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mrg

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This commit is contained in:
Tim Lorsbach
2025-11-11 10:54:36 +01:00
parent 0d9947e6ce 34589efbde
commit 05bee9b718
56 changed files with 560 additions and 230 deletions
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115
epdb/views.py
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@ -10,6 +10,7 @@ from django.urls import reverse
from django.views.decorators.csrf import csrf_exempt
from envipy_additional_information import NAME_MAPPING
from oauth2_provider.decorators import protected_resource
import nh3
from utilities.chem import FormatConverter, IndigoUtils
from utilities.decorators import package_permission_required
@ -85,7 +86,10 @@ def login(request):
from django.contrib.auth import authenticate
from django.contrib.auth import login
username = request.POST.get("username")
username = request.POST.get("username").strip()
if username != request.POST.get("username"):
context["message"] = "Login failed!"
return render(request, "static/login.html", context)
password = request.POST.get("password")
# Get email for username and check if the account is active
@ -673,7 +677,8 @@ def search(request):
if request.method == "GET":
package_urls = request.GET.getlist("packages")
searchterm = request.GET.get("search")
searchterm = request.GET.get("search").strip()
mode = request.GET.get("mode")
# add HTTP_ACCEPT check to differentiate between index and ajax call
@ -774,7 +779,6 @@ def package_models(request, package_uuid):
elif request.method == "POST":
log_post_params(request)
name = request.POST.get("model-name")
description = request.POST.get("model-description")
@ -939,8 +943,14 @@ def package_model(request, package_uuid, model_uuid):
else:
return HttpResponseBadRequest()
else:
name = request.POST.get("model-name", "").strip()
description = request.POST.get("model-description", "").strip()
# 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()
if any([name, description]):
if name:
@ -1042,8 +1052,16 @@ 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"
@ -1152,7 +1170,7 @@ def package_compounds(request, package_uuid):
elif request.method == "POST":
compound_name = request.POST.get("compound-name")
compound_smiles = request.POST.get("compound-smiles")
compound_smiles = request.POST.get("compound-smiles").strip()
compound_description = request.POST.get("compound-description")
c = Compound.create(current_package, compound_smiles, compound_name, compound_description)
@ -1205,8 +1223,16 @@ def package_compound(request, package_uuid, compound_uuid):
return JsonResponse({"success": current_compound.url})
new_compound_name = request.POST.get("compound-name", "").strip()
new_compound_description = request.POST.get("compound-description", "").strip()
# 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()
if new_compound_name:
current_compound.name = new_compound_name
@ -1271,7 +1297,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
elif request.method == "POST":
structure_name = request.POST.get("structure-name")
structure_smiles = request.POST.get("structure-smiles")
structure_smiles = request.POST.get("structure-smiles").strip()
structure_description = request.POST.get("structure-description")
try:
@ -1342,8 +1368,16 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
else:
return HttpResponseBadRequest()
new_structure_name = request.POST.get("compound-structure-name", "").strip()
new_structure_description = request.POST.get("compound-structure-description", "").strip()
# 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()
if new_structure_name:
current_structure.name = new_structure_name
@ -1445,11 +1479,11 @@ def package_rules(request, package_uuid):
# Obtain parameters as required by rule type
if rule_type == "SimpleAmbitRule":
params["smirks"] = request.POST.get("rule-smirks")
params["smirks"] = request.POST.get("rule-smirks").strip()
params["reactant_filter_smarts"] = request.POST.get("rule-reactant-smarts")
params["product_filter_smarts"] = request.POST.get("rule-product-smarts")
elif rule_type == "SimpleRDKitRule":
params["reaction_smarts"] = request.POST.get("rule-reaction-smarts")
params["reaction_smarts"] = request.POST.get("rule-reaction-smarts").strip()
elif rule_type == "ParallelRule":
pass
elif rule_type == "SequentialRule":
@ -1550,8 +1584,14 @@ def package_rule(request, package_uuid, rule_uuid):
return JsonResponse({"success": current_rule.url})
rule_name = request.POST.get("rule-name", "").strip()
rule_description = request.POST.get("rule-description", "").strip()
# 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()
if rule_name:
current_rule.name = rule_name
@ -1640,8 +1680,8 @@ def package_reactions(request, package_uuid):
elif request.method == "POST":
reaction_name = request.POST.get("reaction-name")
reaction_description = request.POST.get("reaction-description")
reactions_smirks = request.POST.get("reaction-smirks")
reactions_smirks = request.POST.get("reaction-smirks").strip()
educts = reactions_smirks.split(">>")[0].split(".")
products = reactions_smirks.split(">>")[1].split(".")
@ -1702,8 +1742,16 @@ def package_reaction(request, package_uuid, reaction_uuid):
return JsonResponse({"success": current_reaction.url})
new_reaction_name = request.POST.get("reaction-name", "").strip()
new_reaction_description = request.POST.get("reaction-description", "").strip()
# 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()
if new_reaction_name:
current_reaction.name = new_reaction_name
@ -1780,8 +1828,9 @@ def package_pathways(request, package_uuid):
name = request.POST.get("name")
description = request.POST.get("description")
pw_mode = request.POST.get("predict", "predict").strip()
smiles = request.POST.get("smiles", "").strip()
pw_mode = request.POST.get("predict", "predict").strip()
if "smiles" in request.POST and smiles == "":
return error(
@ -1790,8 +1839,6 @@ 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:
@ -1950,8 +1997,14 @@ 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() != "":
@ -2039,8 +2092,8 @@ 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)
@ -2202,9 +2255,9 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
elif request.method == "POST":
log_post_params(request)
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")
@ -2291,7 +2344,7 @@ 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)
@ -2339,21 +2392,21 @@ def package_scenarios(request, package_uuid):
"name": "soil",
"widgets": [
HTMLGenerator.generate_html(ai, prefix=f"soil_{0}")
for ai in [x for s in SOIL_ADDITIONAL_INFORMATION.values() for x in s]
for ai in [x for sv in SOIL_ADDITIONAL_INFORMATION.values() for x in sv]
],
},
"Sludge Data": {
"name": "sludge",
"widgets": [
HTMLGenerator.generate_html(ai, prefix=f"sludge_{0}")
for ai in [x for s in SLUDGE_ADDITIONAL_INFORMATION.values() for x in s]
for ai in [x for sv in SLUDGE_ADDITIONAL_INFORMATION.values() for x in sv]
],
},
"Water-Sediment System Data": {
"name": "sediment",
"widgets": [
HTMLGenerator.generate_html(ai, prefix=f"sediment_{0}")
for ai in [x for s in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in s]
for ai in [x for sv in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in sv]
],
},
}
@ -2368,6 +2421,7 @@ 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")
@ -2381,9 +2435,9 @@ 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 s in additional_information.values() for x in s]
additional_information = [x for sv in additional_information.values() for x in sv]
s = Scenario.create(
new_scen = Scenario.create(
current_package,
name=scenario_name,
description=scenario_description,
@ -2392,7 +2446,7 @@ def package_scenarios(request, package_uuid):
additional_information=additional_information,
)
return redirect(s.url)
return redirect(new_scen.url)
else:
return HttpResponseNotAllowed(
[
@ -2692,6 +2746,7 @@ 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(