Make links thicker, reduce timeout trigger time

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

...

epdb/legacy_api.py

@@ -1698,7 +1698,7 @@ class PathwayNode(Schema):
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
-    proposed: List[Dict[str, str]] = []
+    proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
     smiles: str = Field(None, alias="smiles")
     pseudo: bool = Field(False, alias="pseudo")
     pesLink: str | None = Field(None, alias="pes_link")

epdb/models.py

@@ -904,7 +904,6 @@ class Compound(
         # Check if we can find the standardized one
         if qs.exists():
             # TODO should we add a structure?
-            # ->
             found_structure = qs.first()
             found_compound = found_structure.compound
 
@@ -1995,7 +1994,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 # add links start -> pseudo
                 new_link = {
                     "name": link["name"],
-                    "plain_name": link["plain_name"],
                     "id": link["id"],
                     "url": link["url"],
                     "image": link["image"],
@@ -2005,7 +2003,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                     "source": node_url_to_idx[link["start_node_urls"][0]],
                     "target": pseudo_idx,
                     "app_domain": link.get("app_domain", None),
-                    "to_pseudo": True,
                 }
                 adjusted_links.append(new_link)
 
@@ -2013,7 +2010,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 for target in link["end_node_urls"]:
                     new_link = {
                         "name": link["name"],
-                        "plain_name": link["plain_name"],
                         "id": link["id"],
                         "url": link["url"],
                         "image": link["image"],
@@ -2024,7 +2020,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
                         "multi_step": link["multi_step"],
-                        "from_pseudo": True,
                     }
                     adjusted_links.append(new_link)
 
@@ -2334,19 +2329,17 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
-    def get_name(self, include_suffix=True):
+    def get_name(self):
         non_generic_name = True
 
         if 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)"
-            else:
-                return self.default_node_label.name
+        return (
+            self.name
+            if non_generic_name
+            else f"{self.default_node_label.name} (taken from underlying structure)"
+        )
 
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
@@ -2376,7 +2369,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             ),
             "image_type": "svg",
             "name": self.get_name(),
-            "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
@@ -2510,7 +2502,6 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def d3_json(self):
         edge_json = {
             "name": self.get_name(),
-            "plain_name": self.get_name(include_suffix=False),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
@@ -2625,19 +2616,17 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_name(self, include_suffix=True):
+    def get_name(self):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        if non_generic_name:
-            return self.name
-        else:
-            if include_suffix:
-                return f"{self.edge_label.name} (taken from underlying reaction)"
-            else:
-                return self.edge_label.name
+        return (
+            self.name
+            if non_generic_name
+            else f"{self.edge_label.name} (taken from underlying reaction)"
+        )
 
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):

epdb/views.py

@@ -2121,14 +2121,12 @@ def package_pathways(request, package_uuid):
         else:
             prediction_setting = current_user.prediction_settings()
 
-        is_predict_mode = pw_mode in {"predict", "incremental"}
-
         pw = Pathway.create(
             current_package,
-            stand_smiles if is_predict_mode else smiles,
+            stand_smiles,
             name=name,
             description=description,
-            predicted=is_predict_mode,
+            predicted=pw_mode in {"predict", "incremental"},
         )
 
         # set mode

static/js/pw.js

@@ -495,7 +495,7 @@ function draw(pathway, elem) {
         if (n.stereo_removed) {
             popupContent += "<span class='alert alert-warning alert-soft'>Removed stereochemistry for prediction</span>";
         }
-        popupContent += "<a href='" + n.url + "'>" + n.plain_name + "</a><br>";
+        popupContent += "<a href='" + n.url + "'>" + n.name + "</a><br>";
         popupContent += "Depth " + n.depth + "<br>"
 
         if (appDomainViewEnabled) {
@@ -535,22 +535,6 @@ function draw(pathway, elem) {
             popupContent += '<b>Half-lives and related scenarios:</b><br>'
             for (var s of n.scenarios) {
                 popupContent += "<a href='" + s.url + "'>" + s.name + "</a><br>";
-                for (var prop in n.proposed) {
-                    if (n.proposed[prop].scenarioId === s.url) {
-                        if("proposed" in n.proposed[prop]){
-                            popupContent += "This compound is a proposed intermediate" + "<br>";
-                        }
-                        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>";
-                        }
-                    }
-                }
-                popupContent += "<br>";
-
             }
         }
 
@@ -563,7 +547,7 @@ function draw(pathway, elem) {
     }
 
     function edge_popup(e) {
-        popupContent = "<a href='" + e.url + "'>" + e.plain_name + "</a><br><br>";
+        popupContent = "<a href='" + e.url + "'>" + e.name + "</a><br><br>";
 
         if (e.reaction.rules) {
             for (var rule of e.reaction.rules) {
@@ -614,7 +598,7 @@ function draw(pathway, elem) {
 
     // Add background rectangle FIRST to enable pan/zoom on empty space
     // This must be inserted before zoomable group so it's behind everything
-    const rect = svg.insert("rect", "#zoomable")
+    svg.insert("rect", "#zoomable")
         .attr("x", 0)
         .attr("y", 0)
         .attr("width", width)
@@ -623,31 +607,6 @@ function draw(pathway, elem) {
         .attr("pointer-events", "all")
         .style("cursor", "grab");
 
-        // 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)
-        const target = event.target;
-        const isNode = target.closest && (
-            target.closest("circle") !== null ||
-            target.closest("image") !== null ||
-            target.closest(".node") !== null
-        );
-        const isLink = target.closest && (
-            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
-            d3.selectAll("circle").classed("highlighted", false);
-            d3.selectAll("path").classed("highlighted", false);
-            d3.selectAll("path").classed("inedge", false);
-            d3.selectAll("path").classed("outedge", false);
-        }
-    });
-
     // Zoom Funktion aktivieren
     const zoom = d3.zoom()
         .scaleExtent([0.5, 5])
@@ -746,20 +705,6 @@ function draw(pathway, elem) {
           }
         });
 
-    function reaction_name(d) {
-        const to_pseudo = d?.to_pseudo || false;
-
-        if (to_pseudo) {
-            return "";
-        }
-
-        var suffix = "";
-        if ("reaction_probability" in d) {
-            suffix = " (p= " + d["reaction_probability"].toFixed(2) + ")"
-        }
-        return d.plain_name + suffix;
-    }
-
     const linkText = linkGroup
       .append("text")
       .attr("class", "link-label")
@@ -768,7 +713,7 @@ function draw(pathway, elem) {
       .style("font-size", "4px")
       .style("pointer-events", "none")
       .style("display", "none")
-      .text(d => reaction_name(d))
+      .text(d => d.name)
       .attr("x", d => (d.source.x + d.target.x) / 2)
       .attr("y", d => (d.source.y + d.target.y) / 2);
 

templates/objects/pathway.html

@@ -28,7 +28,6 @@
     .link_no_arrow {
       stroke: #999;
       stroke-opacity: 0.6;
-      stroke-width: 1.5px;
     }
 
     .node image {