2 Commits

Author SHA1 Message Date
62e890245e ... 2025-10-29 20:00:41 +01:00
138846d84d ... 2025-10-29 19:46:20 +01:00
198 changed files with 9520 additions and 20354 deletions

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@ -16,5 +16,3 @@ POSTGRES_PORT=
# MAIL
EMAIL_HOST_USER=
EMAIL_HOST_PASSWORD=
# MATOMO
MATOMO_SITE_ID

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@ -1,134 +0,0 @@
name: CI
on:
pull_request:
branches:
- develop
workflow_dispatch:
jobs:
test:
if: ${{ !contains(gitea.event.pull_request.title, 'WIP') }}
runs-on: ubuntu-latest
services:
postgres:
image: postgres:16
env:
POSTGRES_USER: ${{ vars.POSTGRES_USER }}
POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
POSTGRES_DB: ${{ vars.POSTGRES_DB }}
ports:
- ${{ vars.POSTGRES_PORT}}:5432
options: >-
--health-cmd="pg_isready -U postgres"
--health-interval=10s
--health-timeout=5s
--health-retries=5
#redis:
# image: redis:7
# ports:
# - 6379:6379
# options: >-
# --health-cmd "redis-cli ping"
# --health-interval=10s
# --health-timeout=5s
# --health-retries=5
env:
RUNNER_TOOL_CACHE: /toolcache
EP_DATA_DIR: /opt/enviPy/
ALLOWED_HOSTS: 127.0.0.1,localhost
DEBUG: True
LOG_LEVEL: DEBUG
MODEL_BUILDING_ENABLED: True
APPLICABILITY_DOMAIN_ENABLED: True
ENVIFORMER_PRESENT: True
ENVIFORMER_DEVICE: cpu
FLAG_CELERY_PRESENT: False
PLUGINS_ENABLED: True
SERVER_URL: http://localhost:8000
ADMIN_APPROVAL_REQUIRED: True
REGISTRATION_MANDATORY: True
LOG_DIR: ''
# DB
POSTGRES_SERVICE_NAME: postgres
POSTGRES_DB: ${{ vars.POSTGRES_DB }}
POSTGRES_USER: ${{ vars.POSTGRES_USER }}
POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
POSTGRES_PORT: 5432
# SENTRY
SENTRY_ENABLED: False
# MS ENTRA
MS_ENTRA_ENABLED: False
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Install system tools via apt
run: |
sudo apt-get update
sudo apt-get install -y postgresql-client redis-tools openjdk-11-jre-headless
- name: Setup ssh
run: |
echo "${{ secrets.ENVIPY_CI_PRIVATE_KEY }}" > ~/.ssh/id_ed25519
chmod 600 ~/.ssh/id_ed25519
ssh-keyscan git.envipath.com >> ~/.ssh/known_hosts
eval $(ssh-agent -s)
ssh-add ~/.ssh/id_ed25519
- name: Install pnpm
uses: pnpm/action-setup@v4
with:
version: 10
- name: Use Node.js
uses: actions/setup-node@v4
with:
node-version: 20
cache: "pnpm"
- name: Install uv
uses: astral-sh/setup-uv@v6
with:
enable-cache: true
- name: Setup venv
run: |
uv sync --locked --all-extras --dev
source .venv/bin/activate
playwright install --with-deps
- name: Run PNPM Commands
run: |
uv run python scripts/pnpm_wrapper.py install
cat << 'EOF' > pnpm-workspace.yaml
onlyBuiltDependencies:
- '@parcel/watcher'
- '@tailwindcss/oxide'
EOF
uv run python scripts/pnpm_wrapper.py run build
- name: Wait for services
run: |
until pg_isready -h postgres -U postgres; do sleep 2; done
# until redis-cli -h redis ping; do sleep 2; done
- name: Run Django Migrations
run: |
source .venv/bin/activate
python manage.py migrate --noinput
- name: Run frontend tests
run: |
source .venv/bin/activate
python manage.py test --tag frontend
- name: Run Django tests
run: |
source .venv/bin/activate
python manage.py test tests --exclude-tag slow --exclude-tag frontend

6
.gitignore vendored
View File

@ -6,13 +6,7 @@ static/django_extensions/
.env
debug.log
scratches/
test-results/
data/
.DS_Store
node_modules/
static/css/output.css
*.code-workspace

View File

@ -8,7 +8,6 @@ repos:
- id: end-of-file-fixer
- id: check-yaml
- id: check-added-large-files
exclude: ^static/images/
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.13.3
@ -21,15 +20,6 @@ repos:
- id: ruff-format
types_or: [python, pyi]
- repo: local
hooks:
- id: prettier-jinja-templates
name: Format Jinja templates with Prettier
entry: pnpm exec prettier --plugin=prettier-plugin-jinja-template --parser=jinja-template --write
language: system
types: [file]
files: ^templates/.*\.html$
# - repo: local
# hooks:
# - id: django-check

View File

@ -1,11 +0,0 @@
{
"plugins": ["prettier-plugin-jinja-template", "prettier-plugin-tailwindcss"],
"overrides": [
{
"files": "templates/**/*.html",
"options": {
"parser": "jinja-template"
}
}
]
}

View File

@ -7,13 +7,11 @@ These instructions will guide you through setting up the project for local devel
### Prerequisites
- Python 3.11 or later
- [uv](https://github.com/astral-sh/uv) - Python package manager
- **Docker and Docker Compose** - Required for running PostgreSQL database
- [uv](https://github.com/astral-sh/uv) - A fast Python package installer and resolver.
- **Docker and Docker Compose** - Required for running the PostgreSQL database.
- Git
- Make
> **Note:** This application requires PostgreSQL (uses `ArrayField`). Docker is the easiest way to run PostgreSQL locally.
> **Note:** This application requires PostgreSQL, which uses `ArrayField`. Docker is the recommended way to run PostgreSQL locally.
### 1. Install Dependencies
@ -25,12 +23,7 @@ Then, sync the project dependencies. This will create a virtual environment in `
uv sync --dev
```
Note on RDkit installation: if you have rdkit installed on your system globally with a different version of python, the installation will try to link against that and subsequent calls fail. Only option remove global rdkit and rerun sync.
---
The frontend requires `pnpm` to correctly display in development.
[Install it here](https://pnpm.io/installation).
> **Note on RDkit:** If you have a different version of rdkit installed globally, the dependency installation may fail. If this happens, please uninstall the global version and run `uv sync` again.
### 2. Set Up Environment File
@ -51,7 +44,6 @@ uv run poe setup
```
This single command will:
1. Start the PostgreSQL database using Docker Compose.
2. Run database migrations.
3. Bootstrap initial data (anonymous user, default packages, models).
@ -62,12 +54,9 @@ After setup, start the development server:
uv run poe dev
```
This will start the css-watcher as well as the django-development server,
The application will be available at `http://localhost:8000`.
**Note:** The development server automatically starts a CSS watcher (`pnpm run dev`) alongside the Django server to rebuild CSS files when changes are detected. This ensures your styles are always up-to-date during development.
#### Other useful Poe commands
#### Other useful Poe commands:
You can list all available commands by running `uv run poe --help`.
@ -77,7 +66,6 @@ uv run poe db-down # Stop PostgreSQL
uv run poe migrate # Run migrations only
uv run poe bootstrap # Bootstrap data only
uv run poe shell # Open the Django shell
uv run poe build # Build frontend assets and collect static files
uv run poe clean # Remove database volumes (WARNING: destroys all data)
```

View File

@ -49,21 +49,29 @@ INSTALLED_APPS = [
"oauth2_provider",
# Custom
"epdb",
# "migration",
"migration",
]
# Add the TENANT providing implementations for
# Required
# - Package
# - Compound (TODO)
# - CompoundStructure (TODO)
# Optional
# - PackageManager (TODO)
# - GroupManager (TODO)
# - SettingManager (TODO)
TENANT = os.environ.get("TENANT", "public")
if TENANT != "public":
INSTALLED_APPS.append(TENANT)
EPDB_PACKAGE_MODEL = os.environ.get("EPDB_PACKAGE_MODEL", "epdb.Package")
PACKAGE_IMPLEMENTATION = f"{TENANT}.Package"
PACKAGE_MODULE_PATH = f"{TENANT}.models.Package"
def GET_PACKAGE_MODEL():
from django.apps import apps
return apps.get_model(EPDB_PACKAGE_MODEL)
return apps.get_model(TENANT, "Package")
AUTHENTICATION_BACKENDS = [
@ -101,14 +109,11 @@ TEMPLATES = [
"django.template.context_processors.request",
"django.contrib.auth.context_processors.auth",
"django.contrib.messages.context_processors.messages",
"epdb.context_processors.package_context",
],
},
},
]
ALLOWED_HTML_TAGS = {"b", "i", "u", "br", "em", "mark", "p", "s", "strong"}
WSGI_APPLICATION = "envipath.wsgi.application"
# Database
@ -260,7 +265,6 @@ LOGGING = {
ENVIFORMER_PRESENT = os.environ.get("ENVIFORMER_PRESENT", "False") == "True"
ENVIFORMER_DEVICE = os.environ.get("ENVIFORMER_DEVICE", "cpu")
# If celery is not present set always eager to true which will cause delayed tasks to block until finished
FLAG_CELERY_PRESENT = os.environ.get("FLAG_CELERY_PRESENT", "False") == "True"
if not FLAG_CELERY_PRESENT:
@ -361,14 +365,6 @@ LOGIN_EXEMPT_URLS = [
"/password_reset/",
"/reset/",
"/microsoft/",
"/terms",
"/privacy",
"/cookie-policy",
"/about",
"/contact",
"/jobs",
"/cite",
"/legal",
]
# MS AD/Entra
@ -383,6 +379,3 @@ if MS_ENTRA_ENABLED:
MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")
# Site ID 10 -> beta.envipath.org
MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")

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@ -23,20 +23,12 @@ from .api import api_v1, api_legacy
urlpatterns = [
path("", include("epdb.urls")),
path("", include("migration.urls")),
path("admin/", admin.site.urls),
path("api/v1/", api_v1.urls),
path("api/legacy/", api_legacy.urls),
path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
]
if "migration" in s.INSTALLED_APPS:
urlpatterns.append(path("", include("migration.urls")))
if s.MS_ENTRA_ENABLED:
urlpatterns.append(path("", include("epauth.urls")))
# Custom error handlers
handler400 = "epdb.views.handler400"
handler403 = "epdb.views.handler403"
handler404 = "epdb.views.handler404"
handler500 = "epdb.views.handler500"

View File

@ -1,29 +1,29 @@
from django.conf import settings as s
from django.contrib import admin
from django.conf import settings as s
from .models import (
Compound,
CompoundStructure,
Edge,
EnviFormer,
ExternalDatabase,
ExternalIdentifier,
Group,
GroupPackagePermission,
JobLog,
License,
MLRelativeReasoning,
Node,
ParallelRule,
Pathway,
Reaction,
Scenario,
Setting,
SimpleAmbitRule,
User,
UserPackagePermission,
Group,
GroupPackagePermission,
MLRelativeReasoning,
EnviFormer,
Compound,
CompoundStructure,
SimpleAmbitRule,
ParallelRule,
Reaction,
Pathway,
Node,
Edge,
Scenario,
Setting,
ExternalDatabase,
ExternalIdentifier,
JobLog,
)
Package = s.GET_PACKAGE_MODEL()
@ -65,10 +65,6 @@ class EnviFormerAdmin(EPAdmin):
pass
class LicenseAdmin(admin.ModelAdmin):
list_display = ["cc_string", "link", "image_link"]
class CompoundAdmin(EPAdmin):
pass
@ -125,7 +121,6 @@ admin.site.register(JobLog, JobLogAdmin)
admin.site.register(Package, PackageAdmin)
admin.site.register(MLRelativeReasoning, MLRelativeReasoningAdmin)
admin.site.register(EnviFormer, EnviFormerAdmin)
admin.site.register(License, LicenseAdmin)
admin.site.register(Compound, CompoundAdmin)
admin.site.register(CompoundStructure, CompoundStructureAdmin)
admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)

View File

@ -1,9 +1,4 @@
import logging
from django.apps import AppConfig
from django.conf import settings
logger = logging.getLogger(__name__)
class EPDBConfig(AppConfig):
@ -12,6 +7,3 @@ class EPDBConfig(AppConfig):
def ready(self):
import epdb.signals # noqa: F401
model_name = getattr(settings, "EPDB_PACKAGE_MODEL", "epdb.Package")
logger.info(f"Using Package model: {model_name}")

View File

@ -1,32 +0,0 @@
"""
Context processors for enviPy application.
Context processors automatically make variables available to all templates.
"""
from .logic import PackageManager
from django.conf import settings as s
def package_context(request):
"""
Provides package data for the search modal which is included globally
in framework_modern.html.
Returns:
dict: Context dictionary with reviewed and unreviewed packages
"""
current_user = request.user
reviewed_package_qs = PackageManager.get_reviewed_packages()
unreviewed_package_qs = s.GET_PACKAGE_MODEL().objects.none()
# Only get user-specific packages if user is authenticated
if current_user.is_authenticated:
unreviewed_package_qs = PackageManager.get_all_readable_packages(current_user)
return {
"reviewed_packages": reviewed_package_qs,
"unreviewed_packages": unreviewed_package_qs,
}

View File

@ -1,33 +1,28 @@
from typing import Any, Dict, List, Optional
from typing import List, Dict, Optional, Any
import nh3
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.http import HttpResponse
from django.shortcuts import redirect
from ninja import Field, Form, Router, Schema, Query
from ninja.security import SessionAuth
from ninja import Router, Schema, Field, Form
from utilities.chem import FormatConverter
from utilities.misc import PackageExporter
from .logic import GroupManager, PackageManager, SettingManager, UserManager, SearchManager
from .logic import PackageManager, UserManager, SettingManager
from .models import (
Compound,
CompoundStructure,
Edge,
EPModel,
Node,
Pathway,
Reaction,
Rule,
Scenario,
SimpleAmbitRule,
User,
UserPackagePermission,
ParallelRule,
Rule,
Reaction,
Scenario,
Pathway,
Node,
Edge,
SimpleAmbitRule,
)
Package = s.GET_PACKAGE_MODEL()
@ -37,7 +32,8 @@ def _anonymous_or_real(request):
return get_user_model().objects.get(username="anonymous")
router = Router(auth=SessionAuth(csrf=False))
# router = Router(auth=SessionAuth())
router = Router()
class Error(Schema):
@ -125,16 +121,13 @@ class SimpleEdge(SimpleObject):
identifier: str = "edge"
class SimpleModel(SimpleObject):
identifier: str = "relative-reasoning"
################
# Login/Logout #
################
@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
@router.post("/", response={200: SimpleUser, 403: Error})
def login(request, loginusername: Form[str], loginpassword: Form[str]):
from django.contrib.auth import authenticate, login
from django.contrib.auth import authenticate
from django.contrib.auth import login
email = User.objects.get(username=loginusername).email
user = authenticate(username=email, password=loginpassword)
@ -177,13 +170,9 @@ class UserSchema(Schema):
return SettingManager.get_all_settings(obj)
class Me(Schema):
whoami: str | None = None
@router.get("/user", response={200: UserWrapper, 403: Error})
def get_users(request, me: Query[Me]):
if me.whoami:
def get_users(request, whoami: str = None):
if whoami:
return {"user": [request.user]}
else:
return {"user": User.objects.all()}
@ -200,61 +189,6 @@ def get_user(request, user_uuid):
}
class Search(Schema):
packages: List[str] = Field(alias="packages[]")
search: str
method: str
@router.get("/search", response={200: Any, 403: Error})
def search(request, search: Query[Search]):
try:
packs = []
for package in search.packages:
packs.append(PackageManager.get_package_by_url(request.user, package))
method = None
if search.method == "text":
method = "text"
elif search.method == "inchikey":
method = "inchikey"
elif search.method == "defaultSmiles":
method = "default"
elif search.method == "canonicalSmiles":
method = "canonical"
elif search.method == "exactSmiles":
method = "exact"
if method is None:
raise ValueError(f"Search method {search.method} is not supported!")
search_res = SearchManager.search(packs, search.search, method)
res = {}
if "Compounds" in search_res:
res["compound"] = search_res["Compounds"]
if "Compound Structures" in search_res:
res["structure"] = search_res["Compound Structures"]
if "Reaction" in search_res:
res["reaction"] = search_res["Reaction"]
if "Pathway" in search_res:
res["pathway"] = search_res["Pathway"]
if "Rules" in search_res:
res["rule"] = search_res["Rules"]
for key in res:
for v in res[key]:
v["id"] = v["url"].replace("simple-ambit-rule", "simple-rule")
return res
except ValueError as e:
return 403, {"message": f"Search failed due to {e}"}
###########
# Package #
###########
@ -320,110 +254,67 @@ def get_packages(request):
}
class GetPackage(Schema):
exportAsJson: str | None = None
@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 403: Error})
def get_package(request, package_uuid, gp: Query[GetPackage]):
@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema, 403: Error})
def get_package(request, package_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if gp.exportAsJson and gp.exportAsJson.strip() == "true":
return PackageExporter(p).do_export()
return p
return PackageManager.get_package_by_id(request.user, package_uuid)
except ValueError:
return 403, {
"message": f"Getting Package with id {package_uuid} failed due to insufficient rights!"
}
class CreatePackage(Schema):
packageName: str
packageDescription: str | None = None
@router.post("/package")
def create_packages(
request,
p: Form[CreatePackage],
request, packageName: Form[str], packageDescription: Optional[str] = Form(None)
):
try:
if p.packageName.strip() == "":
if packageName.strip() == "":
raise ValueError("Package name cannot be empty!")
new_pacakge = PackageManager.create_package(
request.user, p.packageName, p.packageDescription
)
new_pacakge = PackageManager.create_package(request.user, packageName, packageDescription)
return redirect(new_pacakge.url)
except ValueError as e:
return 400, {"message": str(e)}
class UpdatePackage(Schema):
packageDescription: str | None = None
hiddenMethod: str | None = None
permissions: str | None = None
ppsURI: str | None = None
read: str | None = None
write: str | None = None
@router.post("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 400: Error})
def update_package(request, package_uuid, pack: Form[UpdatePackage]):
def update_package(
request,
package_uuid,
packageDescription: Optional[str] = Form(None),
hiddenMethod: Optional[str] = Form(None),
exportAsJson: Optional[str] = Form(None),
permissions: Optional[str] = Form(None),
ppsURI: Optional[str] = Form(None),
read: Optional[str] = Form(None),
write: Optional[str] = Form(None),
):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if pack.hiddenMethod:
if pack.hiddenMethod == "DELETE":
if hiddenMethod:
if hiddenMethod == "DELETE":
p.delete()
elif pack.packageDescription is not None:
description = nh3.clean(pack.packageDescription, tags=s.ALLOWED_HTML_TAGS).strip()
if description:
p.description = description
elif packageDescription and packageDescription.strip() != "":
p.description = packageDescription
p.save()
return HttpResponse(status=200)
else:
raise ValueError("Package description cannot be empty!")
elif all([pack.permissions, pack.ppsURI, pack.read]):
if "group" in pack.ppsURI:
grantee = GroupManager.get_group_lp(pack.ppsURI)
else:
grantee = UserManager.get_user_lp(pack.ppsURI)
return
elif exportAsJson == "true":
pack_json = PackageManager.export_package(
p, include_models=False, include_external_identifiers=False
)
return pack_json
elif all([permissions, ppsURI, read]):
PackageManager.update_permissions
elif all([permissions, ppsURI, write]):
pass
PackageManager.grant_read(request.user, p, grantee)
return HttpResponse(status=200)
elif all([pack.permissions, pack.ppsURI, pack.write]):
if "group" in pack.ppsURI:
grantee = GroupManager.get_group_lp(pack.ppsURI)
else:
grantee = UserManager.get_user_lp(pack.ppsURI)
PackageManager.grant_write(request.user, p, grantee)
return HttpResponse(status=200)
except ValueError as e:
return 400, {"message": str(e)}
@router.delete("/package/{uuid:package_uuid}")
def delete_package(request, package_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.administrable(request.user, p):
p.delete()
return redirect(f"{s.SERVER_URL}/package")
else:
raise ValueError("You do not have the rights to delete this Package!")
except ValueError:
return 403, {
"message": f"Deleting Package with id {package_uuid} failed due to insufficient rights!"
}
################################
# Compound / CompoundStructure #
################################
@ -621,83 +512,6 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
}
class CreateCompound(Schema):
compoundSmiles: str
compoundName: str | None = None
compoundDescription: str | None = None
inchi: str | None = None
@router.post("/package/{uuid:package_uuid}/compound")
def create_package_compound(
request,
package_uuid,
c: Form[CreateCompound],
):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
# inchi is not used atm
c = Compound.create(
p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
)
return redirect(c.url)
except ValueError as e:
return 400, {"message": str(e)}
@router.delete("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}")
def delete_compound(request, package_uuid, compound_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
c = Compound.objects.get(package=p, uuid=compound_uuid)
c.delete()
return redirect(f"{p.url}/compound")
else:
raise ValueError("You do not have the rights to delete this Compound!")
except ValueError:
return 403, {
"message": f"Deleting Compound with id {compound_uuid} failed due to insufficient rights!"
}
@router.delete(
"/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
)
def delete_compound_structure(request, package_uuid, compound_uuid, structure_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
c = Compound.objects.get(package=p, uuid=compound_uuid)
cs = CompoundStructure.objects.get(compound=c, uuid=structure_uuid)
# Check if we have to delete the compound as no structure is left
if len(cs.compound.structures.all()) == 1:
# This will delete the structure as well
c.delete()
return redirect(p.url + "/compound")
else:
if cs.normalized_structure:
c.delete()
return redirect(p.url + "/compound")
else:
if c.default_structure == cs:
cs.delete()
c.default_structure = c.structures.all().first()
return redirect(c.url + "/structure")
else:
cs.delete()
return redirect(c.url + "/structure")
else:
raise ValueError("You do not have the rights to delete this CompoundStructure!")
except ValueError:
return 403, {
"message": f"Deleting CompoundStructure with id {compound_uuid} failed due to insufficient rights!"
}
#########
# Rules #
#########
@ -861,73 +675,6 @@ def _get_package_rule(request, package_uuid, rule_uuid):
# POST
class CreateSimpleRule(Schema):
smirks: str
name: str | None = None
description: str | None = None
reactantFilterSmarts: str | None = None
productFilterSmarts: str | None = None
immediate: str | None = None
rdkitrule: str | None = None
@router.post("/package/{uuid:package_uuid}/simple-rule")
def create_package_simple_rule(
request,
package_uuid,
r: Form[CreateSimpleRule],
):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if r.rdkitrule and r.rdkitrule.strip() == "true":
raise ValueError("Not yet implemented!")
else:
sr = SimpleAmbitRule.create(
p, r.name, r.description, r.smirks, r.reactantFilterSmarts, r.productFilterSmarts
)
return redirect(sr.url)
except ValueError as e:
return 400, {"message": str(e)}
class CreateParallelRule(Schema):
simpleRules: str
name: str | None = None
description: str | None = None
reactantFilterSmarts: str | None = None
productFilterSmarts: str | None = None
immediate: str | None = None
@router.post("/package/{uuid:package_uuid}/parallel-rule")
def create_package_parallel_rule(
request,
package_uuid,
r: Form[CreateParallelRule],
):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
srs = SimpleRule.objects.filter(package=p, url__in=r.simpleRules)
if srs.count() != len(r.simpleRules):
raise ValueError(
f"Not all SimpleRules could be found in Package with id {package_uuid}!"
)
sr = ParallelRule.create(
p, list(srs), r.name, r.description, r.reactantFilterSmarts, r.productFilterSmarts
)
return redirect(sr.url)
except ValueError as e:
return 400, {"message": str(e)}
@router.post(
"/package/{uuid:package_uuid}/rule/{uuid:rule_uuid}", response={200: str | Any, 403: Error}
)
@ -977,41 +724,6 @@ def _post_package_rule(request, package_uuid, rule_uuid, compound: Form[str]):
}
@router.delete("/package/{uuid:package_uuid}/rule/{uuid:rule_uuid}")
def delete_rule(request, package_uuid, rule_uuid):
return _delete_rule(request, package_uuid, rule_uuid)
@router.delete(
"/package/{uuid:package_uuid}/simple-rule/{uuid:rule_uuid}",
)
def delete_simple_rule(request, package_uuid, rule_uuid):
return _delete_rule(request, package_uuid, rule_uuid)
@router.delete(
"/package/{uuid:package_uuid}/parallel-rule/{uuid:rule_uuid}",
)
def delete_parallel_rule(request, package_uuid, rule_uuid):
return _delete_rule(request, package_uuid, rule_uuid)
def _delete_rule(request, package_uuid, rule_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
r = Rule.objects.get(package=p, uuid=rule_uuid)
r.delete()
return redirect(f"{p.url}/rule")
else:
raise ValueError("You do not have the rights to delete this Rule!")
except ValueError:
return 403, {
"message": f"Deleting Rule with id {rule_uuid} failed due to insufficient rights!"
}
############
# Reaction #
############
@ -1100,82 +812,6 @@ def get_package_reaction(request, package_uuid, reaction_uuid):
}
class CreateReaction(Schema):
reactionName: str | None = None
reactionDescription: str | None = None
smirks: str | None = None
educt: str | None = None
product: str | None = None
rule: str | None = None
@router.post("/package/{uuid:package_uuid}/reaction")
def create_package_reaction(
request,
package_uuid,
r: Form[CreateReaction],
):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if r.smirks is None and (r.educt is None or r.product is None):
raise ValueError("Either SMIRKS or educt/product must be provided")
if r.smirks is not None and (r.educt is not None and r.product is not None):
raise ValueError("SMIRKS and educt/product provided!")
rule = None
if r.rule:
try:
rule = Rule.objects.get(package=p, url=r.rule)
except Rule.DoesNotExist:
raise ValueError(f"Rule with id {r.rule} does not exist!")
if r.educt is not None:
try:
educt_cs = CompoundStructure.objects.get(compound__package=p, url=r.educt)
except CompoundStructure.DoesNotExist:
raise ValueError(f"Compound with id {r.educt} does not exist!")
try:
product_cs = CompoundStructure.objects.get(compound__package=p, url=r.product)
except CompoundStructure.DoesNotExist:
raise ValueError(f"Compound with id {r.product} does not exist!")
new_r = Reaction.create(
p, r.reactionName, r.reactionDescription, [educt_cs], [product_cs], rule
)
else:
educts = r.smirks.split(">>")[0].split("\\.")
products = r.smirks.split(">>")[1].split("\\.")
new_r = Reaction.create(
p, r.reactionName, r.reactionDescription, educts, products, rule
)
return redirect(new_r.url)
except ValueError as e:
return 400, {"message": str(e)}
@router.delete("/package/{uuid:package_uuid}/reaction/{uuid:reaction_uuid}")
def delete_reaction(request, package_uuid, reaction_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
r = Reaction.objects.get(package=p, uuid=reaction_uuid)
r.delete()
return redirect(f"{p.url}/reaction")
else:
raise ValueError("You do not have the rights to delete this Reaction!")
except ValueError:
return 403, {
"message": f"Deleting Reaction with id {reaction_uuid} failed due to insufficient rights!"
}
############
# Scenario #
############
@ -1190,7 +826,7 @@ class ScenarioSchema(Schema):
description: str = Field(None, alias="description")
id: str = Field(None, alias="url")
identifier: str = "scenario"
linkedTo: List[Dict[str, str]] = Field([], alias="linked_to")
linkedTo: List[Dict[str, str]] = Field({}, alias="linked_to")
name: str = Field(None, alias="name")
pathways: List["SimplePathway"] = Field([], alias="related_pathways")
relatedScenarios: List[Dict[str, str]] = Field([], alias="related_scenarios")
@ -1241,38 +877,6 @@ def get_package_scenario(request, package_uuid, scenario_uuid):
}
@router.delete("/package/{uuid:package_uuid}/scenario")
def delete_scenarios(request, package_uuid, scenario_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
scens = Scenario.objects.filter(package=p)
scens.delete()
return redirect(f"{p.url}/scenario")
else:
raise ValueError("You do not have the rights to delete Scenarios!")
except ValueError:
return 403, {"message": "Deleting Scenarios failed due to insufficient rights!"}
@router.delete("/package/{uuid:package_uuid}/scenario/{uuid:scenario_uuid}")
def delete_scenario(request, package_uuid, scenario_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
scen = Scenario.objects.get(package=p, uuid=scenario_uuid)
scen.delete()
return redirect(f"{p.url}/scenario")
else:
raise ValueError("You do not have the rights to delete this Scenario!")
except ValueError:
return 403, {
"message": f"Deleting Scenario with id {scenario_uuid} failed due to insufficient rights!"
}
###########
# Pathway #
###########
@ -1412,67 +1016,46 @@ def get_package_pathway(request, package_uuid, pathway_uuid):
}
class CreatePathway(Schema):
smilesinput: str
name: str | None = None
description: str | None = None
rootOnly: str | None = None
selectedSetting: str | None = None
@router.post("/package/{uuid:package_uuid}/pathway")
def create_pathway(
request,
package_uuid,
pw: Form[CreatePathway],
smilesinput: Form[str],
name: Optional[str] = Form(None),
description: Optional[str] = Form(None),
rootOnly: Optional[str] = Form(None),
selectedSetting: Optional[str] = Form(None),
):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
stand_smiles = FormatConverter.standardize(pw.smilesinput.strip())
stand_smiles = FormatConverter.standardize(smilesinput.strip())
new_pw = Pathway.create(p, stand_smiles, name=pw.name, description=pw.description)
pw = Pathway.create(p, stand_smiles, name=name, description=description)
pw_mode = "predict"
if pw.rootOnly and pw.rootOnly.strip() == "true":
if rootOnly and rootOnly == "true":
pw_mode = "build"
new_pw.kv.update({"mode": pw_mode})
new_pw.save()
pw.kv.update({"mode": pw_mode})
pw.save()
if pw_mode == "predict":
setting = request.user.prediction_settings()
if pw.selectedSetting:
setting = SettingManager.get_setting_by_url(request.user, pw.selectedSetting)
if selectedSetting:
setting = SettingManager.get_setting_by_url(request.user, selectedSetting)
new_pw.setting = setting
new_pw.save()
pw.setting = setting
pw.save()
from .tasks import dispatch, predict
from .tasks import predict
dispatch(request.user, predict, new_pw.pk, setting.pk, limit=-1)
predict.delay(pw.pk, setting.pk, limit=-1)
return redirect(new_pw.url)
return redirect(pw.url)
except ValueError as e:
return 400, {"message": str(e)}
@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
def delete_pathway(request, package_uuid, pathway_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
pw.delete()
return redirect(f"{p.url}/pathway")
else:
raise ValueError("You do not have the rights to delete this pathway!")
except ValueError:
return 403, {
"message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
}
print(e)
########
@ -1563,52 +1146,6 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
}
class CreateNode(Schema):
nodeAsSmiles: str
nodeName: str | None = None
nodeReason: str | None = None
nodeDepth: str | None = None
@router.post(
"/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
response={200: str | Any, 403: Error},
)
def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
if n.nodeDepth is not None and n.nodeDepth.strip() != "":
node_depth = int(n.nodeDepth)
else:
node_depth = -1
n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
return redirect(n.url)
except ValueError:
return 403, {"message": "Adding node failed!"}
@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node/{uuid:node_uuid}")
def delete_node(request, package_uuid, pathway_uuid, node_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
n = Node.objects.get(pathway=pw, uuid=node_uuid)
n.delete()
return redirect(f"{pw.url}/node")
else:
raise ValueError("You do not have the rights to delete this Node!")
except ValueError:
return 403, {
"message": f"Deleting Node with id {node_uuid} failed due to insufficient rights!"
}
########
# Edge #
########
@ -1672,200 +1209,6 @@ def get_package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
}
class CreateEdge(Schema):
edgeAsSmirks: str | None = None
educts: str | None = None # Node URIs comma sep
products: str | None = None # Node URIs comma sep
multistep: str | None = None
edgeReason: str | None = None
@router.post(
"/package/{uuid:package_uuid}/üathway/{uuid:pathway_uuid}/edge",
response={200: str | Any, 403: Error},
)
def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
if e.edgeAsSmirks is None and (e.educts is None or e.products is None):
raise ValueError("Either SMIRKS or educt/product must be provided")
if e.edgeAsSmirks is not None and (e.educts is not None and e.products is not None):
raise ValueError("SMIRKS and educt/product provided!")
educts = []
products = []
if e.edgeAsSmirks:
for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
educts.append(Node.objects.get(pathway=pw, default_node_label__smiles=ed))
for pr in e.edgeAsSmirks.split(">>")[1].split("\\."):
products.append(Node.objects.get(pathway=pw, default_node_label__smiles=pr))
else:
for ed in e.educts.split(","):
educts.append(Node.objects.get(pathway=pw, url=ed.strip()))
for pr in e.products.split(","):
products.append(Node.objects.get(pathway=pw, url=pr.strip()))
new_e = Edge.create(
pathway=pw,
start_nodes=educts,
end_nodes=products,
rule=None,
name=e.name,
description=e.edgeReason,
)
return redirect(new_e.url)
except ValueError:
return 403, {"message": "Adding node failed!"}
@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")
def delete_edge(request, package_uuid, pathway_uuid, edge_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
e = Edge.objects.get(pathway=pw, uuid=edge_uuid)
e.delete()
return redirect(f"{pw.url}/edge")
else:
raise ValueError("You do not have the rights to delete this Edge!")
except ValueError:
return 403, {
"message": f"Deleting Edge with id {edge_uuid} failed due to insufficient rights!"
}
#########
# Model #
#########
class ModelWrapper(Schema):
relative_reasoning: List["SimpleModel"] = Field(..., alias="relative-reasoning")
class ModelSchema(Schema):
aliases: List[str] = Field([], alias="aliases")
description: str = Field(None, alias="description")
evalPackages: List["SimplePackage"] = Field([])
id: str = Field(None, alias="url")
identifier: str = "relative-reasoning"
# "info" : {
# "Accuracy (Single-Gen)" : "0.5932962678936605" ,
# "Area under PR-Curve (Single-Gen)" : "0.5654653182134282" ,
# "Area under ROC-Curve (Single-Gen)" : "0.8178302405034772" ,
# "Precision (Single-Gen)" : "0.6978730822873083" ,
# "Probability Threshold" : "0.5" ,
# "Recall/Sensitivity (Single-Gen)" : "0.4484149210261006"
# } ,
name: str = Field(None, alias="name")
pathwayPackages: List["SimplePackage"] = Field([])
reviewStatus: str = Field(None, alias="review_status")
rulePackages: List["SimplePackage"] = Field([])
scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
status: str
statusMessage: str
threshold: str
type: str
@router.get("/model", response={200: ModelWrapper, 403: Error})
def get_models(request):
pass
@router.get("/package/{uuid:package_uuid}/model", response={200: ModelWrapper, 403: Error})
def get_package_models(request, package_uuid, model_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
return EPModel.objects.filter(package=p)
except ValueError:
return 403, {
"message": f"Getting Reaction with id {model_uuid} failed due to insufficient rights!"
}
class Classify(Schema):
smiles: str | None = None
@router.get(
"/package/{uuid:package_uuid}/model/{uuid:model_uuid}",
response={200: ModelSchema | Any, 403: Error, 400: Error},
)
def get_model(request, package_uuid, model_uuid, c: Query[Classify]):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
mod = EPModel.objects.get(package=p, uuid=model_uuid)
if c.smiles:
if c.smiles == "":
return 400, {"message": "Received empty SMILES"}
try:
stand_smiles = FormatConverter.standardize(c.smiles)
except ValueError:
return 400, {"message": f'"{c.smiles}" is not a valid SMILES'}
from epdb.tasks import dispatch_eager, predict_simple
pred_res = dispatch_eager(request.user, predict_simple, mod.pk, stand_smiles)
result = []
for pr in pred_res:
if len(pr) > 0:
products = []
for prod_set in pr.product_sets:
products.append(tuple([x for x in prod_set]))
res = {
"probability": pr.probability,
"products": list(set(products)),
}
if pr.rule:
res["id"] = pr.rule.url
res["identifier"] = pr.rule.get_rule_identifier()
res["name"] = pr.rule.name
res["reviewStatus"] = (
"reviewed" if pr.rule.package.reviewed else "unreviewed"
)
result.append(res)
return result
return mod
except ValueError:
return 403, {
"message": f"Getting Reaction with id {model_uuid} failed due to insufficient rights!"
}
@router.delete("/package/{uuid:package_uuid}/model/{uuid:model_uuid}")
def delete_model(request, package_uuid, model_uuid):
try:
p = PackageManager.get_package_by_id(request.user, package_uuid)
if PackageManager.writable(request.user, p):
m = EPModel.objects.get(package=p, uuid=model_uuid)
m.delete()
return redirect(f"{p.url}/model")
else:
raise ValueError("You do not have the rights to delete this Model!")
except ValueError:
return 403, {
"message": f"Deleting Model with id {model_uuid} failed due to insufficient rights!"
}
###########
# Setting #
###########

View File

@ -1,35 +1,34 @@
import json
import logging
import re
from typing import Any, Dict, List, Optional, Set, Union
import logging
import json
from typing import Union, List, Optional, Set, Dict, Any
from uuid import UUID
import nh3
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.db import transaction
from django.conf import settings as s
from pydantic import ValidationError
from epdb.models import (
Compound,
CompoundStructure,
Edge,
EnzymeLink,
EPModel,
Group,
GroupPackagePermission,
Node,
Pathway,
Permission,
Reaction,
Rule,
Setting,
User,
UserPackagePermission,
GroupPackagePermission,
Permission,
Group,
Setting,
EPModel,
UserSettingPermission,
Rule,
Pathway,
Node,
Edge,
Compound,
Reaction,
CompoundStructure,
EnzymeLink,
)
from utilities.chem import FormatConverter
from utilities.misc import PackageExporter, PackageImporter
from utilities.misc import PackageImporter, PackageExporter
logger = logging.getLogger(__name__)
@ -187,12 +186,6 @@ class UserManager(object):
def create_user(
username, email, password, set_setting=True, add_to_group=True, *args, **kwargs
):
# Clean for potential XSS
clean_username = nh3.clean(username).strip()
clean_email = nh3.clean(email).strip()
if clean_username != username or clean_email != email:
# This will be caught by the try in view.py/register
raise ValueError("Invalid username or password")
# avoid circular import :S
from .tasks import send_registration_mail
@ -270,9 +263,8 @@ class GroupManager(object):
@staticmethod
def create_group(current_user, name, description):
g = Group()
# Clean for potential XSS
g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
g.name = name
g.description = description
g.owner = current_user
g.save()
@ -527,13 +519,8 @@ class PackageManager(object):
@transaction.atomic
def create_package(current_user, name: str, description: str = None):
p = Package()
# Clean for potential XSS
p.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
if description is not None and description.strip() != "":
p.description = nh3.clean(description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
p.name = name
p.description = description
p.save()
up = UserPackagePermission()
@ -579,39 +566,30 @@ class PackageManager(object):
else:
_ = perm_cls.objects.update_or_create(defaults={"permission": new_perm}, **data)
@staticmethod
def grant_read(caller: User, package: Package, grantee: Union[User, Group]):
PackageManager.update_permissions(caller, package, grantee, Permission.READ[0])
@staticmethod
def grant_write(caller: User, package: Package, grantee: Union[User, Group]):
PackageManager.update_permissions(caller, package, grantee, Permission.WRITE[0])
@staticmethod
@transaction.atomic
def import_legacy_package(
data: dict, owner: User, keep_ids=False, add_import_timestamp=True, trust_reviewed=False
):
from collections import defaultdict
from datetime import datetime
from uuid import UUID, uuid4
from envipy_additional_information import AdditionalInformationConverter
from datetime import datetime
from collections import defaultdict
from .models import (
Package,
Compound,
CompoundStructure,
Edge,
Node,
SimpleRule,
SimpleAmbitRule,
ParallelRule,
Pathway,
Reaction,
Scenario,
SequentialRule,
SequentialRuleOrdering,
SimpleAmbitRule,
SimpleRule,
Reaction,
Pathway,
Node,
Edge,
Scenario,
)
from envipy_additional_information import AdditionalInformationConverter
pack = Package()
pack.uuid = UUID(data["id"].split("/")[-1]) if keep_ids else uuid4()
@ -1117,29 +1095,28 @@ class SettingManager(object):
model: EPModel = None,
model_threshold: float = None,
):
new_s = Setting()
# Clean for potential XSS
new_s.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
new_s.max_nodes = max_nodes
new_s.max_depth = max_depth
new_s.model = model
new_s.model_threshold = model_threshold
s = Setting()
s.name = name
s.description = description
s.max_nodes = max_nodes
s.max_depth = max_depth
s.model = model
s.model_threshold = model_threshold
new_s.save()
s.save()
if rule_packages is not None:
for r in rule_packages:
new_s.rule_packages.add(r)
new_s.save()
s.rule_packages.add(r)
s.save()
usp = UserSettingPermission()
usp.user = user
usp.setting = new_s
usp.setting = s
usp.permission = Permission.ALL[0]
usp.save()
return new_s
return s
@staticmethod
def get_default_setting(user: User):
@ -1568,7 +1545,7 @@ class SPathway(object):
if self.prediction_setting.model.app_domain:
app_domain_assessment = self.prediction_setting.model.app_domain.assess(
sub.smiles
)
)[0]
if self.persist is not None:
n = self.snode_persist_lookup[sub]
@ -1601,7 +1578,9 @@ class SPathway(object):
if self.prediction_setting.model:
if self.prediction_setting.model.app_domain:
app_domain_assessment = (
self.prediction_setting.model.app_domain.assess(c)
self.prediction_setting.model.app_domain.assess(c)[
0
]
)
self.smiles_to_node[c] = SNode(

View File

@ -12,16 +12,10 @@ from epdb.models import (
Permission,
User,
ExternalDatabase,
License,
)
class Command(BaseCommand):
def add_arguments(self, parser):
parser.add_argument(
"-ol", "--only-licenses", action="store_true", help="Only create licenses."
)
def create_users(self):
# Anonymous User
if not User.objects.filter(email="anon@envipath.com").exists():
@ -89,17 +83,6 @@ class Command(BaseCommand):
return anon, admin, g, user0
def create_licenses(self):
"""Create the six default licenses supported by enviPath"""
cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
for cc_string in cc_strings:
if not License.objects.filter(cc_string=cc_string).exists():
new_license = License()
new_license.cc_string = cc_string
new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
new_license.save()
def import_package(self, data, owner):
return PackageManager.import_legacy_package(
data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
@ -174,10 +157,6 @@ class Command(BaseCommand):
@transaction.atomic
def handle(self, *args, **options):
# Create licenses
self.create_licenses()
if options.get("only_licenses", False):
return
# Create users
anon, admin, g, user0 = self.create_users()

View File

@ -0,0 +1,190 @@
# Generated by Django 5.2.7 on 2025-10-29 13:32
import django.db.models.deletion
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0009_joblog"),
("public", "0001_initial"),
]
operations = [
migrations.AlterField(
model_name="userpackagepermission",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Permission on",
),
),
migrations.AlterField(
model_name="grouppackagepermission",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Permission on",
),
),
migrations.AlterField(
model_name="epmodel",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="rule",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="compound",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="scenario",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="pathway",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="reaction",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="user",
name="default_package",
field=models.ForeignKey(
null=True,
on_delete=django.db.models.deletion.SET_NULL,
to="public.package",
verbose_name="Default Package",
),
),
migrations.AlterField(
model_name="enviformer",
name="data_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_data_packages",
to="public.package",
verbose_name="Data Packages",
),
),
migrations.AlterField(
model_name="enviformer",
name="eval_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_eval_packages",
to="public.package",
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="enviformer",
name="rule_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_rule_packages",
to="public.package",
verbose_name="Rule Packages",
),
),
migrations.AlterField(
model_name="mlrelativereasoning",
name="data_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_data_packages",
to="public.package",
verbose_name="Data Packages",
),
),
migrations.AlterField(
model_name="mlrelativereasoning",
name="eval_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_eval_packages",
to="public.package",
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="mlrelativereasoning",
name="rule_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_rule_packages",
to="public.package",
verbose_name="Rule Packages",
),
),
migrations.AlterField(
model_name="rulebasedrelativereasoning",
name="data_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_data_packages",
to="public.package",
verbose_name="Data Packages",
),
),
migrations.AlterField(
model_name="rulebasedrelativereasoning",
name="eval_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_eval_packages",
to="public.package",
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="rulebasedrelativereasoning",
name="rule_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_rule_packages",
to="public.package",
verbose_name="Rule Packages",
),
),
migrations.AlterField(
model_name="setting",
name="rule_packages",
field=models.ManyToManyField(
blank=True,
related_name="setting_rule_packages",
to="public.package",
verbose_name="Setting Rule Packages",
),
),
migrations.DeleteModel(
name="Package",
),
]

View File

@ -1,18 +0,0 @@
# Generated by Django 5.2.7 on 2025-11-11 14:11
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0009_joblog"),
]
operations = [
migrations.AddField(
model_name="license",
name="cc_string",
field=models.TextField(default="by-nc-sa", verbose_name="CC string"),
preserve_default=False,
),
]

View File

@ -1,59 +0,0 @@
# Generated by Django 5.2.7 on 2025-11-11 14:13
import re
from django.contrib.postgres.aggregates import ArrayAgg
from django.db import migrations
from django.db.models import Min
def set_cc(apps, schema_editor):
License = apps.get_model("epdb", "License")
# For all existing licenses extract cc_string from link
for license in License.objects.all():
pattern = r"/licenses/([^/]+)/4\.0"
match = re.search(pattern, license.link)
if match:
license.cc_string = match.group(1)
license.save()
else:
raise ValueError(f"Could not find license for {license.link}")
# Ensure we have all licenses
cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
for cc_string in cc_strings:
if not License.objects.filter(cc_string=cc_string).exists():
new_license = License()
new_license.cc_string = cc_string
new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
new_license.save()
# As we might have existing Licenses representing the same License,
# get min pk and all pks as a list
license_lookup_qs = License.objects.values("cc_string").annotate(
lowest_pk=Min("id"), all_pks=ArrayAgg("id", order_by=("id",))
)
license_lookup = {
row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
}
Packages = apps.get_model("epdb", "Package")
for k, v in license_lookup.items():
# Set min pk to all packages pointing to any of the duplicates
Packages.objects.filter(pk__in=v[1]).update(license_id=v[0])
# remove the min pk from "other" pks as we use them for deletion
v[1].remove(v[0])
# Delete redundant License objects
License.objects.filter(pk__in=v[1]).delete()
class Migration(migrations.Migration):
dependencies = [
("epdb", "0010_license_cc_string"),
]
operations = [migrations.RunPython(set_cc)]

File diff suppressed because it is too large Load Diff

View File

@ -1,22 +1,22 @@
import csv
import io
import logging
from datetime import datetime
from typing import Any, Callable, List, Optional
from uuid import uuid4
from celery import shared_task
from celery.utils.functional import LRUCache
from django.conf import settings as s
from django.utils import timezone
from epdb.logic import SPathway
from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
Package = s.GET_PACKAGE_MODEL()
logger = logging.getLogger(__name__)
ML_CACHE = LRUCache(3) # Cache the three most recent ML models to reduce load times.
Package = s.GET_PACKAGE_MODEL()
def get_ml_model(model_pk: int):
if model_pk not in ML_CACHE:
@ -32,7 +32,7 @@ def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
log.task_id = uuid4()
log.job_name = job.__name__
log.status = "SUCCESS"
log.done_at = timezone.now()
log.done_at = datetime.now()
log.task_result = str(x) if x else None
log.save()

View File

@ -48,7 +48,6 @@ urlpatterns = [
re_path(r"^user$", v.users, name="users"),
re_path(r"^group$", v.groups, name="groups"),
re_path(r"^search$", v.search, name="search"),
re_path(r"^predict$", v.predict_pathway, name="predict_pathway"),
# User Detail
re_path(rf"^user/(?P<user_uuid>{UUID})", v.user, name="user"),
# Group Detail
@ -142,11 +141,6 @@ urlpatterns = [
v.package_pathway,
name="package pathway detail",
),
re_path(
rf"^package/(?P<package_uuid>{UUID})/predict$",
v.package_predict_pathway,
name="package predict pathway",
),
# Pathway Nodes
re_path(
rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
@ -199,13 +193,4 @@ urlpatterns = [
re_path(r"^jobs", v.jobs, name="jobs"),
# OAuth Stuff
path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
# Static Pages
re_path(r"^terms$", v.static_terms_of_use, name="terms_of_use"),
re_path(r"^privacy$", v.static_privacy_policy, name="privacy_policy"),
re_path(r"^cookie-policy$", v.static_cookie_policy, name="cookie_policy"),
re_path(r"^about$", v.static_about_us, name="about_us"),
re_path(r"^contact$", v.static_contact_support, name="contact_support"),
re_path(r"^careers$", v.static_careers, name="careers"),
re_path(r"^cite$", v.static_cite, name="cite"),
re_path(r"^legal$", v.static_legal, name="legal"),
]

View File

@ -2,7 +2,6 @@ import json
import logging
from typing import Any, Dict, List
import nh3
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
@ -51,9 +50,8 @@ from .models import (
UserPackagePermission,
)
logger = logging.getLogger(__name__)
Package = s.GET_PACKAGE_MODEL()
logger = logging.getLogger(__name__)
def log_post_params(request):
@ -62,26 +60,6 @@ def log_post_params(request):
logger.debug(f"{k}\t{v}")
def get_error_handler_context(request, for_user=None) -> Dict[str, Any]:
current_user = _anonymous_or_real(request)
if for_user:
current_user = for_user
ctx = {
"title": "enviPath",
"meta": {
"site_id": s.MATOMO_SITE_ID,
"version": "0.0.1",
"server_url": s.SERVER_URL,
"user": current_user,
"enabled_features": s.FLAGS,
"debug": s.DEBUG,
},
}
return ctx
def error(request, message: str, detail: str, code: int = 400):
context = get_base_context(request)
error_context = {
@ -96,48 +74,6 @@ def error(request, message: str, detail: str, code: int = 400):
return render(request, "errors/error.html", context, status=code)
def handler400(request, exception):
"""Custom 400 Bad Request error handler"""
context = get_error_handler_context(request)
context["public_mode"] = True
return render(request, "errors/400_bad_request.html", context, status=400)
def handler403(request, exception):
"""Custom 403 Forbidden error handler"""
context = get_error_handler_context(request)
context["public_mode"] = True
return render(request, "errors/403_access_denied.html", context, status=403)
def handler404(request, exception):
"""Custom 404 Not Found error handler"""
context = get_error_handler_context(request)
context["public_mode"] = True
return render(request, "errors/404_not_found.html", context, status=404)
def handler500(request):
"""Custom 500 Internal Server Error handler"""
context = get_error_handler_context(request)
error_context = {}
error_context["error_message"] = "Internal Server Error"
error_context["error_detail"] = "An unexpected error occurred. Please try again later."
if request.headers.get("Accept") == "application/json":
return JsonResponse(error_context, status=500)
context["public_mode"] = True
context["error_code"] = 500
context["error_description"] = (
"We encountered an unexpected error while processing your request. Our team has been notified and is working to resolve the issue."
)
context.update(**error_context)
return render(request, "errors/error.html", context, status=500)
def login(request):
context = get_base_context(request)
@ -149,11 +85,7 @@ def login(request):
elif request.method == "POST":
from django.contrib.auth import authenticate, login
username = request.POST.get("username").strip()
if username != request.POST.get("username"):
context["message"] = "Login failed!"
return render(request, "static/login.html", context)
username = request.POST.get("username")
password = request.POST.get("password")
# Get email for username and check if the account is active
@ -168,7 +100,6 @@ def login(request):
except get_user_model().DoesNotExist:
context["message"] = "Login failed!"
return render(request, "static/login.html", context)
try:
user = authenticate(username=email, password=password)
except Exception:
@ -206,14 +137,9 @@ def register(request):
context = get_base_context(request)
if request.method == "GET":
# Redirect to unified login page with signup tab
next_url = request.GET.get("next", "")
redirect_url = reverse("login") + "#signup"
if next_url:
redirect_url += f"?next={next_url}"
return redirect(redirect_url)
context["title"] = "enviPath"
context["next"] = request.GET.get("next", "")
return render(request, "static/register.html", context)
elif request.method == "POST":
context["title"] = "enviPath"
if next := request.POST.get("next"):
@ -226,18 +152,18 @@ def register(request):
if not (username and email and password):
context["message"] = "Invalid username/email/password"
return render(request, "static/login.html", context)
return render(request, "static/register.html", context)
if password != rpassword or password == "":
context["message"] = "Registration failed, provided passwords differ!"
return render(request, "static/login.html", context)
return render(request, "static/register.html", context)
try:
u = UserManager.create_user(username, email, password)
logger.info(f"Created user {u.username} ({u.pk})")
except Exception:
context["message"] = "Registration failed! Couldn't create User Account."
return render(request, "static/login.html", context)
return render(request, "static/register.html", context)
if s.ADMIN_APPROVAL_REQUIRED:
context["success_message"] = (
@ -254,8 +180,8 @@ def register(request):
def editable(request, user):
# if user.is_superuser:
# return True
if user.is_superuser:
return True
url = request.build_absolute_uri(request.path)
if PackageManager.is_package_url(url):
@ -311,7 +237,6 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
"enabled_features": s.FLAGS,
"debug": s.DEBUG,
"external_databases": ExternalDatabase.get_databases(),
"site_id": s.MATOMO_SITE_ID,
},
}
@ -425,34 +350,6 @@ def index(request):
return render(request, "index/index.html", context)
def predict_pathway(request):
"""Top-level predict pathway view using user's default package."""
if request.method != "GET":
return HttpResponseNotAllowed(["GET"])
context = get_base_context(request)
context["title"] = "enviPath - Predict Pathway"
context["meta"]["current_package"] = context["meta"]["user"].default_package
return render(request, "predict_pathway.html", context)
@package_permission_required()
def package_predict_pathway(request, package_uuid):
"""Package-specific predict pathway view."""
if request.method != "GET":
return HttpResponseNotAllowed(["GET"])
current_user = _anonymous_or_real(request)
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
context = get_base_context(request)
context["title"] = f"enviPath - {current_package.name} - Predict Pathway"
context["meta"]["current_package"] = current_package
return render(request, "predict_pathway.html", context)
def packages(request):
current_user = _anonymous_or_real(request)
@ -772,7 +669,7 @@ def search(request):
if request.method == "GET":
package_urls = request.GET.getlist("packages")
searchterm = request.GET.get("search", "").strip()
searchterm = request.GET.get("search")
mode = request.GET.get("mode")
# add HTTP_ACCEPT check to differentiate between index and ajax call
@ -969,10 +866,9 @@ def package_model(request, package_uuid, model_uuid):
if classify:
from epdb.tasks import dispatch_eager, predict_simple
pred_res = dispatch_eager(
current_user, predict_simple, current_model.pk, stand_smiles
)
res = dispatch_eager(current_user, predict_simple, current_model.pk, stand_smiles)
pred_res = current_model.predict(stand_smiles)
res = []
for pr in pred_res:
@ -995,7 +891,7 @@ def package_model(request, package_uuid, model_uuid):
return JsonResponse(res, safe=False)
else:
app_domain_assessment = current_model.app_domain.assess(stand_smiles)
app_domain_assessment = current_model.app_domain.assess(stand_smiles)[0]
return JsonResponse(app_domain_assessment, safe=False)
context = get_base_context(request)
@ -1035,24 +931,12 @@ def package_model(request, package_uuid, model_uuid):
]
dispatch(current_user, evaluate_model, current_model.pk, multigen, eval_package_ids)
return redirect(current_model.url)
elif hidden == "retrain":
from .tasks import dispatch, retrain
dispatch(current_user, retrain, current_model.pk)
return redirect(current_model.url)
else:
return HttpResponseBadRequest()
else:
# TODO: Move cleaning to property updater
name = request.POST.get("model-name")
if name is not None:
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
description = request.POST.get("model-description")
if description is not None:
description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
name = request.POST.get("model-name", "").strip()
description = request.POST.get("model-description", "").strip()
if any([name, description]):
if name:
@ -1132,7 +1016,9 @@ def package(request, package_uuid):
return redirect(s.SERVER_URL + "/package")
elif hidden == "publish-package":
for g in Group.objects.filter(public=True):
PackageManager.grant_read(current_user, current_package, g)
PackageManager.update_permissions(
current_user, current_package, g, Permission.READ[0]
)
return redirect(current_package.url)
elif hidden == "copy":
object_to_copy = request.POST.get("object_to_copy")
@ -1152,23 +1038,17 @@ def package(request, package_uuid):
else:
return HttpResponseBadRequest()
# TODO: Move cleaning to property updater
new_package_name = request.POST.get("package-name")
if new_package_name is not None:
new_package_name = nh3.clean(new_package_name, tags=s.ALLOWED_HTML_TAGS).strip()
new_package_description = request.POST.get("package-description")
if new_package_description is not None:
new_package_description = nh3.clean(
new_package_description, tags=s.ALLOWED_HTML_TAGS
).strip()
grantee_url = request.POST.get("grantee")
read = request.POST.get("read") == "on"
write = request.POST.get("write") == "on"
owner = request.POST.get("owner") == "on"
cc_string = request.POST.get("license")
license = request.POST.get("license")
license_link = request.POST.get("license-link")
license_image_link = request.POST.get("license-image-link")
if new_package_name:
current_package.name = new_package_name
@ -1196,15 +1076,24 @@ def package(request, package_uuid):
PackageManager.update_permissions(current_user, current_package, grantee, max_perm)
return redirect(current_package.url)
elif license is not None:
if license == "no-license":
if current_package.license is not None:
current_package.license.delete()
elif cc_string is not None:
cc_string = cc_string.strip()
if cc_string == "no-license": # Reset the package's license
current_package.license = None
current_package.save()
return redirect(current_package.url)
else: # Get the license and assign it to the package
current_package.license = License.objects.get(cc_string=cc_string)
else:
if current_package.license is not None:
current_package.license.delete()
license = License()
license.link = license_link
license.image_link = license_image_link
license.save()
current_package.license = license
current_package.save()
return redirect(current_package.url)
@ -1312,16 +1201,8 @@ def package_compound(request, package_uuid, compound_uuid):
return JsonResponse({"success": current_compound.url})
# TODO: Move cleaning to property updater
new_compound_name = request.POST.get("compound-name")
if new_compound_name is not None:
new_compound_name = nh3.clean(new_compound_name, tags=s.ALLOWED_HTML_TAGS).strip()
new_compound_description = request.POST.get("compound-description")
if new_compound_description is not None:
new_compound_description = nh3.clean(
new_compound_description, tags=s.ALLOWED_HTML_TAGS
).strip()
new_compound_name = request.POST.get("compound-name", "").strip()
new_compound_description = request.POST.get("compound-description", "").strip()
if new_compound_name:
current_compound.name = new_compound_name
@ -1457,16 +1338,8 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
else:
return HttpResponseBadRequest()
# TODO: Move cleaning to property updater
new_structure_name = request.POST.get("compound-structure-name")
if new_structure_name is not None:
new_structure_name = nh3.clean(new_structure_name, tags=s.ALLOWED_HTML_TAGS).strip()
new_structure_description = request.POST.get("compound-structure-description")
if new_structure_description is not None:
new_structure_description = nh3.clean(
new_structure_description, tags=s.ALLOWED_HTML_TAGS
).strip()
new_structure_name = request.POST.get("compound-structure-name", "").strip()
new_structure_description = request.POST.get("compound-structure-description", "").strip()
if new_structure_name:
current_structure.name = new_structure_name
@ -1673,14 +1546,8 @@ def package_rule(request, package_uuid, rule_uuid):
return JsonResponse({"success": current_rule.url})
# TODO: Move cleaning to property updater
rule_name = request.POST.get("rule-name")
if rule_name is not None:
rule_name = nh3.clean(rule_name, tags=s.ALLOWED_HTML_TAGS).strip()
rule_description = request.POST.get("rule-description")
if rule_description is not None:
rule_description = nh3.clean(rule_description, tags=s.ALLOWED_HTML_TAGS).strip()
rule_name = request.POST.get("rule-name", "").strip()
rule_description = request.POST.get("rule-description", "").strip()
if rule_name:
current_rule.name = rule_name
@ -1770,6 +1637,7 @@ def package_reactions(request, package_uuid):
reaction_name = request.POST.get("reaction-name")
reaction_description = request.POST.get("reaction-description")
reactions_smirks = request.POST.get("reaction-smirks")
educts = reactions_smirks.split(">>")[0].split(".")
products = reactions_smirks.split(">>")[1].split(".")
@ -1830,16 +1698,8 @@ def package_reaction(request, package_uuid, reaction_uuid):
return JsonResponse({"success": current_reaction.url})
# TODO: Move cleaning to property updater
new_reaction_name = request.POST.get("reaction-name")
if new_reaction_name is not None:
new_reaction_name = nh3.clean(new_reaction_name, tags=s.ALLOWED_HTML_TAGS).strip()
new_reaction_description = request.POST.get("reaction-description")
if new_reaction_description is not None:
new_reaction_description = nh3.clean(
new_reaction_description, tags=s.ALLOWED_HTML_TAGS
).strip()
new_reaction_name = request.POST.get("reaction-name", "").strip()
new_reaction_description = request.POST.get("reaction-description", "").strip()
if new_reaction_name:
current_reaction.name = new_reaction_name
@ -1916,9 +1776,8 @@ def package_pathways(request, package_uuid):
name = request.POST.get("name")
description = request.POST.get("description")
smiles = request.POST.get("smiles", "").strip()
pw_mode = request.POST.get("predict", "predict").strip()
smiles = request.POST.get("smiles", "").strip()
if "smiles" in request.POST and smiles == "":
return error(
@ -1927,6 +1786,8 @@ def package_pathways(request, package_uuid):
"Pathway prediction failed due to missing or empty SMILES",
)
smiles = smiles.strip()
try:
stand_smiles = FormatConverter.standardize(smiles)
except ValueError:
@ -2085,14 +1946,8 @@ def package_pathway(request, package_uuid, pathway_uuid):
return JsonResponse({"success": current_pathway.url})
# TODO: Move cleaning to property updater
pathway_name = request.POST.get("pathway-name")
if pathway_name is not None:
pathway_name = nh3.clean(pathway_name, tags=s.ALLOWED_HTML_TAGS).strip()
pathway_description = request.POST.get("pathway-description")
if pathway_description is not None:
pathway_description = nh3.clean(pathway_description, tags=s.ALLOWED_HTML_TAGS).strip()
if any([pathway_name, pathway_description]):
if pathway_name is not None and pathway_name.strip() != "":
@ -2180,8 +2035,8 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
elif request.method == "POST":
node_name = request.POST.get("node-name")
node_description = request.POST.get("node-description")
node_smiles = request.POST.get("node-smiles")
node_smiles = request.POST.get("node-smiles").strip()
current_pathway.add_node(node_smiles, name=node_name, description=node_description)
return redirect(current_pathway.url)
@ -2346,7 +2201,6 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
edge_name = request.POST.get("edge-name")
edge_description = request.POST.get("edge-description")
edge_substrates = request.POST.getlist("edge-substrates")
edge_products = request.POST.getlist("edge-products")
@ -2433,7 +2287,7 @@ def package_scenarios(request, package_uuid):
"all", False
):
scens = Scenario.objects.filter(package=current_package).order_by("name")
res = [{"name": s_.name, "url": s_.url, "uuid": s_.uuid} for s_ in scens]
res = [{"name": s.name, "url": s.url, "uuid": s.uuid} for s in scens]
return JsonResponse(res, safe=False)
context = get_base_context(request)
@ -2481,21 +2335,21 @@ def package_scenarios(request, package_uuid):
"name": "soil",
"widgets": [
HTMLGenerator.generate_html(ai, prefix=f"soil_{0}")
for ai in [x for sv in SOIL_ADDITIONAL_INFORMATION.values() for x in sv]
for ai in [x for s in SOIL_ADDITIONAL_INFORMATION.values() for x in s]
],
},
"Sludge Data": {
"name": "sludge",
"widgets": [
HTMLGenerator.generate_html(ai, prefix=f"sludge_{0}")
for ai in [x for sv in SLUDGE_ADDITIONAL_INFORMATION.values() for x in sv]
for ai in [x for s in SLUDGE_ADDITIONAL_INFORMATION.values() for x in s]
],
},
"Water-Sediment System Data": {
"name": "sediment",
"widgets": [
HTMLGenerator.generate_html(ai, prefix=f"sediment_{0}")
for ai in [x for sv in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in sv]
for ai in [x for s in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in s]
],
},
}
@ -2510,7 +2364,6 @@ def package_scenarios(request, package_uuid):
scenario_name = request.POST.get("scenario-name")
scenario_description = request.POST.get("scenario-description")
scenario_date_year = request.POST.get("scenario-date-year")
scenario_date_month = request.POST.get("scenario-date-month")
scenario_date_day = request.POST.get("scenario-date-day")
@ -2524,9 +2377,9 @@ def package_scenarios(request, package_uuid):
scenario_type = request.POST.get("scenario-type")
additional_information = HTMLGenerator.build_models(request.POST.dict())
additional_information = [x for sv in additional_information.values() for x in sv]
additional_information = [x for s in additional_information.values() for x in s]
new_scen = Scenario.create(
s = Scenario.create(
current_package,
name=scenario_name,
description=scenario_description,
@ -2535,7 +2388,7 @@ def package_scenarios(request, package_uuid):
additional_information=additional_information,
)
return redirect(new_scen.url)
return redirect(s.url)
else:
return HttpResponseNotAllowed(
[
@ -2835,7 +2688,6 @@ def settings(request):
name = request.POST.get("prediction-setting-name")
description = request.POST.get("prediction-setting-description")
new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
max_nodes = min(
@ -2986,60 +2838,3 @@ def userinfo(request):
"email_verified": user.is_active,
}
return JsonResponse(res)
# Static Pages
def static_terms_of_use(request):
context = get_base_context(request)
context["title"] = "enviPath - Terms of Use"
context["public_mode"] = True
return render(request, "static/terms_of_use.html", context)
def static_privacy_policy(request):
context = get_base_context(request)
context["title"] = "enviPath - Privacy Policy"
context["public_mode"] = True
return render(request, "static/privacy_policy.html", context)
def static_cookie_policy(request):
context = get_base_context(request)
context["title"] = "enviPath - Cookie Policy"
context["public_mode"] = True
return render(request, "static/cookie_policy.html", context)
def static_about_us(request):
context = get_base_context(request)
context["title"] = "enviPath - About Us"
context["public_mode"] = True
return render(request, "static/about_us.html", context)
def static_contact_support(request):
context = get_base_context(request)
context["title"] = "enviPath - Contact & Support"
context["public_mode"] = True
return render(request, "static/contact.html", context)
def static_careers(request):
context = get_base_context(request)
context["title"] = "enviPath - Careers"
context["public_mode"] = True
return render(request, "static/careers.html", context)
def static_cite(request):
context = get_base_context(request)
context["title"] = "enviPath - How to Cite"
context["public_mode"] = True
return render(request, "static/cite.html", context)
def static_legal(request):
context = get_base_context(request)
context["title"] = "enviPath - Legal Information"
context["public_mode"] = True
return render(request, "static/legal.html", context)

Binary file not shown.

View File

@ -12,10 +12,10 @@ from epdb.models import CompoundStructure, Rule, SimpleAmbitRule
from epdb.views import get_base_context
from utilities.chem import FormatConverter
logger = logging.getLogger(__name__)
Package = s.GET_PACKAGE_MODEL()
logger = logging.getLogger(__name__)
def normalize_smiles(smiles):
m1 = Chem.MolFromSmiles(smiles)

View File

@ -1,25 +0,0 @@
{
"name": "envipy",
"version": "1.0.0",
"private": true,
"description": "enviPath UI - Tailwind CSS + DaisyUI",
"scripts": {
"dev": "tailwindcss -i static/css/input.css -o static/css/output.css --watch=always",
"build": "tailwindcss -i static/css/input.css -o static/css/output.css --minify"
},
"devDependencies": {
"@tailwindcss/cli": "^4.1.16",
"@tailwindcss/postcss": "^4.1.16",
"daisyui": "^5.4.3",
"postcss": "^8.5.6",
"prettier": "^3.6.2",
"prettier-plugin-jinja-template": "^2.1.0",
"prettier-plugin-tailwindcss": "^0.7.1",
"tailwindcss": "^4.1.16"
},
"keywords": [
"django",
"tailwindcss",
"daisyui"
]
}

740
pnpm-lock.yaml generated
View File

@ -1,740 +0,0 @@
lockfileVersion: '9.0'
settings:
autoInstallPeers: true
excludeLinksFromLockfile: false
importers:
.:
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version: 4.1.16
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specifier: ^5.4.3
version: 5.4.3
postcss:
specifier: ^8.5.6
version: 8.5.6
prettier:
specifier: ^3.6.2
version: 3.6.2
prettier-plugin-jinja-template:
specifier: ^2.1.0
version: 2.1.0(prettier@3.6.2)
prettier-plugin-tailwindcss:
specifier: ^0.7.1
version: 0.7.1(prettier@3.6.2)
tailwindcss:
specifier: ^4.1.16
version: 4.1.16
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1
public/admin.py Normal file
View File

@ -0,0 +1 @@
# Register your models here.

6
public/apps.py Normal file
View File

@ -0,0 +1,6 @@
from django.apps import AppConfig
class PublicConfig(AppConfig):
default_auto_field = "django.db.models.BigAutoField"
name = "public"

View File

@ -0,0 +1,56 @@
# Generated by Django 5.2.7 on 2025-10-29 13:32
import django.utils.timezone
import model_utils.fields
import uuid
from django.db import migrations, models
class Migration(migrations.Migration):
initial = True
dependencies = []
operations = [
migrations.CreateModel(
name="Package",
fields=[
(
"id",
models.BigAutoField(
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
),
),
(
"created",
model_utils.fields.AutoCreatedField(
default=django.utils.timezone.now, editable=False, verbose_name="created"
),
),
(
"modified",
model_utils.fields.AutoLastModifiedField(
default=django.utils.timezone.now, editable=False, verbose_name="modified"
),
),
(
"uuid",
models.UUIDField(
default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
),
),
("name", models.TextField(default="no name", verbose_name="Name")),
(
"description",
models.TextField(default="no description", verbose_name="Descriptions"),
),
("url", models.TextField(null=True, unique=True, verbose_name="URL")),
("kv", models.JSONField(blank=True, default=dict, null=True)),
("reviewed", models.BooleanField(default=False, verbose_name="Reviewstatus")),
],
options={
"db_table": "epdb_package",
"managed": False,
},
),
]

View File

@ -0,0 +1,16 @@
# Generated by Django 5.2.7 on 2025-10-29 18:39
from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
("public", "0001_initial"),
]
operations = [
migrations.AlterModelOptions(
name="package",
options={},
),
]

View File

@ -0,0 +1,25 @@
# Generated by Django 5.2.7 on 2025-10-29 18:40
import django.db.models.deletion
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0010_alter_userpackagepermission_package_and_more"),
("public", "0002_alter_package_options"),
]
operations = [
migrations.AddField(
model_name="package",
name="license",
field=models.ForeignKey(
blank=True,
null=True,
on_delete=django.db.models.deletion.SET_NULL,
to="epdb.license",
verbose_name="License",
),
),
]

View File

6
public/models.py Normal file
View File

@ -0,0 +1,6 @@
from epdb.models import AbstractPackage
class Package(AbstractPackage):
class Meta:
db_table = "epdb_package"

1
public/tests.py Normal file
View File

@ -0,0 +1 @@
# Create your tests here.

1
public/views.py Normal file
View File

@ -0,0 +1 @@
# Create your views here.

View File

@ -27,12 +27,10 @@ dependencies = [
"scikit-learn>=1.6.1",
"sentry-sdk[django]>=2.32.0",
"setuptools>=80.8.0",
"nh3==0.3.2",
"polars==1.35.1",
]
[tool.uv.sources]
enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.4" }
enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.2" }
envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.7"}
envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }
@ -45,8 +43,6 @@ dev = [
"poethepoet>=0.37.0",
"pre-commit>=4.3.0",
"ruff>=0.13.3",
"pytest-playwright>=0.7.1",
"pytest-django>=4.11.1",
]
[tool.ruff]
@ -68,39 +64,23 @@ docstring-code-format = true
[tool.poe.tasks]
# Main tasks
setup = { sequence = [
"db-up",
"migrate",
"bootstrap",
], help = "Complete setup: start database, run migrations, and bootstrap data" }
dev = { cmd = "uv run python scripts/dev_server.py", help = "Start the development server with CSS watcher", deps = [
"db-up",
"js-deps",
] }
build = { sequence = [
"build-frontend",
"collectstatic",
], help = "Build frontend assets and collect static files" }
setup = { sequence = ["db-up", "migrate", "bootstrap"], help = "Complete setup: start database, run migrations, and bootstrap data" }
dev = { cmd = "python manage.py runserver", help = "Start the development server", deps = ["db-up"] }
# Database tasks
db-up = { cmd = "docker compose -f docker-compose.dev.yml up -d", help = "Start PostgreSQL database using Docker Compose" }
db-down = { cmd = "docker compose -f docker-compose.dev.yml down", help = "Stop PostgreSQL database" }
# Frontend tasks
js-deps = { cmd = "uv run python scripts/pnpm_wrapper.py install", help = "Install frontend dependencies" }
# Full cleanup tasks
clean = { sequence = [
"clean-db",
], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
clean = { sequence = ["clean-db"], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
clean-db = { cmd = "docker compose -f docker-compose.dev.yml down -v", help = "Removes the database container and volume." }
# Django tasks
migrate = { cmd = "uv run python manage.py migrate", help = "Run database migrations" }
migrate = { cmd = "python manage.py migrate", help = "Run database migrations" }
bootstrap = { shell = """
echo "Bootstrapping initial data..."
echo "This will take a bit . Get yourself some coffee..."
uv run python manage.py bootstrap
python manage.py bootstrap
echo " Bootstrap complete"
echo ""
echo "Default admin credentials:"
@ -108,16 +88,4 @@ echo " Username: admin"
echo " Email: admin@envipath.com"
echo " Password: SuperSafe"
""", help = "Bootstrap initial data (anonymous user, packages, models)" }
shell = { cmd = "uv run python manage.py shell", help = "Open Django shell" }
build-frontend = { cmd = "uv run python scripts/pnpm_wrapper.py run build", help = "Build frontend assets using pnpm", deps = [
"js-deps",
] } # Build tasks
collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help = "Collect static files for production", deps = [
"build-frontend",
] }
frontend-test-setup = { cmd = "playwright install", help = "Install the browsers required for frontend testing" }
shell = { cmd = "python manage.py shell", help = "Open Django shell" }

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@ -1,201 +0,0 @@
#!/usr/bin/env python3
"""
Cross-platform development server script.
Starts pnpm CSS watcher and Django dev server, handling cleanup on exit.
Works on both Windows and Unix systems.
"""
import atexit
import shutil
import signal
import subprocess
import sys
import time
def find_pnpm():
"""
Find pnpm executable on the system.
Returns the path to pnpm or None if not found.
"""
# Try to find pnpm using shutil.which
# On Windows, this will find pnpm.cmd if it's in PATH
pnpm_path = shutil.which("pnpm")
if pnpm_path:
return pnpm_path
# On Windows, also try pnpm.cmd explicitly
if sys.platform == "win32":
pnpm_cmd = shutil.which("pnpm.cmd")
if pnpm_cmd:
return pnpm_cmd
return None
class DevServerManager:
"""Manages background processes for development server."""
def __init__(self):
self.processes = []
self._cleanup_registered = False
def start_process(self, command, description, shell=False):
"""Start a background process and return the process object."""
print(f"Starting {description}...")
try:
if shell:
# Use shell=True for commands that need shell interpretation
process = subprocess.Popen(
command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
text=True,
bufsize=1,
)
else:
# Split command into list for subprocess
process = subprocess.Popen(
command,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
text=True,
bufsize=1,
)
self.processes.append((process, description))
print(f"✓ Started {description} (PID: {process.pid})")
return process
except Exception as e:
print(f"✗ Failed to start {description}: {e}", file=sys.stderr)
self.cleanup()
sys.exit(1)
def cleanup(self):
"""Terminate all running processes."""
if not self.processes:
return
print("\nShutting down...")
for process, description in self.processes:
if process.poll() is None: # Process is still running
try:
# Try graceful termination first
if sys.platform == "win32":
process.terminate()
else:
process.send_signal(signal.SIGTERM)
# Wait up to 5 seconds for graceful shutdown
try:
process.wait(timeout=5)
except subprocess.TimeoutExpired:
# Force kill if graceful shutdown failed
if sys.platform == "win32":
process.kill()
else:
process.send_signal(signal.SIGKILL)
process.wait()
print(f"{description} stopped")
except Exception as e:
print(f"✗ Error stopping {description}: {e}", file=sys.stderr)
self.processes.clear()
def register_cleanup(self):
"""Register cleanup handlers for various exit scenarios."""
if self._cleanup_registered:
return
self._cleanup_registered = True
# Register atexit handler (works on all platforms)
atexit.register(self.cleanup)
# Register signal handlers (Unix only)
if sys.platform != "win32":
signal.signal(signal.SIGINT, self._signal_handler)
signal.signal(signal.SIGTERM, self._signal_handler)
def _signal_handler(self, signum, frame):
"""Handle Unix signals."""
self.cleanup()
sys.exit(0)
def wait_for_process(self, process, description):
"""Wait for a process to finish and handle its output."""
try:
# Stream output from the process
for line in iter(process.stdout.readline, ""):
if line:
print(f"[{description}] {line.rstrip()}")
process.wait()
return process.returncode
except KeyboardInterrupt:
# Handle Ctrl+C
self.cleanup()
sys.exit(0)
except Exception as e:
print(f"Error waiting for {description}: {e}", file=sys.stderr)
self.cleanup()
sys.exit(1)
def main():
"""Main entry point."""
manager = DevServerManager()
manager.register_cleanup()
# Find pnpm executable
pnpm_path = find_pnpm()
if not pnpm_path:
print("Error: pnpm not found in PATH.", file=sys.stderr)
print("\nPlease install pnpm:", file=sys.stderr)
print(" Windows: https://pnpm.io/installation#on-windows", file=sys.stderr)
print(" Unix: https://pnpm.io/installation#on-posix-systems", file=sys.stderr)
sys.exit(1)
# Determine shell usage based on platform
use_shell = sys.platform == "win32"
# Start pnpm CSS watcher
# Use the found pnpm path to ensure it works on Windows
pnpm_command = f'"{pnpm_path}" run dev' if use_shell else [pnpm_path, "run", "dev"]
manager.start_process(
pnpm_command,
"CSS watcher",
shell=use_shell,
)
# Give pnpm a moment to start
time.sleep(1)
# Start Django dev server
django_process = manager.start_process(
["uv", "run", "python", "manage.py", "runserver"],
"Django server",
shell=False,
)
print("\nDevelopment servers are running. Press Ctrl+C to stop.\n")
try:
# Wait for Django server (main process)
# If Django exits, we should clean up everything
return_code = manager.wait_for_process(django_process, "Django")
# If Django exited unexpectedly, clean up and exit
if return_code != 0:
manager.cleanup()
sys.exit(return_code)
except KeyboardInterrupt:
# Ctrl+C was pressed
manager.cleanup()
sys.exit(0)
if __name__ == "__main__":
main()

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@ -1,59 +0,0 @@
#!/usr/bin/env python3
"""
Cross-platform pnpm command wrapper.
Finds pnpm correctly on Windows (handles pnpm.cmd) and Unix systems.
"""
import shutil
import subprocess
import sys
def find_pnpm():
"""
Find pnpm executable on the system.
Returns the path to pnpm or None if not found.
"""
# Try to find pnpm using shutil.which
# On Windows, this will find pnpm.cmd if it's in PATH
pnpm_path = shutil.which("pnpm")
if pnpm_path:
return pnpm_path
# On Windows, also try pnpm.cmd explicitly
if sys.platform == "win32":
pnpm_cmd = shutil.which("pnpm.cmd")
if pnpm_cmd:
return pnpm_cmd
return None
def main():
"""Main entry point - execute pnpm with provided arguments."""
pnpm_path = find_pnpm()
if not pnpm_path:
print("Error: pnpm not found in PATH.", file=sys.stderr)
print("\nPlease install pnpm:", file=sys.stderr)
print(" Windows: https://pnpm.io/installation#on-windows", file=sys.stderr)
print(" Unix: https://pnpm.io/installation#on-posix-systems", file=sys.stderr)
sys.exit(1)
# Get all arguments passed to this script
args = sys.argv[1:]
# Execute pnpm with the provided arguments
try:
sys.exit(subprocess.call([pnpm_path] + args))
except KeyboardInterrupt:
# Handle Ctrl+C gracefully
sys.exit(130)
except Exception as e:
print(f"Error executing pnpm: {e}", file=sys.stderr)
sys.exit(1)
if __name__ == "__main__":
main()

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@ -1,84 +0,0 @@
/**
* DaisyUI Themes - Generated by Style Dictionary
* Theme mappings defined in tokens/daisyui-themes.json
*/
/* Light theme (default) */
@plugin "daisyui/theme" {
name: "envipath";
default: true;
color-scheme: light;
--color-base-100: var(--color-neutral-50);
--color-base-200: var(--color-neutral-100);
--color-base-300: var(--color-neutral-200);
--color-base-content: var(--color-neutral-900);
--color-primary: var(--color-primary-500);
--color-primary-content: var(--color-primary-50);
--color-secondary: var(--color-secondary-500);
--color-secondary-content: var(--color-secondary-50);
--color-accent: var(--color-accent-500);
--color-accent-content: var(--color-accent-50);
--color-neutral: var(--color-neutral-950);
--color-neutral-content: var(--color-neutral-100);
--color-info: var(--color-info-500);
--color-info-content: var(--color-info-950);
--color-success: var(--color-success-500);
--color-success-content: var(--color-success-950);
--color-warning: var(--color-warning-500);
--color-warning-content: var(--color-warning-950);
--color-error: var(--color-error-500);
--color-error-content: var(--color-error-950);
/* border radius */
--radius-selector: 1rem;
--radius-field: 0.25rem;
--radius-box: 0.5rem;
/* base sizes */
--size-selector: 0.25rem;
--size-field: 0.25rem;
/* border size */
--border: 1px;
/* effects */
--depth: 1;
--noise: 0;
}
/* Dark theme (prefers-color-scheme: dark) */
@plugin "daisyui/theme" {
name: "envipath-dark";
prefersdark: true;
color-scheme: dark;
--color-primary: var(--color-primary-400);
--color-primary-content: var(--color-neutral-950);
--color-secondary: var(--color-secondary-400);
--color-secondary-content: var(--color-neutral-950);
--color-accent: var(--color-primary-500);
--color-accent-content: var(--color-neutral-950);
--color-neutral: var(--color-neutral-300);
--color-neutral-content: var(--color-neutral-900);
--color-base-100: var(--color-neutral-900);
--color-base-200: var(--color-neutral-800);
--color-base-300: var(--color-neutral-700);
--color-base-content: var(--color-neutral-50);
--color-info: var(--color-primary-400);
--color-info-content: var(--color-neutral-950);
--color-success: var(--color-success-400);
--color-success-content: var(--color-neutral-950);
--color-warning: var(--color-warning-400);
--color-warning-content: var(--color-neutral-950);
--color-error: var(--color-error-400);
--color-error-content: var(--color-neutral-950);
--radius-selector: 1rem;
--radius-field: 0.25rem;
--radius-box: 0.5rem;
--size-selector: 0.25rem;
--size-field: 0.25rem;
--border: 1px;
--depth: 1;
--noise: 0;
}

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@ -1,63 +0,0 @@
@import "tailwindcss";
/* fira-code-latin-wght-normal */
@font-face {
font-family: 'Fira Code Variable';
font-style: normal;
font-display: swap;
font-weight: 300 700;
src: url(https://cdn.jsdelivr.net/fontsource/fonts/fira-code:vf@latest/latin-wght-normal.woff2) format('woff2-variations');
unicode-range: U+0000-00FF,U+0131,U+0152-0153,U+02BB-02BC,U+02C6,U+02DA,U+02DC,U+0304,U+0308,U+0329,U+2000-206F,U+20AC,U+2122,U+2191,U+2193,U+2212,U+2215,U+FEFF,U+FFFD;
}
/* inter-latin-wght-normal */
@font-face {
font-family: 'Inter Variable';
font-style: normal;
font-display: swap;
font-weight: 100 900;
src: url(https://cdn.jsdelivr.net/fontsource/fonts/inter:vf@latest/latin-wght-normal.woff2) format('woff2-variations');
unicode-range: U+0000-00FF,U+0131,U+0152-0153,U+02BB-02BC,U+02C6,U+02DA,U+02DC,U+0304,U+0308,U+0329,U+2000-206F,U+20AC,U+2122,U+2191,U+2193,U+2212,U+2215,U+FEFF,U+FFFD;
}
/* Tell Tailwind where to find Django templates and Python files */
@source "../../templates";
/* Custom theme configuration - must come before plugins */
@import "./theme.css";
/* Import DaisyUI plugin */
@plugin "daisyui" {
logs: true;
exclude: rootscrollgutter;
}
@import "./daisyui-theme.css";
/* Loading Spinner - Benzene Ring */
.loading-spinner {
display: flex;
justify-content: center;
align-items: center;
padding: 2rem;
}
.loading-spinner svg {
width: 48px;
height: 48px;
animation: spin 2s linear infinite;
}
.loading-spinner .hexagon,
.loading-spinner .double-bonds {
fill: none;
stroke: currentColor;
stroke-width: 2;
}
@keyframes spin {
100% {
transform: rotate(360deg);
}
}

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@ -1,111 +0,0 @@
/**
* Tailwind v4 Theme - Generated by Style Dictionary
* This creates Tailwind utility classes from design tokens
*/
@theme {
/* Colors */
--color-primary-50: oklch(0.98 0.02 201);
--color-primary-100: oklch(0.96 0.04 203);
--color-primary-200: oklch(0.92 0.08 205);
--color-primary-300: oklch(0.87 0.12 207);
--color-primary-400: oklch(0.80 0.13 212);
--color-primary-500: oklch(0.71 0.13 215);
--color-primary-600: oklch(0.61 0.11 222);
--color-primary-700: oklch(0.52 0.09 223);
--color-primary-800: oklch(0.45 0.08 224);
--color-primary-900: oklch(0.40 0.07 227);
--color-primary-950: oklch(0.30 0.05 230);
--color-secondary-50: oklch(0.98 0.02 166);
--color-secondary-100: oklch(0.95 0.05 163);
--color-secondary-200: oklch(0.90 0.09 164);
--color-secondary-300: oklch(0.85 0.13 165);
--color-secondary-400: oklch(0.77 0.15 163);
--color-secondary-500: oklch(0.70 0.15 162);
--color-secondary-600: oklch(0.60 0.13 163);
--color-secondary-700: oklch(0.51 0.10 166);
--color-secondary-800: oklch(0.43 0.09 167);
--color-secondary-900: oklch(0.38 0.07 169);
--color-secondary-950: oklch(0.26 0.05 173);
--color-success-50: oklch(0.98 0.02 156);
--color-success-100: oklch(0.96 0.04 157);
--color-success-200: oklch(0.93 0.08 156);
--color-success-300: oklch(0.87 0.14 154);
--color-success-400: oklch(0.80 0.18 152);
--color-success-500: oklch(0.72 0.19 150);
--color-success-600: oklch(0.63 0.17 149);
--color-success-700: oklch(0.53 0.14 150);
--color-success-800: oklch(0.45 0.11 151);
--color-success-900: oklch(0.39 0.09 153);
--color-success-950: oklch(0.27 0.06 153);
--color-warning-50: oklch(0.99 0.03 102);
--color-warning-100: oklch(0.97 0.07 103);
--color-warning-200: oklch(0.95 0.12 102);
--color-warning-300: oklch(0.91 0.17 98);
--color-warning-400: oklch(0.86 0.17 92);
--color-warning-500: oklch(0.80 0.16 86);
--color-warning-600: oklch(0.68 0.14 76);
--color-warning-700: oklch(0.55 0.12 66);
--color-warning-800: oklch(0.48 0.10 62);
--color-warning-900: oklch(0.42 0.09 58);
--color-warning-950: oklch(0.29 0.06 54);
--color-error-50: oklch(0.97 0.01 17);
--color-error-100: oklch(0.94 0.03 18);
--color-error-200: oklch(0.88 0.06 18);
--color-error-300: oklch(0.81 0.10 20);
--color-error-400: oklch(0.71 0.17 22);
--color-error-500: oklch(0.64 0.21 25);
--color-error-600: oklch(0.58 0.22 27);
--color-error-700: oklch(0.51 0.19 28);
--color-error-800: oklch(0.44 0.16 27);
--color-error-900: oklch(0.40 0.13 26);
--color-error-950: oklch(0.26 0.09 26);
--color-neutral-50: oklch(0.98 0.00 248);
--color-neutral-100: oklch(0.97 0.01 248);
--color-neutral-200: oklch(0.93 0.01 256);
--color-neutral-300: oklch(0.87 0.02 253);
--color-neutral-400: oklch(0.71 0.04 257);
--color-neutral-500: oklch(0.55 0.04 257);
--color-neutral-600: oklch(0.45 0.04 257);
--color-neutral-700: oklch(0.37 0.04 257);
--color-neutral-800: oklch(0.28 0.04 260);
--color-neutral-900: oklch(0.28 0.04 260);
--color-neutral-950: oklch(0.28 0.04 260);
/* Spacing */
--spacing-0: 0;
--spacing-1: 0.25rem;
--spacing-2: 0.5rem;
--spacing-3: 0.75rem;
--spacing-4: 1rem;
--spacing-5: 1.25rem;
--spacing-6: 1.5rem;
--spacing-7: 1.75rem;
--spacing-8: 2rem;
--spacing-10: 2.5rem;
--spacing-12: 3rem;
--spacing-16: 4rem;
--spacing-20: 5rem;
--spacing-24: 6rem;
--spacing-32: 8rem;
--spacing-40: 10rem;
--spacing-48: 12rem;
--spacing-56: 14rem;
--spacing-64: 16rem;
/* Typography */
--font-family-sans: 'Inter Variable', system-ui, -apple-system, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
--font-family-mono: 'Fira Code Variable', 'Cascadia Code', 'Source Code Pro', Menlo, Consolas, monospace;
--font-family-base: 'Inter Variable', system-ui, -apple-system, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
--font-size-xs: 0.75rem;
--font-size-sm: 0.875rem;
--font-size-base: 1rem;
--font-size-lg: 1.125rem;
--font-size-xl: 1.25rem;
--font-size-2xl: 1.5rem;
--font-size-3xl: 1.875rem;
--font-size-4xl: 2.25rem;
--font-size-5xl: 3rem;
--font-size-6xl: 3.75rem;
--font-size-7xl: 4.5rem;
}

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<svg fill="currentColor" id="ep-logo-square" role="img" viewBox="0 0 65 65" xmlns="http://www.w3.org/2000/svg">
<path d="M26.538 25.283c-.532-1.519-1.274-2.861-2.24-4.037a11.163 11.163 0 0 0-3.522-2.828c-1.381-.712-2.948-1.07-4.697-1.07-1.791 0-3.379.358-4.76 1.07a11.11 11.11 0 0 0-3.522 2.828c-.966 1.176-1.737 2.533-2.308 4.07a19.839 19.839 0 0 0-1.139 4.728h23.047a15.559 15.559 0 0 0-.86-4.76zM5 38.57c.44 1.685 1.143 3.189 2.11 4.527.966 1.333 2.187 2.436 3.656 3.31 1.475.875 3.243 1.308 5.313 1.308 3.178 0 5.665-.83 7.456-2.485 1.793-1.65 3.037-3.867 3.726-6.626h4.35c-.922 4.054-2.613 7.179-5.073 9.39-2.46 2.208-5.947 3.315-10.46 3.315-2.802 0-5.233-.502-7.274-1.489-2.056-.986-3.721-2.348-5.01-4.072-1.284-1.724-2.241-3.725-2.861-6.005C.313 37.465 0 35.058 0 32.529c0-2.343.313-4.649.933-6.9.62-2.254 1.577-4.267 2.861-6.04 1.289-1.772 2.954-3.197 5.01-4.281 2.041-1.08 4.472-1.616 7.275-1.616 2.856 0 5.293.571 7.32 1.724 2.026 1.147 3.666 2.66 4.931 4.521 1.265 1.86 2.177 3.999 2.725 6.416a27.9 27.9 0 0 1 .692 7.348H4.35c0 1.567.215 3.188.65 4.868M49.301 31.456c.914 0 1.793-.07 2.638-.202.845-.136 1.586-.4 2.23-.78.641-.391 1.159-.942 1.548-1.656.387-.702.582-1.64.582-2.782 0-1.148-.195-2.08-.582-2.79-.39-.707-.907-1.26-1.547-1.65-.645-.386-1.386-.65-2.231-.78a16.554 16.554 0 0 0-2.638-.206h-6.176v10.846h6.176zm2.184-17.032c2.26 0 4.189.331 5.776.995 1.592.66 2.88 1.524 3.877 2.608a10.007 10.007 0 0 1 2.177 3.696c.46 1.393.684 2.828.684 4.313 0 1.455-.224 2.88-.684 4.28a9.955 9.955 0 0 1-2.177 3.727c-.997 1.079-2.285 1.953-3.877 2.607-1.587.664-3.516.992-5.776.992h-8.36v12.974h-7.964V14.424h16.324" class="logo-main"/>
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/**
* Alpine.js Components for enviPath
*
* This module provides reusable Alpine.js data components for modals,
* form validation, and form submission.
*/
document.addEventListener('alpine:init', () => {
/**
* Modal Form Component
*
* Provides form validation using HTML5 Constraint Validation API,
* loading states for submission, and error message management.
*
* Basic Usage:
* <dialog x-data="modalForm()" @close="reset()">
* <form id="my-form">
* <input name="field" required>
* </form>
* <button @click="submit('my-form')" :disabled="isSubmitting">Submit</button>
* </dialog>
*
* With Custom State:
* <dialog x-data="modalForm({ state: { selectedItem: '', imageUrl: '' } })" @close="reset()">
* <select x-model="selectedItem" @change="updateImagePreview(selectedItem + '?image=svg')">
* <img :src="imageUrl" x-show="imageUrl">
* </dialog>
*
* With AJAX:
* <button @click="submitAsync('my-form', { onSuccess: (data) => console.log(data) })">
*/
Alpine.data('modalForm', (options = {}) => ({
isSubmitting: false,
errors: {},
// Spread custom initial state from options
...(options.state || {}),
/**
* Validate a single field using HTML5 Constraint Validation API
* @param {HTMLElement} field - The input/select/textarea element
*/
validateField(field) {
const name = field.name || field.id;
if (!name) return;
if (!field.validity.valid) {
this.errors[name] = field.validationMessage;
} else {
delete this.errors[name];
}
},
/**
* Clear error for a field (call on input)
* @param {HTMLElement} field - The input element
*/
clearError(field) {
const name = field.name || field.id;
if (name && this.errors[name]) {
delete this.errors[name];
}
},
/**
* Get error message for a field
* @param {string} name - Field name
* @returns {string|undefined} Error message or undefined
*/
getError(name) {
return this.errors[name];
},
/**
* Check if form has any errors
* @returns {boolean} True if there are errors
*/
hasErrors() {
return Object.keys(this.errors).length > 0;
},
/**
* Validate all fields in a form
* @param {string} formId - The form element ID
* @returns {boolean} True if form is valid
*/
validateAll(formId) {
const form = document.getElementById(formId);
if (!form) return false;
this.errors = {};
const fields = form.querySelectorAll('input, select, textarea');
fields.forEach(field => {
if (field.name && !field.validity.valid) {
this.errors[field.name] = field.validationMessage;
}
});
return !this.hasErrors();
},
/**
* Validate that two password fields match
* @param {string} password1Id - ID of first password field
* @param {string} password2Id - ID of second password field
* @returns {boolean} True if passwords match
*/
validatePasswordMatch(password1Id, password2Id) {
const pw1 = document.getElementById(password1Id);
const pw2 = document.getElementById(password2Id);
if (!pw1 || !pw2) return false;
if (pw1.value !== pw2.value) {
this.errors[pw2.name || password2Id] = 'Passwords do not match';
pw2.setCustomValidity('Passwords do not match');
return false;
}
delete this.errors[pw2.name || password2Id];
pw2.setCustomValidity('');
return true;
},
/**
* Submit a form with loading state
* @param {string} formId - The form element ID
*/
submit(formId) {
const form = document.getElementById(formId);
if (!form) return;
// Validate before submit
if (!form.checkValidity()) {
form.reportValidity();
return;
}
// Set action to current URL if empty
if (!form.action || form.action === window.location.href + '#') {
form.action = window.location.href;
}
// Set loading state and submit
this.isSubmitting = true;
form.submit();
},
/**
* Submit form via AJAX (fetch)
* @param {string} formId - The form element ID
* @param {Object} options - Options { onSuccess, onError, closeOnSuccess }
*/
async submitAsync(formId, options = {}) {
const form = document.getElementById(formId);
if (!form) return;
// Validate before submit
if (!form.checkValidity()) {
form.reportValidity();
return;
}
this.isSubmitting = true;
try {
const formData = new FormData(form);
const response = await fetch(form.action || window.location.href, {
method: form.method || 'POST',
body: formData,
headers: {
'X-Requested-With': 'XMLHttpRequest',
},
});
const data = await response.json().catch(() => ({}));
if (response.ok) {
if (options.onSuccess) {
options.onSuccess(data);
}
if (data.redirect || data.success) {
window.location.href = data.redirect || data.success;
} else if (options.closeOnSuccess) {
this.$el.closest('dialog')?.close();
}
} else {
const errorMsg = data.error || data.message || `Error: ${response.status}`;
this.errors['_form'] = errorMsg;
if (options.onError) {
options.onError(errorMsg, data);
}
}
} catch (error) {
this.errors['_form'] = error.message;
if (options.onError) {
options.onError(error.message);
}
} finally {
this.isSubmitting = false;
}
},
/**
* Set form action URL dynamically
* @param {string} formId - The form element ID
* @param {string} url - The URL to set as action
*/
setFormAction(formId, url) {
const form = document.getElementById(formId);
if (form) {
form.action = url;
}
},
/**
* Update image preview
* @param {string} url - Image URL (with query params)
* @param {string} targetId - Target element ID for the image
*/
updateImagePreview(url) {
// Store URL for reactive binding with :src
this.imageUrl = url;
},
/**
* Reset form state (call on modal close)
* Resets to initial state from options
*/
reset() {
this.isSubmitting = false;
this.errors = {};
this.imageUrl = '';
// Reset custom state to initial values
if (options.state) {
Object.keys(options.state).forEach(key => {
this[key] = options.state[key];
});
}
// Call custom reset handler if provided
if (options.onReset) {
options.onReset.call(this);
}
}
}));
/**
* Simple Modal Component (no form)
*
* For modals that don't need form validation.
*
* Usage:
* <dialog x-data="modal()">
* <button @click="$el.closest('dialog').close()">Close</button>
* </dialog>
*/
Alpine.data('modal', () => ({
// Placeholder for simple modals that may need state later
}));
});

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@ -1,133 +0,0 @@
/**
* Alpine.js Pagination Component
*
* Provides client-side pagination for large lists.
*/
document.addEventListener('alpine:init', () => {
Alpine.data('paginatedList', (initialItems = [], options = {}) => ({
allItems: initialItems,
filteredItems: [],
currentPage: 1,
perPage: options.perPage || 50,
searchQuery: '',
isReviewed: options.isReviewed || false,
instanceId: options.instanceId || Math.random().toString(36).substring(2, 9),
init() {
this.filteredItems = this.allItems;
},
get totalPages() {
return Math.ceil(this.filteredItems.length / this.perPage);
},
get paginatedItems() {
const start = (this.currentPage - 1) * this.perPage;
const end = start + this.perPage;
return this.filteredItems.slice(start, end);
},
get totalItems() {
return this.filteredItems.length;
},
get showingStart() {
if (this.totalItems === 0) return 0;
return (this.currentPage - 1) * this.perPage + 1;
},
get showingEnd() {
return Math.min(this.currentPage * this.perPage, this.totalItems);
},
search(query) {
this.searchQuery = query.toLowerCase();
if (this.searchQuery === '') {
this.filteredItems = this.allItems;
} else {
this.filteredItems = this.allItems.filter(item =>
item.name.toLowerCase().includes(this.searchQuery)
);
}
this.currentPage = 1;
},
nextPage() {
if (this.currentPage < this.totalPages) {
this.currentPage++;
}
},
prevPage() {
if (this.currentPage > 1) {
this.currentPage--;
}
},
goToPage(page) {
if (page >= 1 && page <= this.totalPages) {
this.currentPage = page;
}
},
get pageNumbers() {
const pages = [];
const total = this.totalPages;
const current = this.currentPage;
// Handle empty case
if (total === 0) {
return pages;
}
if (total <= 7) {
// Show all pages if 7 or fewer
for (let i = 1; i <= total; i++) {
pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
}
} else {
// More than 7 pages - show first, last, and sliding window around current
// Always show first page
pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
// Determine the start and end of the middle range
let rangeStart, rangeEnd;
if (current <= 4) {
// Near the beginning: show pages 2-5
rangeStart = 2;
rangeEnd = 5;
} else if (current >= total - 3) {
// Near the end: show last 4 pages before the last page
rangeStart = total - 4;
rangeEnd = total - 1;
} else {
// In the middle: show current page and one on each side
rangeStart = current - 1;
rangeEnd = current + 1;
}
// Add ellipsis before range if there's a gap
if (rangeStart > 2) {
pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
}
// Add pages in the range
for (let i = rangeStart; i <= rangeEnd; i++) {
pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
}
// Add ellipsis after range if there's a gap
if (rangeEnd < total - 1) {
pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
}
// Always show last page
pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
}
return pages;
}
}));
});

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/**
* Search Modal Alpine.js Component
*
* Provides package selection, search mode switching, and results display
* for the search modal.
*/
document.addEventListener('alpine:init', () => {
/**
* Search Modal Component
*
* Usage:
* <dialog x-data="searchModal()" @close="reset()">
* ...
* </dialog>
*/
Alpine.data('searchModal', () => ({
// Package selector state
selectedPackages: [],
// Search state
searchMode: 'text',
searchModeLabel: 'Text',
query: '',
// Results state
results: null,
isSearching: false,
error: null,
// Initialize on modal open
init() {
// Load reviewed packages by default
this.loadInitialSelection();
// Watch for modal open to focus searchbar
this.$watch('$el.open', (open) => {
if (open) {
setTimeout(() => {
this.$refs.searchbar.focus();
}, 320);
}
});
},
loadInitialSelection() {
// Select all reviewed packages by default
const menuItems = this.$refs.packageDropdown.querySelectorAll('li');
for (const item of menuItems) {
// Stop at 'Unreviewed Packages' section
if (item.classList.contains('menu-title') &&
item.textContent.trim() === 'Unreviewed Packages') {
break;
}
const packageOption = item.querySelector('.package-option');
if (packageOption) {
this.selectedPackages.push({
url: packageOption.dataset.packageUrl,
name: packageOption.dataset.packageName
});
}
}
},
togglePackage(url, name) {
const index = this.selectedPackages.findIndex(pkg => pkg.url === url);
if (index !== -1) {
this.selectedPackages.splice(index, 1);
} else {
this.selectedPackages.push({ url, name });
}
},
removePackage(url) {
const index = this.selectedPackages.findIndex(pkg => pkg.url === url);
if (index !== -1) {
this.selectedPackages.splice(index, 1);
}
},
isPackageSelected(url) {
return this.selectedPackages.some(pkg => pkg.url === url);
},
setSearchMode(mode, label) {
this.searchMode = mode;
this.searchModeLabel = label;
this.$refs.modeDropdown.hidePopover();
},
async performSearch(serverBase) {
if (!this.query.trim()) {
return;
}
if (this.selectedPackages.length < 1) {
this.results = { error: 'no_packages' };
return;
}
const params = new URLSearchParams();
this.selectedPackages.forEach(pkg => params.append('packages', pkg.url));
params.append('search', this.query.trim());
params.append('mode', this.searchModeLabel.toLowerCase());
this.isSearching = true;
this.results = null;
this.error = null;
try {
const response = await fetch(`${serverBase}/search?${params.toString()}`, {
method: 'GET',
headers: { 'Accept': 'application/json' }
});
if (!response.ok) {
throw new Error('Search request failed');
}
this.results = await response.json();
} catch (err) {
console.error('Search error:', err);
this.error = 'Search failed. Please try again.';
} finally {
this.isSearching = false;
}
},
hasResults() {
if (!this.results || this.results.error) return false;
const categories = ['Compounds', 'Compound Structures', 'Rules', 'Reactions', 'Pathways'];
return categories.some(cat => this.results[cat] && this.results[cat].length > 0);
},
reset() {
this.query = '';
this.results = null;
this.error = null;
this.isSearching = false;
}
}));
});

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@ -1,173 +0,0 @@
/**
* Discourse API Integration for enviPath Community
* Handles fetching topics from the Discourse forum API
*/
class DiscourseAPI {
constructor() {
this.baseUrl = 'https://community.envipath.org';
this.categoryId = 10; // Announcements category
this.limit = 3; // Number of topics to fetch
}
/**
* Fetch topics from Discourse API
* @param {number} limit - Number of topics to fetch
* @returns {Promise<Array>} Array of topic objects
*/
async fetchTopics(limit = this.limit) {
try {
const url = `${this.baseUrl}/c/announcements/${this.categoryId}.json`;
const response = await fetch(url);
if (!response.ok) {
throw new Error(`HTTP error! status: ${response.status}`);
}
const data = await response.json();
return this.processTopics(data.topic_list.topics, limit);
} catch (error) {
console.error('Error fetching Discourse topics:', error);
return this.getFallbackTopics();
}
}
/**
* Process raw Discourse topics into standardized format
* @param {Array} topics - Raw topics from Discourse API
* @param {number} limit - Number of topics to return
* @returns {Array} Processed topics
*/
processTopics(topics, limit) {
return topics
.slice(0, limit)
.map(topic => ({
id: topic.id,
title: topic.title,
excerpt: this.extractExcerpt(topic.excerpt),
url: `${this.baseUrl}/t/${topic.slug}/${topic.id}`,
replies: topic.reply_count,
views: topic.views,
created_at: topic.created_at,
category: 'Announcements',
category_id: this.categoryId,
author: topic.last_poster_username,
author_avatar: this.getAvatarUrl(topic.last_poster_username)
}))
.sort((a, b) => new Date(b.created_at) - new Date(a.created_at)); // Latest first
}
/**
* Extract excerpt from topic content
* @param {string} excerpt - Raw excerpt from Discourse
* @returns {string} Cleaned excerpt
*/
extractExcerpt(excerpt) {
if (!excerpt) return 'No preview available yet';
// Remove HTML tags and clean up; collapse whitespace; do not add manual ellipsis
const cleaned = excerpt
.replace(/<[^>]*>/g, '') // Remove HTML tags
.replace(/&nbsp;/g, ' ') // Replace &nbsp; with spaces
.replace(/&amp;/g, '&') // Replace &amp; with &
.replace(/&lt;/g, '<') // Replace &lt; with <
.replace(/&gt;/g, '>') // Replace &gt; with >
.replace(/\s+/g, ' ') // Collapse all whitespace/newlines
.trim();
// Check if excerpt is empty after cleaning
return cleaned || 'No preview available yet';
}
/**
* Get avatar URL for user
* @param {string} username - Username
* @returns {string} Avatar URL
*/
getAvatarUrl(username) {
if (!username) return `${this.baseUrl}/letter_avatar_proxy/v4/letter/u/1.png`;
return `${this.baseUrl}/user_avatar/${this.baseUrl.replace('https://', '')}/${username}/40/1_1.png`;
}
/**
* Get fallback topics when API fails
* @returns {Array} Fallback topics
*/
getFallbackTopics() {
return [
{
id: 110,
title: "enviPath Beta Update: Major Improvements to Prediction, Analysis & Collaboration!",
excerpt: "We're excited to announce major updates to the enviPath beta platform! This release includes significant improvements to our prediction algorithms, enhanced analysis tools, and new collaboration features that will make environmental biotransformation research more accessible and efficient.",
url: "https://community.envipath.org/t/envipath-beta-update-major-improvements-to-prediction-analysis-collaboration/110",
replies: 0,
views: 16,
created_at: "2025-09-23T00:00:00Z",
category: "Announcements",
category_id: 10,
author: "wicker",
author_avatar: "https://community.envipath.org/user_avatar/community.envipath.org/wicker/40/1_1.png"
}
];
}
/**
* Format date for display
* @param {string} dateString - ISO date string
* @returns {string} Formatted date
*/
formatDate(dateString) {
const date = new Date(dateString);
return date.toLocaleDateString();
}
/**
* Load topics and call render function
* @param {string} containerId - ID of container element
* @param {Function} renderCallback - Function to render topics
*/
async loadTopics(containerId = 'community-news-container', renderCallback = null) {
const container = document.getElementById(containerId);
if (!container) {
console.error(`Container with ID '${containerId}' not found`);
return;
}
// Hide loading spinner
const loading = document.getElementById('loading');
if (loading) {
loading.style.display = 'none';
}
try {
const topics = await this.fetchTopics();
if (renderCallback && typeof renderCallback === 'function') {
renderCallback(topics);
} else {
// Default rendering - just log topics
console.log('Topics loaded:', topics);
}
} catch (error) {
console.error('Error loading topics:', error);
container.innerHTML = '<p class="text-neutral">No updates found. Head over to the <a href="https://community.envipath.org" target="_blank" class="link link-primary">community</a> to see the latest discussions.</p>';
}
}
}
// Export for use in other scripts
window.DiscourseAPI = DiscourseAPI;
// Auto-initialize if container exists
document.addEventListener('DOMContentLoaded', function() {
if (document.getElementById('community-news-container')) {
const discourseAPI = new DiscourseAPI();
discourseAPI.loadTopics('community-news-container', function(topics) {
// This will be handled by the template's render function
if (window.renderDiscourseTopics) {
window.renderDiscourseTopics(topics);
}
});
}
});

File diff suppressed because it is too large Load Diff

View File

@ -1,21 +1,14 @@
console.log("loaded pw.js")
function predictFromNode(url) {
fetch("", {
method: "POST",
headers: {
"Content-Type": "application/x-www-form-urlencoded",
"X-CSRFToken": document.querySelector('[name=csrfmiddlewaretoken]')?.value || ''
},
body: new URLSearchParams({node: url})
})
.then(response => response.json())
.then(data => {
$.post("", {node: url})
.done(function (data) {
console.log("Success:", data);
window.location.href = data.success;
})
.catch(error => {
console.error("Error:", error);
.fail(function (xhr, status, error) {
console.error("Error:", xhr.status, xhr.responseText);
// show user-friendly message or log error
});
}
@ -110,9 +103,6 @@ function draw(pathway, elem) {
}
function dragstarted(event, d) {
// Prevent zoom pan when dragging nodes
event.sourceEvent.stopPropagation();
if (!event.active) simulation.alphaTarget(0.3).restart();
d.fx = d.x;
d.fy = d.y;
@ -127,9 +117,6 @@ function draw(pathway, elem) {
}
function dragged(event, d) {
// Prevent zoom pan when dragging nodes
event.sourceEvent.stopPropagation();
d.fx = event.x;
d.fy = event.y;
@ -140,9 +127,6 @@ function draw(pathway, elem) {
}
function dragended(event, d) {
// Prevent zoom pan when dragging nodes
event.sourceEvent.stopPropagation();
if (!event.active) simulation.alphaTarget(0);
// Mark that dragging has ended
@ -208,153 +192,52 @@ function draw(pathway, elem) {
d3.select(t).select("circle").classed("highlighted", !d3.select(t).select("circle").classed("highlighted"));
}
// Wait before showing popup (ms)
// Wait one second before showing popup
var popupWaitBeforeShow = 1000;
// Keep Popup at least for one second
var popushowAtLeast = 1000;
// Custom popover element
let popoverTimeout = null;
function pop_show_e(element) {
var e = element;
setTimeout(function () {
if ($(e).is(':hover')) { // if element is still hovered
$(e).popover("show");
function createPopover() {
const popover = document.createElement('div');
popover.id = 'custom-popover';
popover.className = 'fixed z-50';
popover.style.cssText = `
background: #ffffff;
border: 1px solid #d1d5db;
box-shadow: 0 10px 15px -3px rgb(0 0 0 / 0.1), 0 4px 6px -4px rgb(0 0 0 / 0.1);
max-width: 320px;
padding: 0.75rem;
border-radius: 0.5rem;
opacity: 0;
visibility: hidden;
transition: opacity 150ms ease-in-out, visibility 150ms ease-in-out;
pointer-events: auto;
`;
popover.setAttribute('role', 'tooltip');
popover.innerHTML = `
<div class="font-semibold mb-2 popover-title" style="font-weight: 600; margin-bottom: 0.5rem;"></div>
<div class="text-sm popover-content" style="font-size: 0.875rem;"></div>
`;
// Add styles for content images
const style = document.createElement('style');
style.textContent = `
#custom-popover img {
max-width: 100%;
height: auto;
display: block;
margin: 0.5rem 0;
// workaround to set fixed positions
pop = $(e).attr("aria-describedby")
h = $('#' + pop).height();
$('#' + pop).attr("style", `position: fixed; top: ${clientY - (h / 2.0)}px; left: ${clientX + 10}px; margin: 0px; max-width: 1000px; display: block;`)
setTimeout(function () {
var close = setInterval(function () {
if (!$(".popover:hover").length // mouse outside popover
&& !$(e).is(':hover')) { // mouse outside element
$(e).popover('hide');
clearInterval(close);
}
#custom-popover a {
color: #2563eb;
text-decoration: none;
}, 100);
}, popushowAtLeast);
}
#custom-popover a:hover {
text-decoration: underline;
}
`;
if (!document.getElementById('popover-styles')) {
style.id = 'popover-styles';
document.head.appendChild(style);
}
// Keep popover open when hovering over it
popover.addEventListener('mouseenter', () => {
if (popoverTimeout) {
clearTimeout(popoverTimeout);
popoverTimeout = null;
}
});
popover.addEventListener('mouseleave', () => {
hidePopover();
});
document.body.appendChild(popover);
return popover;
}
function getPopover() {
return document.getElementById('custom-popover') || createPopover();
}
function showPopover(element, title, content) {
const popover = getPopover();
popover.querySelector('.popover-title').textContent = title;
popover.querySelector('.popover-content').innerHTML = content;
// Make visible to measure
popover.style.visibility = 'hidden';
popover.style.opacity = '0';
popover.style.display = 'block';
// Smart positioning - avoid viewport overflow
const padding = 10;
const popoverRect = popover.getBoundingClientRect();
const viewportWidth = window.innerWidth;
const viewportHeight = window.innerHeight;
let left = clientX + 15;
let top = clientY - (popoverRect.height / 2);
// Prevent right overflow
if (left + popoverRect.width > viewportWidth - padding) {
left = clientX - popoverRect.width - 15;
}
// Prevent bottom overflow
if (top + popoverRect.height > viewportHeight - padding) {
top = viewportHeight - popoverRect.height - padding;
}
// Prevent top overflow
if (top < padding) {
top = padding;
}
popover.style.top = `${top}px`;
popover.style.left = `${left}px`;
popover.style.visibility = 'visible';
popover.style.opacity = '1';
currentElement = element;
}
function hidePopover() {
const popover = getPopover();
popover.style.opacity = '0';
popover.style.visibility = 'hidden';
currentElement = null;
}, popupWaitBeforeShow);
}
function pop_add(objects, title, contentFunction) {
objects.each(function (d) {
const element = this;
objects.attr("id", "pop")
.attr("data-container", "body")
.attr("data-toggle", "popover")
.attr("data-placement", "right")
.attr("title", title);
element.addEventListener('mouseenter', () => {
if (popoverTimeout) clearTimeout(popoverTimeout);
popoverTimeout = setTimeout(() => {
if (element.matches(':hover')) {
const content = contentFunction(d);
showPopover(element, title, content);
}
}, popupWaitBeforeShow);
objects.each(function (d, i) {
options = {trigger: "manual", html: true, animation: false};
this_ = this;
var p = $(this).popover(options).on("mouseenter", function () {
pop_show_e(this);
});
element.addEventListener('mouseleave', () => {
if (popoverTimeout) {
clearTimeout(popoverTimeout);
popoverTimeout = null;
}
// Delay hide to allow moving to popover
setTimeout(() => {
const popover = getPopover();
if (!popover.matches(':hover') && !element.matches(':hover')) {
hidePopover();
}
}, 100);
p.on("show.bs.popover", function (e) {
// this is to dynamically ajdust the content and bounds of the popup
p.attr('data-content', contentFunction(d));
p.data("bs.popover").setContent();
p.data("bs.popover").tip().css({"max-width": "1000px"});
});
});
}
@ -372,7 +255,7 @@ function draw(pathway, elem) {
}
}
popupContent += "<img src='" + n.image + "'><br>"
popupContent += "<img src='" + n.image + "' width='" + 20 * nodeRadius + "'><br>"
if (n.scenarios.length > 0) {
popupContent += '<b>Half-lives and related scenarios:</b><br>'
for (var s of n.scenarios) {
@ -382,7 +265,7 @@ function draw(pathway, elem) {
var isLeaf = pathway.links.filter(obj => obj.source.id === n.id).length === 0;
if (pathway.isIncremental && isLeaf) {
popupContent += '<br><a class="btn btn-primary btn-sm mt-2" onclick="predictFromNode(\'' + n.url + '\')" href="#">Predict from here</a><br>';
popupContent += '<br><a class="btn btn-primary" onclick="predictFromNode(\'' + n.url + '\')" href="#">Predict from here</a><br>';
}
return popupContent;
@ -402,7 +285,7 @@ function draw(pathway, elem) {
popupContent += adcontent;
}
popupContent += "<img src='" + e.image + "'><br>"
popupContent += "<img src='" + e.image + "' width='" + 20 * nodeRadius + "'><br>"
if (e.reaction_probability) {
popupContent += '<b>Probability:</b><br>' + e.reaction_probability.toFixed(3) + '<br>';
}
@ -425,23 +308,6 @@ function draw(pathway, elem) {
});
const zoomable = d3.select("#zoomable");
const svg = d3.select("#pwsvg");
const container = d3.select("#vizdiv");
// Set explicit SVG dimensions for proper zoom behavior
svg.attr("width", width)
.attr("height", height);
// Add background rectangle FIRST to enable pan/zoom on empty space
// This must be inserted before zoomable group so it's behind everything
svg.insert("rect", "#zoomable")
.attr("x", 0)
.attr("y", 0)
.attr("width", width)
.attr("height", height)
.attr("fill", "transparent")
.attr("pointer-events", "all")
.style("cursor", "grab");
// Zoom Funktion aktivieren
const zoom = d3.zoom()
@ -450,12 +316,7 @@ function draw(pathway, elem) {
zoomable.attr("transform", event.transform);
});
// Apply zoom to the SVG element - this enables wheel zoom
svg.call(zoom);
// Also apply zoom to container to catch events that might not reach SVG
// This ensures drag-to-pan works even when clicking on empty space
container.call(zoom);
d3.select("svg").call(zoom);
nodes = pathway['nodes'];
links = pathway['links'];

View File

@ -1,10 +1,6 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('new_compound_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Compound</a
>
<a role="button" data-toggle="modal" data-target="#new_compound_modal">
<span class="glyphicon glyphicon-plus"></span> New Compound</a>
</li>
{% endif %}

View File

@ -1,10 +1,6 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('new_compound_structure_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Compound Structure</a
>
<a role="button" data-toggle="modal" data-target="#new_compound_structure_modal">
<span class="glyphicon glyphicon-plus"></span> New Compound Structure</a>
</li>
{% endif %}

View File

@ -1,10 +1,6 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('new_edge_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Edge</a
>
<a role="button" data-toggle="modal" data-target="#new_edge_modal">
<span class="glyphicon glyphicon-plus"></span> New Edge</a>
</li>
{% endif %}

View File

@ -1,8 +1,4 @@
<li>
<a
role="button"
onclick="document.getElementById('new_group_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Group</a
>
<a role="button" data-toggle="modal" data-target="#new_group_modal">
<span class="glyphicon glyphicon-plus"></span> New Group</a>
</li>

View File

@ -1,10 +1,6 @@
{% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
<li>
<a
role="button"
onclick="document.getElementById('new_model_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Model</a
>
<a role="button" data-toggle="modal" data-target="#new_model_modal">
<span class="glyphicon glyphicon-plus"></span> New Model</a>
</li>
{% endif %}

View File

@ -1,10 +1,6 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('new_node_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Node</a
>
<a role="button" data-toggle="modal" data-target="#new_node_modal">
<span class="glyphicon glyphicon-plus"></span> New Node</a>
</li>
{% endif %}

View File

@ -1,25 +1,12 @@
<li>
<a
role="button"
onclick="document.getElementById('new_package_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Package</a
>
<a role="button" data-toggle="modal" data-target="#new_package_modal">
<span class="glyphicon glyphicon-plus"></span> New Package</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('import_package_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-import"></span> Import Package from JSON</a
>
<a role="button" data-toggle="modal" data-target="#import_package_modal">
<span class="glyphicon glyphicon-import"></span> Import Package from JSON</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-import"></span> Import Package from legacy
JSON</a
>
<a role="button" data-toggle="modal" data-target="#import_legacy_package_modal">
<span class="glyphicon glyphicon-import"></span> Import Package from legacy JSON</a>
</li>

View File

@ -1,9 +1,6 @@
{% if meta.can_edit %}
<li>
<a
href="{% if meta.current_package %}{{ meta.current_package.url }}/predict{% else %}{{ meta.server_url }}/predict{% endif %}"
>
<span class="glyphicon glyphicon-plus"></span> New Pathway</a
>
<a role="button" data-toggle="modal" data-target="#predict_modal">
<span class="glyphicon glyphicon-plus"></span> New Pathway</a>
</li>
{% endif %}

View File

@ -1,10 +1,6 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('new_reaction_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Reaction</a
>
<a role="button" data-toggle="modal" data-target="#new_reaction_modal">
<span class="glyphicon glyphicon-plus"></span> New Reaction</a>
</li>
{% endif %}

View File

@ -1,10 +1,6 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('new_rule_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Rule</a
>
<a role="button" data-toggle="modal" data-target="#new_rule_modal">
<span class="glyphicon glyphicon-plus"></span> New Rule</a>
</li>
{% endif %}

View File

@ -1,10 +1,6 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('new_scenario_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Scenario</a
>
<a role="button" data-toggle="modal" data-target="#new_scenario_modal">
<span class="glyphicon glyphicon-plus"></span> New Scenario</a>
</li>
{% endif %}

View File

@ -1,10 +1,6 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('new_setting_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span>New Setting</a
>
<a role="button" data-toggle="modal" data-target="#new_setting_modal">
<span class="glyphicon glyphicon-plus"></span>New Setting</a>
</li>
{% endif %}

View File

@ -1,60 +1,32 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_compound_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Compound</a
>
<a role="button" data-toggle="modal" data-target="#edit_compound_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Compound</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('add_structure_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Add Structure</a
>
<a role="button" data-toggle="modal" data-target="#add_structure_modal">
<i class="glyphicon glyphicon-plus"></i> Add Structure</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a
>
<a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
</li>
{% endif %}
<li>
<a
role="button"
onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a>
</li>
{% if meta.can_edit %}
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
</li>
{% endif %}

View File

@ -1,42 +1,22 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_compound_structure_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a
>
<a role="button" data-toggle="modal" data-target="#edit_compound_structure_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a
>
<a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
</li>
{% endif %}

View File

@ -1,26 +1,14 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Edge</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Edge</a>
</li>
{% endif %}

View File

@ -1,18 +1,10 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_group_member_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a
>
<a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
<i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Group</a
>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Group</a>
</li>
{% endif %}

View File

@ -1,34 +1,18 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_model_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Model</a
>
<a role="button" data-toggle="modal" data-target="#edit_model_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Model</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('evaluate_model_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-ok"></i> Evaluate Model</a
>
<a role="button" data-toggle="modal" data-target="#evaluate_model_modal">
<i class="glyphicon glyphicon-ok"></i> Evaluate Model</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('retrain_model_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-repeat"></i> Retrain Model</a
>
<a role="button" data-toggle="modal" data-target="#retrain_model_modal">
<i class="glyphicon glyphicon-repeat"></i> Retrain Model</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Model</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Model</a>
</li>
{% endif %}

View File

@ -1,34 +1,18 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_node_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Node</a
>
<a role="button" data-toggle="modal" data-target="#edit_node_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Node</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Node</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Node</a>
</li>
{% endif %}

View File

@ -1,50 +1,26 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_package_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Package</a
>
<a role="button" data-toggle="modal" data-target="#edit_package_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Package</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('edit_package_permissions_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-user"></i> Edit Permissions</a
>
<a role="button" data-toggle="modal" data-target="#edit_package_permissions_modal">
<i class="glyphicon glyphicon-user"></i> Edit Permissions</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('publish_package_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
>
<a role="button" data-toggle="modal" data-target="#publish_package_modal">
<i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('export_package_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a
>
<a role="button" data-toggle="modal" data-target="#export_package_modal">
<i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_license_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> License</a
>
<a role="button" data-toggle="modal" data-target="#set_license_modal">
<i class="glyphicon glyphicon-duplicate"></i> License</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Package</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Package</a>
</li>
{% endif %}

View File

@ -1,104 +1,59 @@
{% if meta.can_edit %}
<li>
<a
class="button"
onclick="document.getElementById('add_pathway_node_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Add Compound</a
>
<a class="button" data-toggle="modal" data-target="#add_pathway_node_modal">
<i class="glyphicon glyphicon-plus"></i> Add Compound</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('add_pathway_edge_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Add Reaction</a
>
<a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
<i class="glyphicon glyphicon-plus"></i> Add Reaction</a>
</li>
<li role="separator" class="divider"></li>
{% endif %}
<li>
<a
role="button"
onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('download_pathway_csv_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a
>
<a class="button" data-toggle="modal" data-target="#download_pathway_csv_modal">
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('download_pathway_image_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a
>
<a class="button" data-toggle="modal" data-target="#download_pathway_image_modal">
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a>
</li>
{% if meta.can_edit %}
<li>
<a
class="button"
onclick="document.getElementById('identify_missing_rules_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-question-sign"></i> Identify Missing
Rules</a
>
<a class="button" data-toggle="modal" data-target="#identify_missing_rules_modal">
<i class="glyphicon glyphicon-question-sign"></i> Identify Missing Rules</a>
</li>
<li role="separator" class="divider"></li>
<li>
<a
class="button"
onclick="document.getElementById('edit_pathway_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Pathway</a
>
<a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Pathway</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
{# <li>#}
{# <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
{# <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}
{# </li>#}
<li role="separator" class="divider"></li>
<li>
<a
class="button"
onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a
>
<a class="button" data-toggle="modal" data-target="#delete_pathway_node_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
>
<a class="button" data-toggle="modal" data-target="#delete_pathway_edge_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Pathway</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
</li>
{% endif %}

View File

@ -1,52 +1,28 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_reaction_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Reaction</a
>
<a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a
>
<a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
</li>
{% endif %}
<li>
<a
role="button"
onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a>
</li>
{% if meta.can_edit %}
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
</li>
{% endif %}

View File

@ -1,44 +1,24 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_rule_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Rule</a
>
<a role="button" data-toggle="modal" data-target="#edit_rule_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
{% endif %}
<li>
<a
role="button"
onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a>
</li>
{% if meta.can_edit %}
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Rule</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Rule</a>
</li>
{% endif %}

View File

@ -1,26 +1,14 @@
{% if meta.can_edit %}
<li>
<a
class="button"
onclick="document.getElementById('add_additional_information_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Add Additional Information</a
>
<a class="button" data-toggle="modal" data-target="#add_additional_information_modal">
<i class="glyphicon glyphicon-trash"></i> Add Additional Information</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('update_scenario_additional_information_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Set Additional Information</a
>
<a class="button" data-toggle="modal" data-target="#update_scenario_additional_information_modal">
<i class="glyphicon glyphicon-trash"></i> Set Additional Information</a>
</li>
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Scenario</a
>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Scenario</a>
</li>
{% endif %}

View File

@ -1,38 +1,22 @@
{% if meta.can_edit %}
<li>
<a
role="button"
onclick="document.getElementById('edit_user_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Update</a
>
<a role="button" data-toggle="modal" data-target="#edit_user_modal">
<i class="glyphicon glyphicon-edit"></i> Update</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('edit_password_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-lock"></i> Update Password</a
>
<a role="button" data-toggle="modal" data-target="#edit_password_modal">
<i class="glyphicon glyphicon-lock"></i> Update Password</a>
</li>
<li>
<a
role="button"
onclick="document.getElementById('new_prediction_setting_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a
>
<a role="button" data-toggle="modal" data-target="#new_prediction_setting_modal">
<i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a>
</li>
{# <li>#}
{# <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">#}
{# <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
{# </li>#}
<li>
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Account</a
>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Account</a>
</li>
{% endif %}

View File

@ -1,17 +1,12 @@
{% extends "framework.html" %}
{% load static %}
{% block content %}
<div id="searchContent">
<div id=searchContent>
<form id="admin-form" action="{{ SERVER_BASE }}/admin" method="post">
<div class="form-group">
<label for="textarea">Query</label>
<textarea
id="textarea"
class="form-control"
rows="10"
placeholder="Paste query here"
required
>
<textarea id="textarea" class="form-control" rows="10" placeholder="Paste query here" required>
PREFIX pps: <http://localhost:8080/vocabulary#>
SELECT ?name (count(?objId) as ?xcnt)
WHERE {
@ -20,29 +15,32 @@ WHERE {
?packageId pps:reviewStatus 'reviewed' .
?packageId pps:pathway ?objId .
} GROUP BY ?name
</textarea
>
</textarea>
</div>
<button id="submit" type="button" class="btn btn-primary">Submit</button>
</form>
<p></p>
</div>
<div id="results"></div>
<div id="results">
</div>
<div id="loading"></div>
</div>
<script>
$(function() {
$("#submit").on("click", function () {
$('#submit').on('click', function() {
makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
data = {
query: $("#textarea").val(),
};
"query": $("#textarea").val()
}
$.post("{{ SERVER_BASE }}/expire", data, function(result) {
$("#loading").empty();
queryResultToTable("results", result);
})
});
});
});
})
</script>
{% endblock content %}

View File

@ -1,52 +1,49 @@
{% extends "framework_modern.html" %}
{% extends "framework.html" %}
{% load static %}
{% load envipytags %}
{% block content %}
<div class="space-y-2 p-4">
<!-- Header Section -->
<div class="card bg-base-100">
<div class="card-body">
<h2 class="card-title text-2xl">User Prediction Jobs</h2>
<p class="mt-2">Job Logs Desc</p>
<div class="panel-group" id="reviewListAccordion">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
Jobs
</div>
<div class="panel-body">
<p>
Job Logs Desc
</p>
</div>
<!-- Jobs -->
<div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked />
<div class="collapse-title text-xl font-medium">Recent Jobs</div>
<div class="collapse-content" id="job-content">
<div class="overflow-x-auto">
<table class="table-zebra table">
<thead>
<tr>
<th>ID</th>
<th>Name</th>
<th>Status</th>
<th>Queued</th>
<th>Done</th>
<th>Result</th>
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="job-accordion-link" data-toggle="collapse" data-parent="#job-accordion" href="#jobs">
Jobs
</a>
</h4>
</div>
<div id="jobs"
class="panel-collapse collapse in">
<div class="panel-body list-group-item" id="job-content">
<table class="table table-bordered table-hover">
<tr style="background-color: rgba(0, 0, 0, 0.08);">
<th scope="col">ID</th>
<th scope="col">Name</th>
<th scope="col">Status</th>
<th scope="col">Queued</th>
<th scope="col">Done</th>
<th scope="col">Result</th>
</tr>
</thead>
<tbody>
{% for job in jobs %}
<tr>
{% if meta.user.is_superuser %}
<td>
<a href="{{ job.user.url }}">{{ job.user.username }}</a>
</td>
{% endif %}
<td>{{ job.task_id }}</td>
<td>{{ job.job_name }}</td>
<td>{{ job.status }}</td>
<td>{{ job.created }}</td>
<td>{{ job.done_at }}</td>
{% if job.task_result and job.task_result|is_url == True %}
<td>
<a href="{{ job.task_result }}" class="link link-primary"
>Result</a
>
</td>
<td><a href="{{ job.task_result }}">Result</a></td>
{% elif job.task_result %}
<td>{{ job.task_result|slice:"40" }}...</td>
{% else %}
@ -58,31 +55,17 @@
</table>
</div>
</div>
</div>
{% if objects %}
<!-- Unreviewable objects such as User / Group / Setting -->
<div class="card bg-base-100 shadow-xl">
<div class="card-body">
<ul class="menu bg-base-200 rounded-box">
<ul class='list-group'>
{% for obj in objects %}
{% if object_type == 'user' %}
<li>
<a href="{{ obj.url }}" class="hover:bg-base-300"
>{{ obj.username }}</a
>
</li>
<a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
{% else %}
<li>
<a href="{{ obj.url }}" class="hover:bg-base-300"
>{{ obj.name }}</a
>
</li>
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
{% endif %}
{% endfor %}
</ul>
</div>
</div>
{% endif %}
</div>
{% endblock content %}

View File

@ -1,32 +1,20 @@
{% extends "framework_modern.html" %}
{% extends "framework.html" %}
{% load static %}
{% block content %}
{# Serialize objects data for Alpine pagination #}
{# prettier-ignore-start #}
{# FIXME: This is a hack to get the objects data into the JavaScript code. #}
<script>
window.reviewedObjects = [
{% for obj in reviewed_objects %}
{ "name": "{{ obj.name|escapejs }}", "url": "{{ obj.url }}" }{% if not forloop.last %},{% endif %}
{% endfor %}
];
window.unreviewedObjects = [
{% for obj in unreviewed_objects %}
{ "name": "{{ obj.name|escapejs }}", "url": "{{ obj.url }}" }{% if not forloop.last %},{% endif %}
{% endfor %}
];
</script>
{# prettier-ignore-end #}
{% if object_type != 'package' %}
<div class="px-8 py-4">
<input
type="text"
id="object-search"
class="input input-bordered hidden w-full max-w-xs"
placeholder="Search by name"
/>
<div>
<div id="load-all-error" style="display: none;">
<div class="alert alert-danger" role="alert">
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
<span class="sr-only">Error:</span>
Getting objects failed!
</div>
</div>
<input type="text" id="object-search" class="form-control" placeholder="Search by name"
style="display: none;">
<p></p>
</div>
{% endif %}
@ -60,12 +48,9 @@
{% endif %}
{% endblock action_modals %}
<div class="px-8 py-4">
<!-- Header Section -->
<div class="card bg-base-100">
<div class="card-body px-0 py-4">
<div class="flex items-center justify-between">
<h2 class="card-title text-2xl">
<div class="panel-group" id="reviewListAccordion">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{% if object_type == 'package' %}
Packages
{% elif object_type == 'compound' %}
@ -93,31 +78,13 @@
{% elif object_type == 'group' %}
Groups
{% endif %}
</h2>
<div id="actionsButton" class="dropdown dropdown-end hidden">
<div tabindex="0" role="button" class="btn btn-ghost btn-sm">
<svg
xmlns="http://www.w3.org/2000/svg"
width="16"
height="16"
viewBox="0 0 24 24"
fill="none"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
class="lucide lucide-wrench"
>
<path
d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
/>
</svg>
Actions
</div>
<ul
tabindex="-1"
class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
>
<div id="actionsButton"
style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-haspopup="true" aria-expanded="false"><span
class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
style="padding-right:1em"></span></a>
<ul id="actionsList" class="dropdown-menu">
{% block actions %}
{% if object_type == 'package' %}
{% include "actions/collections/package.html" %}
@ -148,386 +115,205 @@
</ul>
</div>
</div>
<div class="mt-2">
<div class="panel-body">
<!-- Set Text above links -->
{% if object_type == 'package' %}
<p>
A package contains pathways, rules, etc. and can reflect specific
experimental conditions.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/packages"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>A package contains pathways, rules, etc. and can reflect specific experimental
conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
more &gt;&gt;</a></p>
{% elif object_type == 'compound' %}
<p>
A compound stores the structure of a molecule and can include
meta-information.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/compounds"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>A compound stores the structure of a molecule and can include meta-information.
<a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'structure' %}
<p>
The structures stored in this compound
<a
target="_blank"
href="https://wiki.envipath.org/index.php/compounds"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>The structures stored in this compound
<a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'rule' %}
<p>
A rule describes a biotransformation reaction template that is
defined as SMIRKS.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/Rules"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>A rule describes a biotransformation reaction template that is defined as SMIRKS.
<a target="_blank" href="https://wiki.envipath.org/index.php/Rules" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'reaction' %}
<p>
A reaction is a specific biotransformation from educt compounds to
product compounds.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/reactions"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>A reaction is a specific biotransformation from educt compounds to product compounds.
<a target="_blank" href="https://wiki.envipath.org/index.php/reactions" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'pathway' %}
<p>
A pathway displays the (predicted) biodegradation of a compound as
graph.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/pathways"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>A pathway displays the (predicted) biodegradation of a compound as graph.
<a target="_blank" href="https://wiki.envipath.org/index.php/pathways" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'node' %}
<p>
Nodes represent the (predicted) compounds in a graph.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/nodes"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>Nodes represent the (predicted) compounds in a graph.
<a target="_blank" href="https://wiki.envipath.org/index.php/nodes" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'edge' %}
<p>
Edges represent the links between Nodes in a graph
<a
target="_blank"
href="https://wiki.envipath.org/index.php/edges"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>Edges represent the links between Nodes in a graph
<a target="_blank" href="https://wiki.envipath.org/index.php/edges" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'scenario' %}
<p>
A scenario contains meta-information that can be attached to other
data (compounds, rules, ..).
<a
target="_blank"
href="https://wiki.envipath.org/index.php/scenarios"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>A scenario contains meta-information that can be attached to other data (compounds, rules, ..).
<a target="_blank" href="https://wiki.envipath.org/index.php/scenarios" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'model' %}
<p>
A model applies machine learning to limit the combinatorial
explosion.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/relative_reasoning"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>A model applies machine learning to limit the combinatorial explosion.
<a target="_blank" href="https://wiki.envipath.org/index.php/relative_reasoning" role="button">Learn
more
&gt;&gt;</a></p>
{% elif object_type == 'setting' %}
<p>
A setting includes configuration parameters for pathway
predictions.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/settings"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>A setting includes configuration parameters for pathway predictions.
<a target="_blank" href="https://wiki.envipath.org/index.php/settings" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'user' %}
<p>
Register now to create own packages and to submit and manage your
data.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/users"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>Register now to create own packages and to submit and manage your data.
<a target="_blank" href="https://wiki.envipath.org/index.php/users" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'group' %}
<p>
Users can team up in groups to share packages.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/groups"
class="link link-primary"
>Learn more &gt;&gt;</a
>
</p>
<p>Users can team up in groups to share packages.
<a target="_blank" href="https://wiki.envipath.org/index.php/groups" role="button">Learn more
&gt;&gt;</a></p>
{% endif %}
<!-- If theres nothing to show extend the text above -->
{% if reviewed_objects and unreviewed_objects %}
{% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
<p class="mt-4">
Nothing found. There are two possible reasons: <br /><br />1.
There is no content yet.<br />2. You have no reading
permissions.<br /><br />Please be sure you have at least reading
permissions.
</p>
<p>Nothing found. There are two possible reasons: <br><br>1. There is no content yet.<br>2. You have no
reading permissions.<br><br>Please be sure you have at least reading permissions.</p>
{% endif %}
{% endif %}
</div>
</div>
</div>
<!-- Lists Container - Full Width with Reviewed on Right -->
<div class="w-full">
{% if reviewed_objects %}
{% if reviewed_objects|length > 0 %}
<!-- Reviewed -->
<div
class="collapse-arrow bg-base-200 collapse order-2 w-full"
x-data="paginatedList(window.reviewedObjects || [], { isReviewed: true, instanceId: 'reviewed' })"
>
<input type="checkbox" checked />
<div class="collapse-title text-xl font-medium">
Reviewed
<span
class="badge badge-sm badge-neutral ml-2"
x-text="totalItems"
></span>
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="ReviewedLink" data-toggle="collapse" data-parent="#reviewListAccordion"
href="#Reviewed">Reviewed</a>
</h4>
</div>
<div class="collapse-content w-full">
<ul class="menu bg-base-100 rounded-box w-full">
<template x-for="obj in paginatedItems" :key="obj.url">
<li>
<a :href="obj.url" class="hover:bg-base-200">
<span x-text="obj.name"></span>
<span
class="tooltip tooltip-left ml-auto"
data-tip="Reviewed"
>
<svg
xmlns="http://www.w3.org/2000/svg"
width="16"
height="16"
viewBox="0 0 24 24"
fill="none"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
class="lucide lucide-star"
>
<polygon
points="12 2 15.09 8.26 22 9.27 17 14.14 18.18 21.02 12 17.77 5.82 21.02 7 14.14 2 9.27 8.91 8.26 12 2"
/>
</svg>
<div id="Reviewed" class="panel-collapse collapse in">
<div class="panel-body list-group-item" id="ReviewedContent">
{% if object_type == 'package' %}
{% for obj in reviewed_objects %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}
<span class="glyphicon glyphicon-star" aria-hidden="true"
style="float:right" data-toggle="tooltip"
data-placement="top" title="" data-original-title="Reviewed">
</span>
</a>
</li>
</template>
</ul>
<!-- Pagination Controls -->
<div
x-show="totalPages > 1"
class="mt-4 flex items-center justify-between px-2"
>
<span class="text-base-content/70 text-sm">
Showing <span x-text="showingStart"></span>-<span
x-text="showingEnd"
></span>
of <span x-text="totalItems"></span>
{% endfor %}
{% else %}
{% for obj in reviewed_objects|slice:":50" %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}{# <i>({{ obj.package.name }})</i> #}
<span class="glyphicon glyphicon-star" aria-hidden="true"
style="float:right" data-toggle="tooltip"
data-placement="top" title="" data-original-title="Reviewed">
</span>
<div class="join">
<button
class="join-item btn btn-sm"
:disabled="currentPage === 1"
@click="prevPage()"
>
«
</button>
<template x-for="item in pageNumbers" :key="item.key">
<button
class="join-item btn btn-sm"
:class="{ 'btn-active': item.page === currentPage }"
:disabled="item.isEllipsis"
@click="!item.isEllipsis && goToPage(item.page)"
x-text="item.page"
></button>
</template>
<button
class="join-item btn btn-sm"
:disabled="currentPage === totalPages"
@click="nextPage()"
>
»
</button>
</div>
</div>
</a>
{% endfor %}
{% endif %}
</div>
</div>
{% endif %}
{% endif %}
{% if unreviewed_objects %}
<!-- Unreviewed -->
<div
class="collapse-arrow bg-base-200 collapse order-1 w-full"
x-data="paginatedList(window.unreviewedObjects || [], { isReviewed: false, instanceId: 'unreviewed' })"
>
<input
type="checkbox"
{% if reviewed_objects|length == 0 or object_type == 'package' %}checked{% endif %}
/>
<div class="collapse-title text-xl font-medium">
Unreviewed
<span
class="badge badge-sm badge-neutral ml-2"
x-text="totalItems"
></span>
</div>
<div class="collapse-content w-full">
<ul class="menu bg-base-100 rounded-box w-full">
<template x-for="obj in paginatedItems" :key="obj.url">
<li>
<a
:href="obj.url"
class="hover:bg-base-200"
x-text="obj.name"
></a>
</li>
</template>
</ul>
<!-- Pagination Controls -->
<div
x-show="totalPages > 1"
class="mt-4 flex items-center justify-between px-2"
>
<span class="text-base-content/70 text-sm">
Showing <span x-text="showingStart"></span>-<span
x-text="showingEnd"
></span>
of <span x-text="totalItems"></span>
</span>
<div class="join">
<button
class="join-item btn btn-sm"
:disabled="currentPage === 1"
@click="prevPage()"
>
«
</button>
<template x-for="item in pageNumbers" :key="item.key">
<button
class="join-item btn btn-sm"
:class="{ 'btn-active': item.page === currentPage }"
:disabled="item.isEllipsis"
@click="!item.isEllipsis && goToPage(item.page)"
x-text="item.page"
></button>
</template>
<button
class="join-item btn btn-sm"
:disabled="currentPage === totalPages"
@click="nextPage()"
>
»
</button>
</div>
</div>
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver"><h4
class="panel-title"><a id="UnreviewedLink" data-toggle="collapse" data-parent="#unReviewListAccordion"
href="#Unreviewed">Unreviewed</a></h4></div>
<div id="Unreviewed" class="panel-collapse collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %}">
<div class="panel-body list-group-item" id="UnreviewedContent">
{% if object_type == 'package' %}
{% for obj in unreviewed_objects %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
{% endfor %}
{% else %}
{% for obj in unreviewed_objects|slice:":50" %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
{% endfor %}
{% endif %}
</div>
</div>
{% endif %}
</div>
{% if objects %}
<!-- Unreviewable objects such as User / Group / Setting -->
<div class="card bg-base-100">
<div class="card-body">
<ul class="menu bg-base-200 rounded-box">
<ul class='list-group'>
{% for obj in objects %}
{% if object_type == 'user' %}
<li>
<a href="{{ obj.url }}" class="hover:bg-base-300"
>{{ obj.username }}</a
>
</li>
<a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
{% else %}
<li>
<a href="{{ obj.url }}" class="hover:bg-base-300"
>{{ obj.name }}</a
>
</li>
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
{% endif %}
{% endfor %}
</ul>
</div>
</div>
{% endif %}
</div>
<style>
.spinner-widget {
position: fixed; /* stays in place on scroll */
bottom: 20px; /* distance from bottom */
right: 20px; /* distance from right */
z-index: 9999; /* above most elements */
width: 60px; /* adjust to gif size */
height: 60px;
}
.spinner-widget img {
width: 100%;
height: auto;
}
</style>
<div id="load-all-loading" class="spinner-widget" style="display: none">
<img id="loading-gif" src="{% static '/images/wait.gif' %}" alt="Loading...">
</div>
</div>
<script>
document.addEventListener("DOMContentLoaded", function () {
// Show actions button if there are actions
const actionsButton = document.getElementById("actionsButton");
const actionsList = actionsButton?.querySelector("ul");
if (actionsList && actionsList.children.length > 0) {
actionsButton?.classList.remove("hidden");
$(function () {
$('#object-search').show();
{% if object_type != 'package' and object_type != 'user' and object_type != 'group' %}
{% if reviewed_objects|length > 50 or unreviewed_objects|length > 50 %}
$('#load-all-loading').show()
setTimeout(function () {
$('#load-all-error').hide();
$.getJSON('?all=true', function (resp) {
$('#ReviewedContent').empty();
$('#UnreviewedContent').empty();
for (o in resp.objects) {
obj = resp.objects[o];
if (obj.reviewed) {
$('#ReviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + ' <span class="glyphicon glyphicon-star" aria-hidden="true" style="float:right" data-toggle="tooltip" data-placement="top" title="" data-original-title="Reviewed"></span></a>');
} else {
$('#UnreviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + '</a>');
}
}
// Show search input and connect to Alpine pagination
const objectSearch = document.getElementById("object-search");
if (objectSearch) {
objectSearch.classList.remove("hidden");
objectSearch.addEventListener("input", function () {
const query = this.value;
// Dispatch search to all paginatedList components
document
.querySelectorAll('[x-data*="paginatedList"]')
.forEach((el) => {
if (el._x_dataStack && el._x_dataStack[0]) {
el._x_dataStack[0].search(query);
}
$('#load-all-loading').hide();
$('#load-remaining').hide();
}).fail(function (resp) {
$('#load-all-loading').hide();
$('#load-all-error').show();
});
});
}
// Delete form submit handler
const deleteSubmit = document.getElementById("modal-form-delete-submit");
const deleteForm = document.getElementById("modal-form-delete");
if (deleteSubmit && deleteForm) {
deleteSubmit.addEventListener("click", function (e) {
}, 2500);
{% endif %}
{% endif %}
$('#modal-form-delete-submit').on('click', function (e) {
e.preventDefault();
deleteForm.submit();
$('#modal-form-delete').submit();
});
}
$('#object-search').on('keyup', function () {
let query = $(this).val().toLowerCase();
$('a.list-group-item').each(function () {
let text = $(this).text().toLowerCase();
$(this).toggle(text.indexOf(query) !== -1);
});
});
});
</script>
{% endblock content %}

View File

@ -4,32 +4,16 @@
<div>
<form action="" method="post">
{% csrf_token %}
<input
type="text"
class="form-control"
id="smiles"
name="smiles"
placeholder="SMILES"
value="{{ smiles }}"
/>
<input
type="text"
class="form-control"
id="smiles"
name="smirks"
placeholder="SMIRKS"
value="{{ smirks }}"
/>
<input type="text" class="form-control" id="smiles" name="smiles" placeholder="SMILES"
value="{{ smiles }}"/>
<input type="text" class="form-control" id="smiles" name="smirks" placeholder="SMIRKS"
value="{{ smirks }}"/>
<button type="submit" class="btn btn-primary">Test</button>
</form>
</div>
{% if result %}
{{ smiles }}
<p></p>
<img
width="400"
src="{% url 'depict' %}?smiles={{ smiles|urlencode }}"
/><br />
{{ smiles }}<p></p>
<img width='400' src='{% url 'depict' %}?smiles={{ smiles|urlencode }}'><br>
<p></p>
{% if rule %}
{{ smirks }}
@ -38,7 +22,9 @@
<p></p>
{{ rule.products_smarts }}
<p></p>
<div>{{ rule.as_svg|safe }}</div>
<div>
{{ rule.as_svg|safe }}
</div>
{% endif %}
<h2>Diff</h2>
{% if diff %}
@ -52,22 +38,16 @@
<div class="col-md-6">
<h2>Ambit</h2>
{% for p in ambit_res %}
{{ p }}<br />
<img
width="400"
src="{% url 'depict' %}?smiles={{ p|urlencode }}"
/><br />
{{ p }}<br>
<img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
{% endfor %}
</div>
<div class="col-md-6">
<h2>RDKit</h2>
{% for p in rdkit_res %}
{{ p }}<br />
<img
width="400"
src="{% url 'depict' %}?smiles={{ p|urlencode }}"
/><br />
{{ p }}<br>
<img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
{% endfor %}
</div>
</div>

View File

@ -1,77 +1,15 @@
{% extends "framework_modern.html" %}
{% extends "framework.html" %}
{% load static %}
{% block content %}
<div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
<div class="w-full max-w-2xl">
<div class="alert alert-error mb-6 shadow-lg">
<svg
xmlns="http://www.w3.org/2000/svg"
class="h-8 w-8 shrink-0 stroke-current"
fill="none"
viewBox="0 0 24 24"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z"
/>
</svg>
<div class="flex flex-col">
<h3 class="text-lg font-bold">Bad Request</h3>
<p class="text-sm">The request you sent was invalid or malformed.</p>
</div>
<div class="alert alert-error" role="alert">
<h4 class="alert-heading">Bad Request!</h4>
<p>Lorem</p>
<hr>
<p class="mb-0">
You can find out more about permissions in our <a target="_blank"
href="https://wiki.envipath.org/index.php/packages"
role="button">Wiki &gt;&gt;</a></p>
</div>
<div class="card bg-base-100 shadow-xl">
<div class="card-body">
<h2 class="card-title mb-4 text-2xl">What happened?</h2>
<p class="text-base-content/70 mb-4">
The server couldn't process your request because it contains invalid
data or parameters.
</p>
<div class="card-actions mt-6 justify-end">
<a href="/" class="btn btn-primary">
<svg
xmlns="http://www.w3.org/2000/svg"
class="mr-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
/>
</svg>
Go Home
</a>
<a
href="https://wiki.envipath.org/index.php/packages"
target="_blank"
class="btn btn-outline"
>
Learn More
<svg
xmlns="http://www.w3.org/2000/svg"
class="ml-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M10 6H6a2 2 0 00-2 2v10a2 2 0 002 2h10a2 2 0 002-2v-4M14 4h6m0 0v6m0-6L10 14"
/>
</svg>
</a>
</div>
</div>
</div>
</div>
</div>
{% endblock content %}

View File

@ -1,80 +1,15 @@
{% extends "framework_modern.html" %}
{% extends "framework.html" %}
{% load static %}
{% block content %}
<div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
<div class="w-full max-w-2xl">
<div class="alert alert-warning mb-6 shadow-lg">
<svg
xmlns="http://www.w3.org/2000/svg"
class="h-8 w-8 shrink-0 stroke-current"
fill="none"
viewBox="0 0 24 24"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z"
/>
</svg>
<div class="flex flex-col">
<h3 class="text-lg font-bold">Access Denied</h3>
<p class="text-sm">
You don't have permission to access this resource.
</p>
</div>
<div class="alert alert-error" role="alert">
<h4 class="alert-heading">Access Denied!</h4>
<p>Access to X denied. </p>
<hr>
<p class="mb-0">
You can find out more about permissions in our <a target="_blank"
href="https://wiki.envipath.org/index.php/packages"
role="button">Wiki &gt;&gt;</a></p>
</div>
<div class="card bg-base-100 shadow-xl">
<div class="card-body">
<h2 class="card-title mb-4 text-2xl">Permission Required</h2>
<p class="text-base-content/70 mb-4">
You need the appropriate permissions to access this content. If you
believe this is an error, please contact the package owner or
administrator.
</p>
<div class="card-actions mt-6 justify-end">
<a href="/" class="btn btn-primary">
<svg
xmlns="http://www.w3.org/2000/svg"
class="mr-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
/>
</svg>
Go Home
</a>
<a
href="https://wiki.envipath.org/index.php/packages"
target="_blank"
class="btn btn-outline"
>
Learn More
<svg
xmlns="http://www.w3.org/2000/svg"
class="ml-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M10 6H6a2 2 0 00-2 2v10a2 2 0 002 2h10a2 2 0 002-2v-4M14 4h6m0 0v6m0-6L10 14"
/>
</svg>
</a>
</div>
</div>
</div>
</div>
</div>
{% endblock content %}

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@ -1,77 +1,15 @@
{% extends "framework_modern.html" %}
{% extends "framework.html" %}
{% load static %}
{% block content %}
<div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
<div class="w-full max-w-2xl">
<div class="alert alert-info mb-6 shadow-lg">
<svg
xmlns="http://www.w3.org/2000/svg"
class="h-8 w-8 shrink-0 stroke-current"
fill="none"
viewBox="0 0 24 24"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
/>
</svg>
<div class="flex flex-col">
<h3 class="text-lg font-bold">Page Not Found</h3>
<p class="text-sm">The page you're looking for doesn't exist.</p>
</div>
<div class="alert alert-error" role="alert">
<h4 class="alert-heading">Not Found!</h4>
<p>Does not exist</p>
<hr>
<p class="mb-0">
You can find out more about permissions in our <a target="_blank"
href="https://wiki.envipath.org/index.php/packages"
role="button">Wiki &gt;&gt;</a></p>
</div>
<div class="card bg-base-100 shadow-xl">
<div class="card-body">
<h2 class="card-title mb-4 text-2xl">404 Error</h2>
<p class="text-base-content/70 mb-4">
The page or resource you requested could not be found. It may have
been moved, deleted, or the URL might be incorrect.
</p>
<div class="card-actions mt-6 justify-end">
<a href="/" class="btn btn-primary">
<svg
xmlns="http://www.w3.org/2000/svg"
class="mr-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
/>
</svg>
Go Home
</a>
<a
href="https://wiki.envipath.org/index.php/packages"
target="_blank"
class="btn btn-outline"
>
Learn More
<svg
xmlns="http://www.w3.org/2000/svg"
class="ml-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M10 6H6a2 2 0 00-2 2v10a2 2 0 002 2h10a2 2 0 002-2v-4M14 4h6m0 0v6m0-6L10 14"
/>
</svg>
</a>
</div>
</div>
</div>
</div>
</div>
{% endblock content %}

View File

@ -1,76 +1,13 @@
{% extends "framework_modern.html" %}
{% extends "framework.html" %}
{% load static %}
{% block content %}
<div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
<div class="w-full max-w-2xl">
<div class="alert alert-error mb-6 shadow-lg">
<svg
xmlns="http://www.w3.org/2000/svg"
class="h-8 w-8 shrink-0 stroke-current"
fill="none"
viewBox="0 0 24 24"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M10 14l2-2m0 0l2-2m-2 2l-2-2m2 2l2 2m7-2a9 9 0 11-18 0 9 9 0 0118 0z"
/>
</svg>
<div class="flex flex-col">
<h3 class="text-lg font-bold">
{{ error_message|default:"An Error Occurred" }}
</h3>
<p class="text-sm">
{{ error_detail|default:"Something went wrong. Please try again later." }}
<div class="alert alert-danger" role="alert">
<h4 class="alert-heading">{{ error_message }}</h4>
<hr>
<p class="mb-0">
{{ error_detail }}
</p>
</div>
</div>
<div class="card bg-base-100 shadow-xl">
<div class="card-body">
<h2 class="card-title mb-4 text-2xl">Oops! Something went wrong</h2>
<p class="text-base-content/70 mb-4">
{{ error_description|default:"We encountered an unexpected error while processing your request. Our team has been notified and is working to resolve the issue." }}
</p>
<div class="card-actions mt-6 justify-end">
<a href="/" class="btn btn-primary">
<svg
xmlns="http://www.w3.org/2000/svg"
class="mr-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
/>
</svg>
Go Home
</a>
<button onclick="window.history.back()" class="btn btn-outline">
<svg
xmlns="http://www.w3.org/2000/svg"
class="mr-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M10 19l-7-7m0 0l7-7m-7 7h18"
/>
</svg>
Go Back
</button>
</div>
</div>
</div>
</div>
</div>
{% endblock content %}

View File

@ -1,81 +1,12 @@
{% extends "framework_modern.html" %}
{% extends "framework.html" %}
{% load static %}
{% block content %}
<div class="flex min-h-[60vh] flex-col items-center justify-center p-8">
<div class="w-full max-w-2xl">
<div class="alert alert-warning mb-6 shadow-lg">
<svg
xmlns="http://www.w3.org/2000/svg"
class="h-8 w-8 shrink-0 stroke-current"
fill="none"
viewBox="0 0 24 24"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z"
/>
</svg>
<div class="flex flex-col">
<h3 class="text-lg font-bold">Account Not Activated</h3>
<p class="text-sm">Your account is pending activation.</p>
</div>
<div class="alert alert-danger" role="alert">
<h4 class="alert-heading">Your account has not been activated yet!</h4>
<p>Your account has not been activated yet. If you have questions <a href="mailto:admin@envipath.org">contact
us.</a>
</p>
</div>
<div class="card bg-base-100 shadow-xl">
<div class="card-body">
<h2 class="card-title mb-4 text-2xl">Account Activation Required</h2>
<p class="text-base-content/70 mb-4">
Your account has not been activated yet. An administrator needs to
approve your account before you can access all features. This
process typically takes 24-48 hours.
</p>
<div class="divider"></div>
<p class="text-base-content/70 mb-4">
If you have questions or believe this is an error, please
<a href="mailto:admin@envipath.org" class="link link-primary"
>contact us</a
>.
</p>
<div class="card-actions mt-6 justify-end">
<a href="/" class="btn btn-primary">
<svg
xmlns="http://www.w3.org/2000/svg"
class="mr-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M3 12l2-2m0 0l7-7 7 7M5 10v10a1 1 0 001 1h3m10-11l2 2m-2-2v10a1 1 0 01-1 1h-3m-6 0a1 1 0 001-1v-4a1 1 0 011-1h2a1 1 0 011 1v4a1 1 0 001 1m-6 0h6"
/>
</svg>
Go Home
</a>
<a href="mailto:admin@envipath.org" class="btn btn-outline">
<svg
xmlns="http://www.w3.org/2000/svg"
class="mr-2 h-5 w-5"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M3 8l7.89 5.26a2 2 0 002.22 0L21 8M5 19h14a2 2 0 002-2V7a2 2 0 00-2-2H5a2 2 0 00-2 2v10a2 2 0 002 2z"
/>
</svg>
Contact Admin
</a>
</div>
</div>
</div>
</div>
</div>
{% endblock content %}

View File

@ -1,52 +1,28 @@
<!doctype html>
<html data-theme="envipath">
<!DOCTYPE html>
<html>
{% load static %}
<head>
<title>{{ title }}</title>
<meta name="csrf-token" content="{{ csrf_token }}" />
{# Favicon #}
<link
rel="shortcut icon"
type="image/png"
href="{% static 'images/favicon.ico' %}"
/>
{# Tailwind CSS disabled for legacy Bootstrap framework #}
{# Pages using this framework will be migrated to framework_modern.html incrementally #}
{# <link href="{% static 'css/output.css' %}" rel="stylesheet" type="text/css"/> #}
{# Legacy Bootstrap 3.3.7 - scoped to .legacy-bootstrap #}
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
<link
rel="stylesheet"
href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
/>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
<script src="https://ajax.aspnetcdn.com/ajax/jquery.templates/beta1/jquery.tmpl.js"></script>
<link
href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
rel="stylesheet"
/>
<link
rel="stylesheet"
href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css"
/>
<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/js/bootstrap-select.min.js"></script>
<script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
<!-- CDN END -->
{# Bootstrap compatibility styles #}
<style>
/* Ensure proper viewport behavior */
html,
body {
html, body {
height: 100%; /* ensure body fills viewport */
overflow-x: hidden; /* prevent horizontal scroll */
}
</style>
{# TODO use bundles from bootstrap 3.3.7 #}
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
<script src="https://ajax.aspnetcdn.com/ajax/jquery.templates/beta1/jquery.tmpl.js"></script>
<link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
<link rel="stylesheet"
href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css">
<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/js/bootstrap-select.min.js"></script>
<script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
<!-- CDN END -->
<meta name="csrf-token" content="{{ csrf_token }}">
<script>
const csrftoken = document.querySelector("[name=csrf-token]").content;
const csrftoken = document.querySelector('[name=csrf-token]').content;
// Setup CSRF header for all jQuery AJAX requests
$.ajaxSetup({
@ -54,15 +30,17 @@
if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
xhr.setRequestHeader("X-CSRFToken", csrftoken);
}
},
}
});
</script>
{# Favicon #}
<link rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
<!-- {# C3 CSS #}-->
<!-- <link id="css-c3" href="{% static 'css/c3.css' %}" rel="stylesheet" type="text/css"/>-->
<!-- {# EP CSS #}-->
<!-- <link id="css-pps_white_general" href="{% static 'css/epp.css' %}" rel="stylesheet" type="text/css"/>-->
{# General EP JS #}
<script src="{% static 'js/pps.js' %}"></script>
{# Modal Steps for Stepwise Modal Wizards #}
@ -71,33 +49,26 @@
{% if not debug %}
<!-- Matomo -->
<script>
var _paq = (window._paq = window._paq || []);
var _paq = window._paq = window._paq || [];
/* tracker methods like "setCustomDimension" should be called before "trackPageView" */
_paq.push(["trackPageView"]);
_paq.push(["enableLinkTracking"]);
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function () {
var u = "//matomo.envipath.com/";
_paq.push(["setTrackerUrl", u + "matomo.php"]);
_paq.push(["setSiteId", "{{ meta.site_id }}"]);
var d = document,
g = d.createElement("script"),
s = d.getElementsByTagName("script")[0];
_paq.push(['setTrackerUrl', u + 'matomo.php']);
_paq.push(['setSiteId', '10']);
var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
g.async = true;
g.src = u + "matomo.js";
g.src = u + 'matomo.js';
s.parentNode.insertBefore(g, s);
})();
</script>
<!-- End Matomo Code -->
{% endif %}
</head>
<body>
<!-- Legacy Bootstrap navbar - isolated from Tailwind -->
<div class="legacy-bootstrap">
<nav
class="navbar navbar-default navbar-inverse"
style="border-radius:0px;"
role="navigation"
>
<nav class="navbar navbar-default navbar-inverse" style="border-radius:0px;" role="navigation">
<div class="container-fluid">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header navbar-header-framework">
@ -108,28 +79,19 @@
<!-- <span class="icon-bar"></span>-->
<!-- <span class="icon-bar"></span>-->
<!-- </button>-->
<a
id="pictureLink"
href="{{ meta.server_url }}"
class="navbar-brand"
>
<img
id="image-logo-short-white.svg"
src="{% static "/images/logo-short-white.svg" %}"
width="100"
alt="enviPath"
/>
<a id="pictureLink" href="{{ meta.server_url }}" class="navbar-brand">
<img id="image-logo-short-white.svg" src='{% static "/images/logo-short-white.svg" %}' width="100"
alt="enviPath">
</a>
</div>
<!-- Collect the nav links, forms, and other content for toggling -->
<div
class="navbar-collapse collapse-framework navbar-collapse-framework collapse"
id="navbarCollapse"
>
<div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
<ul class="nav navbar-nav navbar-nav-framework">
<li>
<a href="{{ meta.server_url }}/predict"> Predict Pathway </a>
<a href="#" data-toggle="modal" data-target="#predict_modal">
Predict Pathway
</a>
</li>
{# <li class="dropdown">#}
{# <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
@ -146,135 +108,67 @@
{# </li>#}
{# </ul>#}
{# </li>#}
<li>
<a href="{{ meta.server_url }}/package" id="packageLink"
>Package</a
>
</li>
<li>
<a href="{{ meta.server_url }}/model" id="modelLink"
>Modelling</a
>
</li>
<li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li>
<li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>
<li><a href="{{ meta.server_url }}/model" id="modelLink">Modelling</a></li>
<li class="dropdown">
<a data-toggle="dropdown" class="dropdown-toggle" href="#"
>Browse Data<b class="caret"></b
></a>
<a data-toggle="dropdown" class="dropdown-toggle" href="#">Browse Data<b class="caret"></b></a>
<ul role="menu" class="dropdown-menu">
<li>
<a href="{{ meta.server_url }}/pathway" id="pathwayLink"
>Pathway</a
>
</li>
<li>
<a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a>
</li>
<li>
<a href="{{ meta.server_url }}/compound" id="compoundLink"
>Compound</a
>
</li>
<li>
<a href="{{ meta.server_url }}/reaction" id="reactionLink"
>Reaction</a
>
</li>
<li>
<a
href="{{ meta.server_url }}/model"
id="relative-reasoningLink"
>Model</a
>
</li>
<li>
<a href="{{ meta.server_url }}/scenario" id="scenarioLink"
>Scenario</a
>
</li>
<li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
<li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
<li><a href="{{ meta.server_url }}/compound" id="compoundLink">Compound</a></li>
<li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
<li><a href="{{ meta.server_url }}/model" id="relative-reasoningLink">Model</a></li>
<li><a href="{{ meta.server_url }}/scenario" id="scenarioLink">Scenario</a></li>
{# <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>#}
{# <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>#}
{# <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>#}
</ul>
</li>
</ul>
<ul
class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework"
>
<li>
<a href="https://community.envipath.org/" id="communityLink"
>Community</a
>
</li>
<ul class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework">
<li><a href="https://community.envipath.org/" id="communityLink">Community</a></li>
<li class="dropdown">
<a data-toggle="dropdown" class="dropdown-toggle" href="#"
>Info <b class="caret"></b
></a>
<a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
<ul role="menu" class="dropdown-menu">
<!--<li><a href="{{ meta.server_url }}/funding" id="fundingLink">Funding</a></li>-->
<li>
<a
href="https://community.envipath.org/t/envipath-license/109"
id="licenceLink"
>Licences</a
>
</li>
<li><a href="https://community.envipath.org/t/envipath-license/109" id="licenceLink">Licences</a></li>
<li class="divider"></li>
<li>
<a
target="_blank"
href="https://wiki.envipath.org/"
id="wikiLink"
>Documentation Wiki</a
>
<li><a target="_blank" href="https://wiki.envipath.org/" id="wikiLink">Documentation Wiki</a>
</li>
<li><a href="#" id="citeButton" data-toggle="modal" data-target="#citemodal">How to cite
enviPath</a></li>
<li class="divider"></li>
<li><a>Version: {{ meta.version }}</a></li>
</ul>
</li>
{% if meta.user.username == 'anonymous' %}
<li>
<a
href="{% url 'login' %}"
id="loginButton"
style="margin-right:10px"
>Login</a
>
<a href="#signup" id="loginButton" data-toggle="modal" data-target="#signupmodal"
style="margin-right:10px">Login</a>
</li>
{% else %}
<li class="dropdown">
<a
data-toggle="dropdown"
id="loggedInButton"
class="dropdown-toggle"
id="logedInButton"
href="#"
>
<a data-toggle="dropdown" id="loggedInButton" class="dropdown-toggle" id="logedInButton"
href="#">
<div id="username">
{{ user.username }}<b class="caret"></b>
</div>
</a>
<ul role="menu" class="dropdown-menu">
<li>
<a href="{{ meta.user.url }}" id="accountbutton"
>My Account</a
>
<a href="{{ meta.user.url }}" id="accountbutton">My Account</a>
</li>
<li class="divider"></li>
<form
class="navbar-form navbar-left navbar-left-framework"
role="logout"
action="{% url 'logout' %}"
method="post"
>
<form class="navbar-form navbar-left navbar-left-framework" role="logout"
action="{% url 'logout' %}" method="post">
{% csrf_token %}
<div class="form-group">
<input type="hidden" name="logout" value="true" />
<input type="hidden" name="logout" value="true">
</div>
<button type="submit" class="btn btn-default">
Logout
</button>
<button type="submit" class="btn btn-default">Logout</button>
</form>
</ul>
</li>
@ -283,9 +177,6 @@
</div>
</div>
</nav>
</div>
<!-- End legacy Bootstrap navbar -->
<div id="docContent" class="content container">
{% if breadcrumbs %}
<div id="bread">
@ -305,30 +196,24 @@
</div>
{% endif %}
{% if message %}
<div id="message">{{ message }}</div>
<div id="message">
{{ message }}
</div>
{% endif %}
{% block content %}
{% endblock content %}
{% if meta.url_contains_package and meta.current_package.license %}
<p></p>
<div class="panel-group" id="license_accordion">
<div
class="panel panel-default list-group-item"
style="background-color:#f5f5f5"
>
<div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
<div class="panel-title">
<a
data-toggle="collapse"
data-parent="#licence_accordion"
href="#license"
>License</a
>
<a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
</div>
</div>
<div id="license" class="panel-collapse in collapse">
<div id="license" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<a target="_blank" href="{{ meta.current_package.license.link }}">
<img src="{{ meta.current_package.license.image_link }}" />
<img src="{{ meta.current_package.license.image_link }}">
</a>
</div>
</div>
@ -336,8 +221,7 @@
{% endif %}
</div>
<!-- FOOTER - Legacy Bootstrap -->
<div class="legacy-bootstrap">
<!-- FOOTER -->
<div class="container text-center">
<hr/>
<div class="row">
@ -345,32 +229,19 @@
<ul class="nav nav-pills nav-justified">
<li>
<a href="http://ml.auckland.ac.nz" target="_blank">
<img
id="image-uoalogo"
height="60"
src="{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}"
alt="The Univserity of Auckland"
/>
<img id="image-uoalogo" height="60" src='{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}'
alt="The Univserity of Auckland"/>
</a>
</li>
<li>
<a href="https://eawag.ch" target="_blank">
<img
id="image-ealogo"
height="60"
src="{% static "/images/ealogo.gif" %}"
alt="Eawag"
/>
<img id="image-ealogo" height="60" src='{% static "/images/ealogo.gif" %}' alt="Eawag"/>
</a>
</li>
<li>
<a href="https://www.uzh.ch/" target="_blank">
<img
id="image-ufzlogo"
height="60"
src="{% static "/images/uzh-logo.svg" %}"
alt="University of Zurich"
/>
<img id="image-ufzlogo" height="60" src='{% static "/images/uzh-logo.svg" %}'
alt="University of Zurich"/>
</a>
</li>
</ul>
@ -381,24 +252,25 @@
<div class="col-lg-12">
<ul class="nav nav-pills nav-justified">
<!-- <li><a href="https://envipath.com/imprint/" target="_blank">Impressum/Imprint</a></li>-->
<li>
<a href="mailto:admin@envipath.org" target="_blank">Contact</a>
</li>
<li><a href="mailto:admin@envipath.org" target="_blank">Contact</a></li>
<!-- <li><a href="http://envipath.com" target="_blank"> enviPath UG (haftungsbeschr&auml;nkt) &amp; Co. KG &copy;-->
<!-- {{ YEAR }}</a></li>-->
</ul>
</div>
</div>
</div>
<!-- End legacy Bootstrap footer -->
<script>
$(function () {
// Hide actionsbutton if theres no action defined
if ($("#actionsButton ul").children().length > 0) {
$("#actionsButton").show();
if ($('#actionsButton ul').children().length > 0) {
$('#actionsButton').show();
}
});
</script>
{% block modals %}
{% include "modals/cite_modal.html" %}
{% include "modals/signup_modal.html" %}
{% include "modals/predict_modal.html" %}
{% include "modals/batch_predict_modal.html" %}
{% endblock %}
</body>
</html>

View File

@ -1,219 +0,0 @@
<!doctype html>
<html data-theme="envipath" lang="en">
{% load static %}
<head>
<title>{{ title }}</title>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<meta name="csrf-token" content="{{ csrf_token }}" />
{# Favicon #}
<link
rel="shortcut icon"
type="image/png"
href="{% static 'images/favicon.ico' %}"
/>
{# Tailwind CSS + DaisyUI Output #}
<link
href="{% static 'css/output.css' %}"
rel="stylesheet"
type="text/css"
/>
{# Alpine.js - For reactive components #}
<script
defer
src="https://cdn.jsdelivr.net/npm/alpinejs@3.x.x/dist/cdn.min.js"
></script>
<script src="{% static 'js/alpine/index.js' %}"></script>
<script src="{% static 'js/alpine/search.js' %}"></script>
<script src="{% static 'js/alpine/pagination.js' %}"></script>
{# Font Awesome #}
<link
href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
rel="stylesheet"
/>
{# Discourse embed for community #}
<script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
<script>
const csrftoken = document.querySelector("[name=csrf-token]").content;
</script>
{# General EP JS #}
<script src="{% static 'js/pps.js' %}"></script>
{% if not debug %}
<!-- Matomo -->
<script>
var _paq = (window._paq = window._paq || []);
_paq.push(["trackPageView"]);
_paq.push(["enableLinkTracking"]);
(function () {
var u = "//matomo.envipath.com/";
_paq.push(["setTrackerUrl", u + "matomo.php"]);
_paq.push(["setSiteId", "{{ meta.site_id }}"]);
var d = document,
g = d.createElement("script"),
s = d.getElementsByTagName("script")[0];
g.async = true;
g.src = u + "matomo.js";
s.parentNode.insertBefore(g, s);
})();
</script>
<!-- End Matomo Code -->
{% endif %}
</head>
<body class="bg-base-300 min-h-screen">
{% include "includes/navbar.html" %}
{# Main Content Area #}
<main class="w-full">
{% block main_content %}
{# Breadcrumbs - outside main content, optional #}
{% if breadcrumbs %}
<div id="bread" class="mx-auto max-w-7xl px-4 py-4">
<div class="breadcrumbs text-sm">
<ul>
{% for elem in breadcrumbs %}
{% for name, url in elem.items %}
{% if forloop.parentloop.last %}
<li>{{ name }}</li>
{% else %}
<li><a href="{{ url }}">{{ name }}</a></li>
{% endif %}
{% endfor %}
{% endfor %}
</ul>
</div>
</div>
{% endif %}
{# Main content container - paper effect on medium+ screens #}
<div
id="docContent"
class="bg-base-100 mx-auto md:my-8 md:max-w-6xl md:rounded-lg md:shadow-xl"
>
{# Messages - inside paper #}
{% if message %}
<div id="message" class="alert alert-info m-4">{{ message }}</div>
{% endif %}
{# Page content - no enforced styles #}
{% block content %}
{% endblock content %}
{# License - inside paper if present #}
{% if meta.url_contains_package and meta.current_package.license %}
<div class="collapse-arrow bg-base-200 collapse p-8">
<input type="checkbox" checked />
<div class="collapse-title text-xl font-medium">License</div>
<div class="collapse-content">
<a
target="_blank"
href="{{ meta.current_package.license.link }}"
>
<img
src="{{ meta.current_package.license.image_link }}"
alt="License"
/>
</a>
</div>
</div>
{% endif %}
</div>
{% endblock main_content %}
</main>
{% include "includes/footer.html" %}
{# Floating Help Tab #}
{% if not public_mode %}
<div class="fixed top-1/2 right-0 z-50 -translate-y-1/2">
<a
href="https://community.envipath.org/"
target="_blank"
class="btn btn-secondary hover:btn-secondary-focus text-secondary-content flex items-center justify-center text-sm shadow-lg transition-all duration-300 hover:-translate-x-1 hover:scale-105"
title="Get Help from the Community"
>
<svg
xmlns="http://www.w3.org/2000/svg"
width="24"
height="24"
viewBox="0 0 24 24"
fill="none"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
class="lucide lucide-message-circle-question-mark-icon lucide-message-circle-question-mark"
>
<path
d="M2.992 16.342a2 2 0 0 1 .094 1.167l-1.065 3.29a1 1 0 0 0 1.236 1.168l3.413-.998a2 2 0 0 1 1.099.092 10 10 0 1 0-4.777-4.719"
/>
<path d="M9.09 9a3 3 0 0 1 5.83 1c0 2-3 3-3 3" />
<path d="M12 17h.01" />
</svg>
</a>
</div>
{% endif %}
{% block modals %}
{% include "modals/search_modal.html" %}
{% endblock %}
<script>
document.addEventListener("DOMContentLoaded", function () {
// Show actions button if there are actions defined
const actionsButtonUl = document.querySelector("#actionsButton ul");
if (actionsButtonUl && actionsButtonUl.children.length > 0) {
document.getElementById("actionsButton").style.display = "";
}
});
// Open search modal function
function openSearchModal() {
const searchModal = document.getElementById("search_modal");
if (searchModal) {
searchModal.showModal();
}
}
// Click handler for search badge
const searchTrigger = document.getElementById("search-trigger");
if (searchTrigger) {
searchTrigger.addEventListener("click", function (event) {
event.preventDefault();
openSearchModal();
});
}
// Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
document.addEventListener("keydown", function (event) {
// Check if user is typing in an input field
const activeElement = document.activeElement;
const isInputField =
activeElement &&
(activeElement.tagName === "INPUT" ||
activeElement.tagName === "TEXTAREA" ||
activeElement.contentEditable === "true");
if (isInputField) {
return; // Don't trigger shortcut when typing in input fields
}
// Check for Cmd+K (Mac) or Ctrl+K (Windows/Linux)
const isMac = /Mac/.test(navigator.platform);
const isCorrectModifier = isMac ? event.metaKey : event.ctrlKey;
if (isCorrectModifier && event.key === "k") {
event.preventDefault();
openSearchModal();
}
});
</script>
</body>
</html>

View File

@ -1,94 +0,0 @@
{% load static %}
<div class="bg-base-300 text-base-content mx-auto mt-10 lg:max-w-5xl">
<footer class="footer sm:footer-horizontal p-10">
{% if not public_mode %}
<nav>
<h6 class="footer-title">Services</h6>
<a class="link link-hover" href="/predict">Predict</a>
<a class="link link-hover" href="/package">Packages</a>
{% if user.is_authenticated %}
<a class="link link-hover" href="/model">Your Collections</a>
{% endif %}
<a
href="https://wiki.envipath.org/"
target="_blank"
class="link link-hover"
>Documentation</a
>
</nav>
{% endif %}
<nav>
<h6 class="footer-title">Company</h6>
<a class="link link-hover" href="/about">About us</a>
<a class="link link-hover" href="/contact">Contact us</a>
<a class="link link-hover" href="/careers">Careers</a>
<a class="link link-hover" href="/legal">Legal</a>
</nav>
<nav>
<h6 class="footer-title">Legal</h6>
<a class="link link-hover" href="/terms">Terms of use</a>
<a class="link link-hover" href="/privacy">Privacy policy</a>
<a class="link link-hover" href="/cookie-policy">Cookie policy</a>
<a class="link link-hover" href="/cite">Cite enviPath</a>
</nav>
</footer>
<footer class="footer border-t-2 border-neutral-300 px-10 py-4">
<div class="flex w-full flex-row items-start justify-between">
<aside class="grid-flow-col items-center">
<svg
class="fill-neutral-content m-2 h-14 flex-shrink-0"
viewbox="0 0 65 65"
>
<use
href="{% static "/images/logo-square.svg" %}#ep-logo-square"
></use>
</svg>
enviPath Ltd.
<br />
Biodegredation prediction since 2015.
</aside>
<aside class="text-base-200 mt-2 text-sm">
<span class="text-xs tracking-tight">Version</span>
<span class="text-base font-bold">{{ meta.version }}</span>
</aside>
</div>
<nav class="md:place-self-center md:justify-self-end">
<div class="grid grid-flow-col gap-4">
<a href="https://www.youtube.com/@envipath7231" target="_blank">
<svg
role="img"
viewBox="0 0 24 24"
xmlns="http://www.w3.org/2000/svg"
class="h-6 w-6 fill-current"
>
<title>YouTube</title>
<path
d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"
/>
</svg>
</a>
<a href="https://community.envipath.org/" target="_blank">
<svg
role="img"
viewBox="0 0 24 24"
xmlns="http://www.w3.org/2000/svg"
class="h-6 w-6 fill-current"
>
<title>Discourse</title>
<path
d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"
/>
</svg>
</a>
<a href="https://www.linkedin.com/company/envipath/" target="_blank">
<img
src="{% static "/images/linkedin.png" %}"
alt="LinkedIn"
class="h-6 w-6"
/>
</a>
</div>
</nav>
</footer>
</div>

View File

@ -1,277 +0,0 @@
{% load static %}
{# Modern DaisyUI Navbar with Mobile Drawer Menu #}
<div class="drawer drawer-mobile">
<input id="drawer-toggle" type="checkbox" class="drawer-toggle" />
<div class="drawer-content flex flex-col">
{# Navbar #}
<div class="navbar x-50 bg-neutral-50 text-neutral-950 shadow-lg">
<div class="navbar-start">
{# Hamburger menu button - visible on mobile, hidden on desktop #}
{% if not public_mode %}
<label
for="drawer-toggle"
class="btn btn-square btn-ghost drawer-button lg:hidden"
>
<svg
xmlns="http://www.w3.org/2000/svg"
fill="none"
viewBox="0 0 24 24"
class="inline-block h-5 w-5 stroke-current"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M4 6h16M4 12h16M4 18h16"
></path>
</svg>
</label>
{% endif %}
<a
href="{{ meta.server_url }}"
class="btn btn-ghost text-xl normal-case"
>
<svg class="fill-base-content h-8" viewBox="0 0 104 26" role="img">
<use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
</svg>
</a>
</div>
{% if not public_mode %}
{# Desktop menu - hidden on mobile, visible on desktop #}
<div class="navbar-center hidden lg:flex">
<a
href="{{ meta.server_url }}/predict"
role="button"
class="btn btn-ghost"
id="predictLink"
>Predict</a
>
<div class="dropdown dropdown-center">
<div tabindex="0" role="button" class="btn btn-ghost">Browse</div>
<ul
tabindex="-1"
class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm"
>
<li>
<a href="{{ meta.server_url }}/package" id="packageLink"
>Package</a
>
</li>
<li>
<a href="{{ meta.server_url }}/pathway" id="pathwayLink"
>Pathway</a
>
</li>
<li>
<a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a>
</li>
<li>
<a href="{{ meta.server_url }}/compound" id="compoundLink"
>Compound</a
>
</li>
<li>
<a href="{{ meta.server_url }}/reaction" id="reactionLink"
>Reaction</a
>
</li>
<li>
<a
href="{{ meta.server_url }}/model"
id="relative-reasoningLink"
>Model</a
>
</li>
<li>
<a href="{{ meta.server_url }}/scenario" id="scenarioLink"
>Scenario</a
>
</li>
</ul>
</div>
</div>
{% endif %}
<div class="navbar-end">
{% if not public_mode %}
<a id="search-trigger" role="button" class="cursor-pointer">
<div
class="badge badge-dash bg-base-200 text-base-content/50 m-1 flex items-center space-x-1 p-2"
>
<svg
xmlns="http://www.w3.org/2000/svg"
width="16"
height="16"
viewBox="0 0 24 24"
fill="none"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
class="lucide lucide-search-icon lucide-search"
>
<path d="m21 21-4.34-4.34" />
<circle cx="11" cy="11" r="8" />
</svg>
<span id="search-shortcut">⌘K</span>
</div>
</a>
{% endif %}
{% if meta.user.username == 'anonymous' or public_mode %}
<a href="{% url 'login' %}" id="loginButton" class="p-2">Login</a>
{% else %}
<div class="dropdown dropdown-end">
<div
tabindex="0"
role="button"
class="btn btn-ghost btn-circle m-1"
id="loggedInButton"
>
<svg
xmlns="http://www.w3.org/2000/svg"
width="24"
height="24"
viewBox="0 0 24 24"
fill="none"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
class="lucide lucide-circle-user-icon lucide-circle-user"
>
<circle cx="12" cy="12" r="10" />
<circle cx="12" cy="10" r="3" />
<path d="M7 20.662V19a2 2 0 0 1 2-2h6a2 2 0 0 1 2 2v1.662" />
</svg>
</div>
<ul
tabindex="-1"
class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2 shadow-sm"
>
<li>
<a href="{{ meta.user.url }}" id="accountbutton">Settings</a>
</li>
<li>
<form
id="logoutForm"
action="{% url 'logout' %}"
method="post"
style="display: none;"
>
{% csrf_token %}
<input type="hidden" name="logout" value="true" />
</form>
<a
href="#"
id="logoutButton"
onclick="event.preventDefault(); document.getElementById('logoutForm').submit();"
>Logout</a
>
</li>
</ul>
</div>
{% endif %}
</div>
</div>
</div>
{# Mobile drawer menu - slides in from the left #}
<div class="drawer-side">
<label for="drawer-toggle" class="drawer-overlay"></label>
<ul class="menu min-h-full w-80 bg-base-200 p-4 text-base-content">
{# Drawer header with close button #}
<li class="mb-4">
<div class="flex items-center justify-between">
<span class="font-bold text-lg">Menu</span>
<label
for="drawer-toggle"
class="btn btn-sm btn-circle btn-ghost"
aria-label="Close menu"
>
<svg
xmlns="http://www.w3.org/2000/svg"
class="h-6 w-6"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
stroke-width="2"
d="M6 18L18 6M6 6l12 12"
/>
</svg>
</label>
</div>
</li>
{% if not public_mode %}
{# Predict link #}
<li>
<a
href="{{ meta.server_url }}/predict"
class="text-lg"
id="predictLinkMobile"
>Predict</a
>
</li>
{# Browse menu with submenu #}
<li>
<details>
<summary class="text-lg">Browse</summary>
<ul>
<li>
<a href="{{ meta.server_url }}/package" id="packageLinkMobile"
>Package</a
>
</li>
<li>
<a href="{{ meta.server_url }}/pathway" id="pathwayLinkMobile"
>Pathway</a
>
</li>
<li>
<a href="{{ meta.server_url }}/rule" id="ruleLinkMobile"
>Rule</a
>
</li>
<li>
<a href="{{ meta.server_url }}/compound" id="compoundLinkMobile"
>Compound</a
>
</li>
<li>
<a href="{{ meta.server_url }}/reaction" id="reactionLinkMobile"
>Reaction</a
>
</li>
<li>
<a
href="{{ meta.server_url }}/model"
id="relative-reasoningLinkMobile"
>Model</a
>
</li>
<li>
<a href="{{ meta.server_url }}/scenario" id="scenarioLinkMobile"
>Scenario</a
>
</li>
</ul>
</details>
</li>
{% endif %}
</ul>
</div>
</div>
<script>
// OS-aware search shortcut display
(function () {
const isMac = /Mac/.test(navigator.platform);
const shortcutElement = document.getElementById("search-shortcut");
if (shortcutElement) {
shortcutElement.textContent = isMac ? "⌘K" : "Ctrl+K";
}
})();
</script>

View File

@ -1,424 +1,186 @@
{% extends "framework_modern.html" %}
{% extends "framework.html" %}
{% load static %}
{% block main_content %}
<!-- Hero Section with Logo and Search -->
<section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
<div
class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
>
<div class="hero-overlay"></div>
<!-- Predict Pathway text over the image -->
<div class="absolute bottom-40 left-1/8 -translate-x-8">
<h2 class="text-base-100 text-left text-3xl text-shadow-lg">
Predict Your Pathway
</h2>
</div>
</div>
</section>
<div class="bg-base-200 mx-auto max-w-5xl shadow-md">
<!-- Predict Pathway Section -->
<div
class="relative mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
>
<div
class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
x-data="{
drawMode: false,
smiles: '',
loadExample(smilesStr, linkEl) {
if (this.drawMode && window.indexKetcher && window.indexKetcher.setMolecule) {
window.indexKetcher.setMolecule(smilesStr);
} else {
this.smiles = smilesStr;
}
const original = linkEl.textContent;
linkEl.textContent = 'loaded!';
setTimeout(() => linkEl.textContent = original, 1000);
},
syncFromKetcher() {
const ketcher = getKetcherInstance('index-ketcher');
if (ketcher && ketcher.getSmiles) {
try {
const s = ketcher.getSmiles();
if (s && s.trim()) this.smiles = s;
} catch (err) {
console.error('Failed to sync from Ketcher:', err);
}
}
},
submitForm() {
let finalSmiles = '';
if (this.drawMode) {
const ketcher = getKetcherInstance('index-ketcher');
if (ketcher && ketcher.getSmiles) {
try {
finalSmiles = ketcher.getSmiles().trim();
} catch (err) {
console.error('Failed to get SMILES from Ketcher:', err);
alert('Unable to extract structure. Please try again or switch to SMILES input.');
return;
}
} else {
alert('The drawing editor is still loading. Please wait and try again.');
return;
}
} else {
finalSmiles = this.smiles.trim();
}
if (!finalSmiles) {
alert('Please enter a SMILES string or draw a structure.');
return;
}
document.getElementById('index-form-smiles').value = finalSmiles;
document.getElementById('index-form').submit();
}
}"
x-init="$watch('drawMode', value => { if (!value) syncFromKetcher(); })"
>
<div class="card-body">
<div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
<div class="flex items-center gap-1">
<label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
<input type="checkbox" x-model="drawMode" />
<span class="swap-on flex items-center gap-1">
<div
class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
>
<svg
aria-label="smiles mode"
xmlns="http://www.w3.org/2000/svg"
viewBox="0 0 20 20"
class="size-5"
>
<g
stroke-linejoin="round"
stroke-linecap="round"
stroke-width="2"
fill="currentColor"
stroke="none"
>
<path
fill-rule="evenodd"
d="M8 2.75A.75.75 0 0 1 8.75 2h7.5a.75.75 0 0 1 0 1.5h-3.215l-4.483 13h2.698a.75.75 0 0 1 0 1.5h-7.5a.75.75 0 0 1 0-1.5h3.215l4.483-13H8.75A.75.75 0 0 1 8 2.75Z"
clip-rule="evenodd"
/>
</g>
</svg>
</div>
<span class="ext-xs">SMILES</span>
</span>
<span class="swap-off flex items-center gap-1">
<div
class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
>
<svg
aria-label="draw mode"
xmlns="http://www.w3.org/2000/svg"
viewBox="0 0 20 20"
fill="currentColor"
stroke="none"
class="size-5"
>
<path
d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z"
/>
</svg>
</div>
<span class="text-base/50 text-xs">Draw</span>
</span>
</label>
</div>
</div>
<fieldset
class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
:class="drawMode ? 'p-4' : 'p-8'"
>
<form
id="index-form"
action="{{ meta.current_package.url }}/pathway"
method="POST"
@submit.prevent="submitForm()"
>
{% csrf_token %}
<div
id="text-input-container"
x-show="!drawMode"
x-transition:enter="transition ease-out duration-300"
x-transition:enter-start="opacity-0 scale-95"
x-transition:enter-end="opacity-100 scale-100"
x-transition:leave="transition ease-in duration-300"
x-transition:leave-start="opacity-100 scale-100"
x-transition:leave-end="opacity-0 scale-95"
>
<div class="join mx-auto w-full">
<input
type="text"
id="index-form-text-input"
placeholder="canonical SMILES string"
class="input input-md join-item grow"
x-model="smiles"
/>
<button class="btn btn-neutral join-item">Predict!</button>
</div>
<div class="label relative mt-1 w-full">
<div class="flex gap-2">
<a
href="#"
class="example-link hover:text-primary cursor-pointer"
title="load example"
@click.prevent="loadExample('CN1C=NC2=C1C(=O)N(C(=O)N2C)C', $el)"
>Caffeine</a
>
<a
href="#"
class="example-link hover:text-primary cursor-pointer"
title="load example"
@click.prevent="loadExample('CC(C)CC1=CC=C(C=C1)C(C)C(=O)O', $el)"
>Ibuprofen</a
>
</div>
<a
class="absolute top-0 left-[calc(100%-5.4rem)]"
href="/predict"
>Advanced</a
>
</div>
</div>
<div
id="ketcher-container"
x-show="drawMode"
x-transition:enter="transition ease-out duration-300"
x-transition:enter-start="opacity-0 scale-95"
x-transition:enter-end="opacity-100 scale-100"
x-transition:leave="transition ease-in duration-300"
x-transition:leave-start="opacity-100 scale-100"
x-transition:leave-end="opacity-0 scale-95"
class="w-full"
>
<iframe
id="index-ketcher"
src="{% static '/js/ketcher2/ketcher.html' %}"
width="100%"
height="400"
class="rounded-lg"
></iframe>
<button
class="btn btn-lg bg-primary-950 text-primary-50 join-item mt-2 w-full"
>
Predict!
{% block content %}
<!-- TODO rename ids as well as remove pathways if modal is closed!-->
<div class="modal fade" tabindex="-1" id="foundMatching" role="dialog" aria-labelledby="foundModal"
aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal">
<span aria-hidden="true">&times;</span>
<span class="sr-only">Close</span>
</button>
<div class="mt-1 flex w-full justify-end">
<a class="label justify-end" href="/predict">Advanced</a>
<h4 class="modal-title" id="newPackMod">Found Pathway in Database</h4>
</div>
<div class="modal-body">
<p>We found at least one pathway in the database with the given root
compound. Do you want to open any of the existing pathways or
predict a new one? To open an existing pathway, simply click
on the pathway, to predict a new one, click Predict. The predicted
pathway might differ from the ones in the database due to the
settings used in the prediction.</p>
<div id="foundPathways"></div>
</div>
<input
type="hidden"
id="index-form-smiles"
name="smiles"
value="smiles"
/>
<input
type="hidden"
id="index-form-predict"
name="predict"
value="predict"
/>
<input type="hidden" id="current-action" value="predict" />
</form>
</fieldset>
<div class="modal-footer">
<a id="modal-predict" class="btn btn-primary" href="#">Predict</a>
<button type="button" id="cancel-predict" class="btn btn-default" data-dismiss="modal">Cancel
</button>
</div>
</div>
</div>
<!-- Community News Section -->
<section class="bg-base-200 z-10 mx-8 py-16">
<div class="mx-auto max-w-7xl px-4">
<h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
<div id="community-news-container" class="flex justify-center gap-4">
<!-- News cards will be populated here -->
<div id="loading" class="flex w-full justify-center">
<span class="loading loading-spinner loading-lg"></span>
</div>
</div>
<div class="mt-6 text-right">
<a
href="https://community.envipath.org/c/announcements/10"
target="_blank"
class="btn btn-ghost btn-sm"
>
Read More Announcements
</a>
</div>
<!-- Discourse API integration -->
<script src="{% static 'js/discourse-api.js' %}"></script>
</div>
</section>
<!-- Mission Statement Section -->
<section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
<div class="mx-auto px-8 md:px-12">
<div class="flex flex-row gap-4">
<div class="w-1/3">
<img
src="{% static "/images/ep-rule-artwork.png" %}"
alt="rule-based iterative tree greneration"
class="h-full w-full object-contain"
/>
</div>
<div class="mr-8 w-2/3 space-y-4 text-left">
<h2 class="h2 mb-8 font-bold">About enviPath</h2>
<p class="">
enviPath is a database and prediction system for the microbial
<div class="row">
<div class="col-xs-8">
<div class="jumbotron">
<h1>
<img id="image-logo-long" class="img-responsive" alt="enviPath" width="1000ex"
src='{% static "/images/logo-long.svg" %}'/>
</h1>
<p>enviPath is a database and prediction system for the microbial
biotransformation of organic environmental contaminants. The
database provides the possibility to store and view experimentally
observed biotransformation pathways.
observed biotransformation pathways. The pathway prediction system
provides different relative reasoning models to predict likely biotransformation
pathways and products. You can try it out below.
</p>
<p class="">
The pathway prediction system provides different relative
reasoning models to predict likely biotransformation pathways and
products. Explore our tools and contribute to advancing
environmental biotransformation research.
<p>
<a class="btn" style="background-color:#222222;color:#9d9d9d" role="button" target="_blank"
href="https://wiki.envipath.org/index.php/Main_Page">Learn more &gt;&gt;</a>
</p>
<div class="float-right flex flex-row gap-4">
<a href="/about" class="btn btn-ghost-neutral">Read More</a>
<a href="/about" class="btn btn-neutral">Publications</a>
</div>
</div>
</div>
</div>
</section>
<!-- Partners Section -->
<section class="bg-base-100 py-14 sm:py-12">
<div class="mx-auto px-6 lg:px-8">
<div class="divider">
<h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
</div>
<div
class="mx-auto mt-10 grid max-w-lg grid-cols-4 items-center gap-x-8 gap-y-10 sm:max-w-xl sm:grid-cols-6 sm:gap-x-10 lg:mx-0 lg:max-w-none lg:grid-cols-3"
>
<img
src="{% static "/images/uoa-logo-small.png" %}"
alt="The University of Auckland"
class="max-h-20 w-full object-contain lg:col-span-1"
/>
<img
src="{% static "/images/logo-eawag.svg" %}"
alt="Eawag"
class="max-h-12 w-full object-contain lg:col-span-1"
/>
<img
src="{% static "/images/uzh-logo.svg" %}"
alt="University of Zurich"
class="2 max-h-16 w-full object-contain lg:col-span-1"
/>
</div>
</div>
</section>
</div>
</div>
<div id="loading"></div>
<div class="col-xs-4">
<d-topics-list discourse-url="https://community.envipath.org" per-page="10" category="10"
template="complete"></d-topics-list>
</div>
</div>
<div class="row">
<form id="index-form" action="{{ meta.current_package.url }}/pathway" method="POST">
{% csrf_token %}
<div class="input-group" id="index-form-bar">
<div class="input-group-btn">
<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
aria-expanded="false">
<span class="caret"></span>
</button>
<ul class="dropdown-menu" role="menu">
<li>
<iframe id="index-form-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
height="510"></iframe>
</li>
</ul>
</div>
<input type="text" class="form-control" id='index-form-text-input'
placeholder="Enter a SMILES to predict a Pathway or type something to search">
<div class="input-group-btn">
<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
aria-haspopup="true"
aria-expanded="false" id="action-button">Predict <span class="caret"></span></button>
<ul class="dropdown-menu">
<li><a id="dropdown-predict">Predict</a></li>
<li><a id="dropdown-search">Search</a></li>
</ul>
<button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="run-button">Go!
</button>
</div>
</div>
<input type="hidden" id="index-form-smiles" name="smiles" value="smiles">
<input type="hidden" id="index-form-predict" name="predict" value="predict">
</form>
</div>
<p></p>
<script language="javascript">
var currentPackage = "{{ meta.current_package.url }}";
// Helper function to safely get Ketcher instance from iframe
function getKetcherInstance(iframeId) {
const ketcherFrame = document.getElementById(iframeId);
if (!ketcherFrame) {
console.error("Ketcher iframe not found:", iframeId);
return null;
function goButtonClicked() {
$(this).prop("disabled", true);
var action = $('#action-button').text().trim();
var textSmiles = $('#index-form-text-input').val().trim();
if (textSmiles === '') {
$(this).prop("disabled", false);
return;
}
try {
if (
"contentWindow" in ketcherFrame &&
ketcherFrame.contentWindow.ketcher
) {
return ketcherFrame.contentWindow.ketcher;
}
} catch (err) {
console.error(
"Cannot access Ketcher iframe - possible CORS issue:",
err,
);
var ketcherSmiles = getKetcher('index-form-ketcher').getSmiles().trim();
if (action !== 'Search' && ketcherSmiles !== '' && textSmiles !== ketcherSmiles) {
console.log("Ketcher and TextInput differ!");
}
return null;
if (action === 'Search') {
var par = {};
par['search'] = textSmiles;
par['mode'] = 'text';
var queryString = $.param(par, true);
window.location.href = "/search?" + queryString;
} else {
$('#index-form-smiles').val(textSmiles);
$('#index-form').submit();
}
}
// Discourse API integration is now handled by discourse-api.js
function actionDropdownClicked() {
var suffix = ' <span class="caret"></span>';
var dropdownVal = $(this).text();
// Function to render Discourse topics into cards
function renderDiscourseTopics(topics) {
const container = document.getElementById("community-news-container");
if (!container) return;
if (dropdownVal === 'Search') {
$("#index-form").attr("action", '/search');
$("#index-form").attr("method", 'GET');
} else {
$("#index-form").attr("action", currentPackage + "/pathway");
}
// Clear container
container.innerHTML = "";
$('#action-button').html(dropdownVal + suffix);
}
// Create cards for each topic
topics.forEach((topic) => {
const card = createDiscourseCard(topic);
container.insertAdjacentHTML("beforeend", card);
function ketcherToTextInput() {
$('#index-form-text-input').val(this.ketcher.getSmiles());
}
$(function () {
$('#index-form').on("keydown", function (e) {
if (e.key === "Enter") {
e.preventDefault();
goButtonClicked();
}
});
}
// Function to create HTML card for a topic
function createDiscourseCard(topic) {
const date = new Date(topic.created_at).toLocaleDateString();
// Code that should be executed once DOM is ready goes here
$('#dropdown-predict').on('click', actionDropdownClicked);
$('#dropdown-search').on('click', actionDropdownClicked);
return `
<div class="card bg-white shadow-sm hover:shadow-lg transition-shadow duration-300 h-52 w-75 flex-shrink-0">
<div class="card-body flex flex-col h-full justify-between">
<h3 class="card-title leading-tight font-normal tracking-tight mb-2 line-clamp-5 overflow-hidden">
<a href="${topic.url}" target="_blank" class="hover:text-primary">
${topic.title}
</a>
</h3>
$('#run-button').on('click', goButtonClicked);
<div class="flex flex-row items-center justify-between">
<div class="flex items-center gap-2">
<div class="avatar tooltip tooltip-right" data-tip="${topic.author}">
<div class="w-8 rounded-full">
<img src="${topic.author_avatar}" alt="${topic.author}" />
</div>
</div>
<span class="text-xs text-gray-500">${date}</span>
</div>
<a href="${topic.url}" target="_blank" class="btn btn-ghost text-neutral-500 rounded-full p-2">
<svg xmlns="http://www.w3.org/2000/svg" class="h-5 w-5" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
<path d="M12 7v14"/>
<path d="M3 18a1 1 0 0 1-1-1V4a1 1 0 0 1 1-1h5a4 4 0 0 1 4 4 4 4 0 0 1 4-4h5a1 1 0 0 1 1 1v13a1 1 0 0 1-1 1h-6a3 3 0 0 0-3 3 3 3 0 0 0-3-3z"/>
</svg>
</a>
</div>
</div>
</div>
`;
}
// Update Ketcher Width
var fullWidth = $('#index-form-bar').width();
$('#index-form-ketcher').width(fullWidth);
// Make render function globally available
window.renderDiscourseTopics = renderDiscourseTopics;
// Ketcher iframe load handler - set up change event to sync SMILES
document.addEventListener("DOMContentLoaded", function () {
const indexKetcher = document.getElementById("index-ketcher");
indexKetcher.addEventListener("load", function () {
// add a listener that gets triggered whenever the structure in ketcher has changed
$('#index-form-ketcher').on('load', function () {
const checkKetcherReady = () => {
const win = this.contentWindow;
if (win.ketcher && "editor" in win.ketcher) {
window.indexKetcher = win.ketcher;
win = this.contentWindow
if (win.ketcher && 'editor' in win.ketcher) {
win.ketcher.editor.event.change.handlers.push({
once: false,
priority: 0,
f: ketcherToTextInput,
ketcher: win.ketcher
});
} else {
setTimeout(checkKetcherReady, 100);
}
};
checkKetcherReady();
});
});
</script>
{% endblock main_content %}
{% endblock content %}

View File

@ -3,11 +3,7 @@
{% block content %}
<div class="panel-group" id="migration-detail">
<div class="panel panel-default">
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
Migration Status BT Rules
</div>
<div class="panel-body">
@ -16,56 +12,33 @@
</div>
{% for obj in results %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
{% if obj.status %}
<span
class="glyphicon glyphicon-ok"
aria-hidden="true"
style="float:right"
data-toggle="tooltip"
data-placement="top"
title=""
data-original-title="Reviewed"
>
<span class="glyphicon glyphicon-ok" aria-hidden="true"
style="float:right" data-toggle="tooltip"
data-placement="top" title="" data-original-title="Reviewed">
</span>
{% else %}
<span
class="glyphicon glyphicon-remove"
aria-hidden="true"
style="float:right"
data-toggle="tooltip"
data-placement="top"
title=""
data-original-title="Reviewed"
>
<span class="glyphicon glyphicon-remove" aria-hidden="true"
style="float:right" data-toggle="tooltip"
data-placement="top" title="" data-original-title="Reviewed">
</span>
{% endif %}
<h4 class="panel-title">
<a
id="{{ obj.id }}-link"
data-toggle="collapse"
data-parent="#migration-detail"
href="#{{ obj.id }}"
>{{ obj.name|safe }}</a
>
<a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
href="#{{ obj.id }}">{{ obj.name }}</a>
</h4>
</div>
<div
id="{{ obj.id }}"
class="panel-collapse {% if not obj.status %}in{% endif %} collapse"
>
<div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
<div class="panel-body list-group-item">
<a class="list-group-item" href="{{ obj.detail_url }}"
>{{ obj.name|safe }} Migration Detail Page</a
>
<a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name }} Migration Detail Page</a>
</div>
</div>
{% endfor %}
</div>
</div>
<script></script>
<script>
</script>
{% endblock content %}

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