forked from enviPath/enviPy
adjusted migration
Initial bayer app Show Pack Classification Adjusted docker compose to bayer specifics Adjusted Dockerfile for Bayer Adding secret flags to group, add secret pools to packages Adjusted View for Package creation Prep configs, added Package Create Modal wip More on PES wip wip Wip minor PW interactions API PES wip Make Select Widget reflect required make required generallay available Update UI if pathway mode is set to build Added ais circle adjustments Initial Zoom, fix AD Creation wip auth log, bb4g fix missing import Added viz hint if PES is part of reaction Add Edge check for pes flip boolean ... pes Added extra ... In / Out Edges Viz, Submitting Button Text ... Make PES Link clickable Return proper http response instead of error Fixed error return, removed unused options Fix PES Link HTML for other entities Fixed molfile assignment, adjusted Export Package Export/Import cycle highlight Description links implemented non persistent Harmonised proposed field in Json output Added pesLink field to PW Api output PES Fields in API Output removed debug Fix Classification import, Fix PES Deserialization underline pes link in templates Fix alter name/desc for node, make /node /edge funcitonal provide setting link and copy button Implemented Compound Names / Reaction Names View Option Unconnected Nodes Make links thicker, reduce timeout trigger time Show proposed info in popover Pathway Build no stereo removal Include probs in reaction name option viz Detect clicks outside nodes/edges Provide proper Error Pages View Package Perm wip sync Auth log auth log leftovers ... secret packs viz auth log for api model stats Fix Package Adjustment Adjust Group Auth Log Fix Secret image size in Navbar leftover ... minor
This commit is contained in:
Tim Lorsbach
213
bayer/views.py
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213
bayer/views.py
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import base64
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import logging
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import requests
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from django.conf import settings as s
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from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed
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from django.shortcuts import redirect
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from bayer.models import PESCompound
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from epdb.logic import PackageManager
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from epdb.models import Pathway, Node
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from epdb.views import _anonymous_or_real, error
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from utilities.decorators import package_permission_required
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Package = s.GET_PACKAGE_MODEL()
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logger = logging.getLogger(__name__)
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@package_permission_required()
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def create_pes(request, package_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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if request.method == "POST":
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if current_package.classification_level == Package.Classification.INTERNAL:
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return error(
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request,
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f'Creation of PESs for package {current_package.name} failed!',
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"Creating PESs for internal packages is not allowed.",
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)
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compound_name = request.POST.get('compound-name')
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compound_description = request.POST.get('compound-description')
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pes_link = request.POST.get('pes-link')
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if pes_link:
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try:
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pes_data = fetch_pes(request, pes_link)
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except ValueError as e:
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return error(
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request,
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"Could not fetch PES",
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f"Could not fetch PES data for {pes_link}"
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)
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classification = pes_data.get("classificationLevel", "")
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if "secret" == classification.lower():
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if current_package.classification_level != Package.Classification.SECRET:
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return error(
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request,
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"Classification Mismatch!",
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"Cannot create secret PESs in non-secret packages."
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)
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if not current_package.data_pool or not current_package.data_pool.secret:
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logger.info(f"The current package does not have a secret data pool.")
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return error(
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request,
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"The current package does not have a secret data pool.",
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"Cannot create secret PESs in package without a secret data pool."
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)
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pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
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return redirect(pes.url)
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else:
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return error(
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request,
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"No PES link received",
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"Please provide a PES link."
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)
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else:
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return HttpResponseNotAllowed(["POST"])
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@package_permission_required()
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def create_pes_node(request, package_uuid, pathway_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
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if request.method == "POST":
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if current_package.classification_level == Package.Classification.INTERNAL:
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return error(
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request,
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f'Creation of PESs for package {current_package.name} failed!',
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"Creating PESs for internal packages is not allowed.",
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)
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compound_name = request.POST.get('compound-name')
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compound_description = request.POST.get('compound-description')
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pes_link = request.POST.get('pes-link')
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if pes_link:
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try:
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pes_data = fetch_pes(request, pes_link)
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except ValueError as e:
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return error(
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request,
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"Could not fetch PES",
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f"Could not fetch PES data for {pes_link}"
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)
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classification = pes_data.get("classificationLevel", "")
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if "secret" == classification.lower():
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if current_package.classification_level != Package.Classification.SECRET:
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return error(
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request,
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"Classification Mismatch!",
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"Cannot create secret PESs in non-secret packages."
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)
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if not current_package.data_pool or not current_package.data_pool.secret:
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logger.info(f"The current package does not have a secret data pool.")
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return error(
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request,
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"The current package does not have a secret data pool.",
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"Cannot create secret PESs in package without a secret data pool."
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)
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pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
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node_qs = Node.objects.filter(
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pathway=current_pathway,
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default_node_label=pes.default_structure
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)
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if node_qs.exists():
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return redirect(current_pathway.url)
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n = Node()
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n.stereo_removed = False
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n.pathway = current_pathway
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n.depth = 0
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n.default_node_label = pes.default_structure
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n.save()
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n.node_labels.add(pes.default_structure)
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n.save()
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return redirect(current_pathway.url)
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else:
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return error(
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request,
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"No PES link received",
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"Please provide a PES link."
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)
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else:
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return HttpResponseNotAllowed(["POST"])
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def fetch_pes(request, pes_url) -> dict:
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from epauth.views import get_access_token_from_request
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token = get_access_token_from_request(request)
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if token is None:
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token = pes_url.split('/')[-1] == 'dummy'
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if token:
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for k, v in s.PES_API_MAPPING.items():
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if pes_url.startswith(k):
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pes_id = pes_url.split('/')[-1]
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if pes_id == 'dummy':
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import json
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res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
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res_data["pes_url"] = pes_url
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return res_data
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else:
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headers = {"Authorization": f"Bearer {token['access_token']}"}
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params = {"pes_reg_entity_corporate_id": pes_id}
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res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
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try:
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res.raise_for_status()
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pes_data = res.json()
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if len(pes_data) == 0:
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raise ValueError(f"PES with id {pes_id} not found")
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res_data = pes_data[0]
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res_data["pes_url"] = pes_url
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return res_data
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except requests.exceptions.HTTPError as e:
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raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
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else:
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raise ValueError(f"Unknown URL {pes_url}")
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else:
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raise ValueError("Could not fetch access token from request.")
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def visualize_pes(request):
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pes_link = request.GET.get('pesLink')
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if pes_link:
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pes_data = fetch_pes(request, pes_link)
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representations = pes_data.get('representations')
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for rep in representations:
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if rep.get('type') == 'color':
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image_data = base64.b64decode(rep.get('base64').replace("data:image/png;base64,", ""))
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return HttpResponse(image_data, content_type="image/png")
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