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

epdb/exceptions.py

@@ -8,4 +8,3 @@ class InvalidMolfileException(Exception):
 
 class PackageImportException(Exception):
     pass
-

epdb/legacy_api.py

@@ -2412,17 +2412,12 @@ class NonPersistent(Schema):
 @router.post("/util", response={200: Any, 403: Error})
 def predict(request, np: Form[NonPersistent]):
     try:
-        print(request.user)
-        print(np.setting_url)
-        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
-
         from epdb.logic import SPathway
 
+        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
         spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
         spw.predict()
-
         return spw.to_json()
-
     except ValueError:
         return 403, {
             "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"

epdb/models.py

@@ -1834,7 +1834,7 @@ class Reaction(
         r = Reaction()
         r.package = package
 
-        if r is not None:
+        if name is not None:
             r.name = name
 
         if description is not None and description.strip() != "":
@@ -2414,14 +2414,14 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def get_name(self, include_suffix=True):
         non_generic_name = True
 
-        if self.name == "no name":
+        if self.name is None or self.name == "no name":
             non_generic_name = False
 
         if non_generic_name:
             return self.name
         else:
             if include_suffix:
-                f"{self.default_node_label.name} (taken from underlying structure)"
+                return f"{self.default_node_label.name} (taken from underlying structure)"
             else:
                 return self.default_node_label.name
 
@@ -2556,8 +2556,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def is_proposed_intermediate(self):
         collected = defaultdict(dict)
         for ai in self.additional_information.filter(
-                type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"]
+            type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],
-                , scenario__isnull=False
+            scenario__isnull=False,
         ):
             collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
             collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
@@ -2569,7 +2569,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
                 collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
 
             if ai.type == "TransformationProductImportance":
-                collected[str(ai.scenario.uuid)]["Transformation product importance"] = ai.get().importance.value
+                collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
+                    ai.get().importance.value
+                )
 
         return list(collected.values())
 

epdb/views.py

@@ -2506,13 +2506,17 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
                 current_node.name = new_node_name
 
             if new_node_description is not None and new_node_description.strip() != "":
-                new_node_description = nh3.clean(new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
+                new_node_description = nh3.clean(
+                    new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS
+                ).strip()
                 current_node.description = new_node_description
 
             current_node.save()
+
             return redirect(current_node.url)
 
         return error(request, "Node update failed!", "No changes were made to the node")
+
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 

static/js/alpine/pagination.js

@@ -122,7 +122,8 @@ document.addEventListener('alpine:init', () => {
         return this.items.slice(start, end);
       }
 
-    }));
+    })
+  );
 
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],

static/js/pw.js

@@ -161,6 +161,7 @@ function draw(pathway, elem) {
         linkText
          .attr("x", d => (d.source.x + d.target.x) / 2)
          .attr("y", d => (d.source.y + d.target.y) / 2);
+
     }
 
     function dragstarted(event, d) {
@@ -542,7 +543,6 @@ function draw(pathway, elem) {
                         }
                         if("Confidence" in n.proposed[prop]){
                             popupContent += "Confidence: " + n.proposed[prop]["Confidence"] + "<br>";
-
                         }
                         if("Transformation product importance" in n.proposed[prop]){
                             popupContent += "Transformation product importance: " + n.proposed[prop]["Transformation product importance"] + "<br>";
@@ -623,7 +623,7 @@ function draw(pathway, elem) {
         .attr("pointer-events", "all")
         .style("cursor", "grab");
 
-        // Click on empty SVG space (not on a node or link)
+    // Click on empty SVG space (not on a node or link)
     rect.on("click", function(event) {
         // Only treat it as a background click if the direct target is the rect itself
         // (clicks on nodes/links bubble up but originate from different elements)
@@ -637,7 +637,6 @@ function draw(pathway, elem) {
             target.closest("path.link") !== null ||
             target.closest("path.link_no_arrow") !== null
         );
-
         if (!isNode && !isLink) {
             // console.log("Clicked outside a node or link");
             // Clear all highlights
@@ -694,7 +693,7 @@ function draw(pathway, elem) {
         .force("center", d3.forceCenter(width / 2, height / 4))
         .on("tick", ticked);
 
-    // Kanten zeichnen
+    // Draw Edges
     const linkGroup = zoomable.append("g")
       .selectAll("g")
       .data(links)
@@ -754,7 +753,7 @@ function draw(pathway, elem) {
         }
 
         var suffix = "";
-        if ("reaction_probability" in d) {
+        if ("reaction_probability" in d && d["reaction_probability"] !== null) {
             suffix = " (p= " + d["reaction_probability"].toFixed(2) + ")"
         }
         return d.plain_name + suffix;
@@ -779,7 +778,7 @@ function draw(pathway, elem) {
 
     pop_add(link, "Reaction", edge_popup);
 
-    // Knoten zeichnen
+    // Draw Nodes
     const node = zoomable.append("g")
         .selectAll("g")
         .data(nodes)

templates/objects/node.html

@@ -63,7 +63,6 @@
         <div class="collapse-content">{{ node.description }}</div>
       </div>
     {% endif %}
-
     {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
 
     {% for tpl in viz_templates %}

templates/objects/pathway.html

@@ -22,7 +22,6 @@
       stroke: #999;
       stroke-opacity: 0.6;
       stroke-width: 1.5px;
-      /* marker-end: url(#arrow); */
     }
 
     .link_no_arrow {
@@ -182,46 +181,46 @@
                   <li>
                     <a id="compound-names-toggle-button" class="cursor-pointer">
                       <svg
-                          id="compound-names-icon"
+                        id="compound-names-icon"
-                          xmlns="http://www.w3.org/2000/svg"
+                        xmlns="http://www.w3.org/2000/svg"
-                          width="16"
+                        width="16"
-                          height="16"
+                        height="16"
-                          viewBox="0 0 24 24"
+                        viewBox="0 0 24 24"
-                          fill="none"
+                        fill="none"
-                          stroke="currentColor"
+                        stroke="currentColor"
-                          stroke-width="2"
+                        stroke-width="2"
-                          stroke-linecap="round"
+                        stroke-linecap="round"
-                          stroke-linejoin="round"
+                        stroke-linejoin="round"
-                          class="lucide lucide-eye"
+                        class="lucide lucide-eye"
-                        >
+                      >
-                          <path
+                        <path
-                            d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
+                          d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
-                          />
+                        />
-                          <circle cx="12" cy="12" r="3" />
+                        <circle cx="12" cy="12" r="3" />
-                        </svg>
+                      </svg>
                       Compound Names
                     </a>
                   </li>
                   <li>
                     <a id="reaction-names-toggle-button" class="cursor-pointer">
                       <svg
-                          id="reaction-names-icon"
+                        id="reaction-names-icon"
-                          xmlns="http://www.w3.org/2000/svg"
+                        xmlns="http://www.w3.org/2000/svg"
-                          width="16"
+                        width="16"
-                          height="16"
+                        height="16"
-                          viewBox="0 0 24 24"
+                        viewBox="0 0 24 24"
-                          fill="none"
+                        fill="none"
-                          stroke="currentColor"
+                        stroke="currentColor"
-                          stroke-width="2"
+                        stroke-width="2"
-                          stroke-linecap="round"
+                        stroke-linecap="round"
-                          stroke-linejoin="round"
+                        stroke-linejoin="round"
-                          class="lucide lucide-eye"
+                        class="lucide lucide-eye"
-                        >
+                      >
-                          <path
+                        <path
-                            d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
+                          d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
-                          />
+                        />
-                          <circle cx="12" cy="12" r="3" />
+                        <circle cx="12" cy="12" r="3" />
-                        </svg>
+                      </svg>
                       Reaction Names
                     </a>
                   </li>
@@ -584,22 +583,22 @@
         descContent.innerHTML = newDesc;
       }
 
-      const compoundNamesBtn = document.getElementById("compound-names-toggle-button");
+      const compoundNamesBtn = document.getElementById(
+        "compound-names-toggle-button",
+      );
       if (compoundNamesBtn) {
         compoundNamesBtn.addEventListener("click", function () {
           compoundNamesViewEnabled = !compoundNamesViewEnabled;
           const icon = document.getElementById("compound-names-icon");
-
           if (compoundNamesViewEnabled) {
             // Change to eye-off icon
             icon.innerHTML =
               '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
-
             nodes.forEach((x) => {
               if (x.name) {
                 d3.select(x.el)
                   .append("text")
-                  .text(d => d.name)
+                  .text((d) => d.plain_name)
                   .attr("text-anchor", "middle")
                   .attr("y", -20)
                   .style("font-size", "4px");
@@ -609,38 +608,29 @@
             // Change back to eye icon
             icon.innerHTML =
               '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
-
             nodes.forEach((x) => {
-              d3.select(x.el)
+              d3.select(x.el).select("text").remove();
-                .select("text")
+            });
-                .remove()
-            })
           }
         });
       }
-
+      const reactionNamesBtn = document.getElementById(
-      const reactionNamesBtn = document.getElementById("reaction-names-toggle-button");
+        "reaction-names-toggle-button",
+      );
       if (reactionNamesBtn) {
         reactionNamesBtn.addEventListener("click", function () {
           reactionNamesViewEnabled = !reactionNamesViewEnabled;
           const icon = document.getElementById("reaction-names-icon");
-
           if (reactionNamesViewEnabled) {
             // Change to eye-off icon
             icon.innerHTML =
               '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
-
+            d3.selectAll(".link-label").style("display", null);
-              d3.selectAll(".link-label")
-                .style("display", null);
-
           } else {
             // Change back to eye icon
             icon.innerHTML =
               '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
-
+            d3.selectAll(".link-label").style("display", "none");
-            d3.selectAll(".link-label")
-                .style("display", "none");
-
           }
         });
       }

tests/views/test_package_views.py

@@ -72,8 +72,10 @@ class PackageViewTest(TestCase):
 
     def test_import_package(self):
         file = SimpleUploadedFile(
-            "Fixture_Package.json",
+            "EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json",
-            open(s.FIXTURE_DIRS[0] / "Fixture_Package.json", "rb").read(),
+            open(
+                s.FIXTURE_DIRS[0] / "EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json", "rb"
+            ).read(),
             content_type="application/json",
         )
 
@@ -86,10 +88,11 @@ class PackageViewTest(TestCase):
 
         p = Package.objects.get(url=package_url)
 
-        self.assertEqual(p.pathways.count(), 22)
+        self.assertEqual(p.pathways.count(), 219)
-        self.assertEqual(p.rules.count(), 45)
+        self.assertEqual(p.rules.count(), 498)
-        self.assertEqual(p.compounds.count(), 223)
+        self.assertEqual(p.compounds.count(), 1399)
-        self.assertEqual(p.reactions.count(), 212)
+        self.assertEqual(p.reactions.count(), 1480)
+        self.assertEqual(p.scenarios.count(), 1914)
 
         upp = UserPackagePermission.objects.get(package=p, user=self.user1)
         self.assertEqual(upp.permission, Permission.ALL[0])

utilities/misc.py

@@ -9,7 +9,6 @@ from datetime import datetime
 from typing import Any, Dict, List, Optional, TYPE_CHECKING
 
 from django.conf import settings as s
-from django.db import transaction
 from ninja import Schema
 from pydantic import HttpUrl, ValidationError
 
@@ -20,23 +19,15 @@ from epdb.models import (
     Compound,
     CompoundStructure,
     Edge,
-    EnviFormer,
-    EPModel,
-    ExternalDatabase,
-    ExternalIdentifier,
     License,
-    MLRelativeReasoning,
     Node,
     ParallelRule,
     Pathway,
     Reaction,
     Rule,
-    RuleBasedRelativeReasoning,
     Scenario,
     Setting,
     SimpleAmbitRule,
-    SimpleRDKitRule,
-    SimpleRule, Group,
 )
 from utilities.chem import FormatConverter
 
@@ -353,7 +344,6 @@ class PackageExporter:
 
 
 class PackageImporter:
-
     def __init__(self, package: Dict[str, Any], preserve_uuids: bool = False):
         self.preserve_uuids = preserve_uuids
         self._raw_package = package
@@ -412,11 +402,7 @@ class PackageImporter:
             new_c.default_structure = self._cache[c.default_structure.uuid]
             new_c.save()
 
-    def _import_simple_rules(
+    def _import_simple_rules(self, package: Package, rules: List[RuleExportSchema]):
-            self,
-            package: Package,
-            rules: List[RuleExportSchema]
-    ):
         for r in rules:
             new_r = SimpleAmbitRule()
             new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
@@ -431,11 +417,7 @@ class PackageImporter:
 
             self._cache[r.uuid] = new_r
 
-    def _import_composite_rules(
+    def _import_composite_rules(self, package: Package, rules: List[ParallelRuleExportSchema]):
-        self,
-        package: Package,
-        rules: List[ParallelRuleExportSchema]
-    ):
         for r in rules:
             new_r = ParallelRule()
             new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
@@ -451,9 +433,9 @@ class PackageImporter:
             self._cache[r.uuid] = new_r
 
     def _import_reactions(
-            self,
+        self,
-            package: Package,
+        package: Package,
-            reactions: List[ReactionExportSchema],
+        reactions: List[ReactionExportSchema],
     ):
         for r in reactions:
             new_r = Reaction()
@@ -477,11 +459,7 @@ class PackageImporter:
 
             self._cache[r.uuid] = new_r
 
-    def _import_pathways(
+    def _import_pathways(self, package: Package, pathways: List[PathwayExportSchema]):
-            self,
-            package: Package,
-            pathways: List[PathwayExportSchema]
-    ):
         for pw in pathways:
             new_pw = Pathway()
             new_pw.uuid = str(uuid.uuid4()) if not self.preserve_uuids else pw.uuid
@@ -529,27 +507,21 @@ class PackageImporter:
 
                 self._cache[e.uuid] = new_e
 
-    def _import_scenarios(
+    def _import_scenarios(self, package: Package, scenarios: List[ScenarioExportSchema]):
-            self,
+        for scen in scenarios:
-            package: Package,
-            scenarios: List[ScenarioExportSchema]
-    ):
-        for s in scenarios:
             new_s = Scenario()
-            new_s.uuid = str(uuid.uuid4()) if not self.preserve_uuids else s.uuid
+            new_s.uuid = str(uuid.uuid4()) if not self.preserve_uuids else scen.uuid
             new_s.package = package
-            new_s.name = s.name
+            new_s.name = scen.name
-            new_s.description = s.description
+            new_s.description = scen.description
-            new_s.scenario_date = s.scenario_date
+            new_s.scenario_date = scen.scenario_date
-            new_s.scenario_type = s.scenario_type
+            new_s.scenario_type = scen.scenario_type
             new_s.save()
 
-            self._cache[s.uuid] = new_s
+            self._cache[scen.uuid] = new_s
 
     def _import_additional_information(
-            self,
+        self, package: Package, additional_information: List[AdditionalInformationExportSchema]
-            package: Package,
-            additional_information: List[AdditionalInformationExportSchema]
     ):
         for ai in additional_information:
             new_ai = AdditionalInformation()
@@ -582,12 +554,11 @@ class PackageImporter:
         for coll in collections:
             for elem in coll:
                 elem_obj = self._cache[elem.uuid]
-                for s in elem.scenarios:
+                for scen in elem.scenarios:
-                    elem_obj.scenarios.add(self._cache[s.uuid])
+                    elem_obj.scenarios.add(self._cache[scen.uuid])
-
 
     def _import_package_from_json(
-            self,
+        self,
     ) -> Package:
         try:
             parsed = PackageExportSchema.model_validate(self._raw_package)
@@ -602,8 +573,6 @@ class PackageImporter:
         package_license = License.objects.get(link=parsed.license.link) if parsed.license else None
         package_classification_level = Package.Classification[parsed.classification_level.upper()]
 
-        print(parsed.classification_level, "->", package_classification_level)
-
         package = Package()
         package.uuid = package_uuid
         package.name = f"{parsed.name} - Imported at {datetime.now()}"