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

...

bayer/models.py

@@ -185,7 +185,7 @@ class PESStructure(CompoundStructure):
     def create(
             compound: Compound,
             pes_link: str,
-            molfile: str,
+            mol_file: str,
             smiles: str,
             name: str = None,
             description: str = None,
@@ -204,7 +204,7 @@ class PESStructure(CompoundStructure):
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         cs.smiles = smiles
-        cs.molfile = molfile
+        cs.mol_file = mol_file
         cs.pes_link = pes_link
         cs.compound = compound
 

bayer/templates/objects/compound_structure_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ compound_structure.pes_link }}" class="hover:bg-base-200">{{ compound_structure.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ compound_structure.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/compound_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ compound.default_structure.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/node_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ node.default_node_label.pes_link }}" class="hover:bg-base-200">{{ node.default_node_label.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ node.default_node_label.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/views.py

@@ -2,13 +2,14 @@ import base64
 
 import requests
 from django.conf import settings as s
-from django.http import HttpResponse, HttpResponseBadRequest
+from django.core.exceptions import BadRequest
+from django.http import HttpResponse
 from django.shortcuts import redirect
 
 from bayer.models import PESCompound
 from epdb.logic import PackageManager
 from epdb.models import Pathway, Node
-from epdb.views import _anonymous_or_real, error
+from epdb.views import _anonymous_or_real
 from utilities.decorators import package_permission_required
 
 Package = s.GET_PACKAGE_MODEL()
@@ -22,11 +23,7 @@ def create_pes(request, package_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
+            raise BadRequest("Cannot create PESs for internal packages.")
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -36,25 +33,25 @@ def create_pes(request, package_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
+                    return BadRequest("Cannot create PESs for non-secret packages.")
 
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return HttpResponseBadRequest(
+                        return BadRequest(
                             f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
             return redirect(pes.url)
         else:
-            return HttpResponseBadRequest("Please provide a PES link.")
+            return BadRequest("Please provide a PES link.")
     else:
         pass
 
@@ -68,11 +65,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
+            raise BadRequest("Cannot create PESs for internal packages.")
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -82,18 +75,18 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
+                    return BadRequest("Cannot create PESs for non-secret packages.")
 
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        return HttpResponseBadRequest(
+                        return BadRequest(
                             f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
@@ -116,7 +109,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             return redirect(current_pathway.url)
 
         else:
-            return HttpResponseBadRequest("Please provide a PES link.")
+            return BadRequest("Please provide a PES link.")
     else:
         pass
 

epdb/exceptions.py

@@ -1,5 +1,2 @@
 class InvalidSMILESException(Exception):
     pass
-
-class PackageImportException(Exception):
-    pass

epdb/legacy_api.py

@@ -633,14 +633,9 @@ class CompoundSchema(Schema):
     reviewStatus: str = Field(False, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     structures: List["CompoundStructureSchema"] = []
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
-    def resolve_pes_link(obj: Compound):
-        return getattr(obj.default_structure, "pes_link", None)
-
-    @staticmethod
-    def resolve_review_status(obj: Compound):
+    def resolve_review_status(obj: CompoundStructure):
         return "reviewed" if obj.package.reviewed else "unreviewed"
 
     @staticmethod
@@ -714,7 +709,6 @@ class CompoundStructureSchema(Schema):
     reviewStatus: str = Field(None, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     smiles: str = Field(None, alias="smiles")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_review_status(obj: CompoundStructure):
@@ -1701,7 +1695,6 @@ class PathwayNode(Schema):
     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")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1714,10 +1707,24 @@ class PathwayNode(Schema):
         # TODO
         return []
 
+    @staticmethod
+    def resolve_engineered_intermediate(obj: Node):
+        # TODO
+        return False
+
+    @staticmethod
+    def resolve_image(obj: Node):
+        return f"{obj.default_node_label.url}?image=svg"
+
     @staticmethod
     def resolve_image_size(obj: Node):
         return 400
 
+    @staticmethod
+    def resolve_proposed_intermediate(obj: Node):
+        # TODO
+        return []
+
 
 class PathwaySchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
@@ -2385,31 +2392,3 @@ def get_setting(request, setting_uuid):
         return 403, {
             "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
         }
-
-
-########
-# Util #
-########
-class NonPersistent(Schema):
-    smiles: str
-    setting_url: str = Field(..., alias="settingUri")
-
-
-@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
-
-        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/logic.py

@@ -1078,8 +1078,10 @@ class PackageManager(object):
         data: Dict[str, Any],
         owner: User,
         preserve_uuids=False,
+        add_import_timestamp=True,
+        trust_reviewed=False,
     ) -> Package:
-        importer = PackageImporter(data, preserve_uuids)
+        importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1896,12 +1898,6 @@ class SPathway(object):
                 "to": to_indices,
             }
 
-            if edge.rule:
-                e["rule"] = edge.rule.simple_json()
-
-            if edge.probability:
-                e["probability"] = edge.probability
-
             edges.append(e)
 
         return {

epdb/models.py

@@ -2379,7 +2379,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
-            "proposed": self.is_proposed_intermediate(),
             "timeseries": self.get_timeseries_data(),
             **structure_data,
         }
@@ -2453,26 +2452,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return data
 
-    def is_proposed_intermediate(self):
-        collected = defaultdict(dict)
-        for ai in self.additional_information.filter(
-                type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"]
-                , scenario__isnull=False
-        ):
-            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
-            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
-
-            if ai.type == "ProposedIntermediate":
-                collected[str(ai.scenario.uuid)]["proposed"] = True
-
-            if ai.type == "Confidence":
-                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
-
-        return list(collected.values())
-
     def simple_json(self, include_description=False):
         res = super().simple_json()
         name = res.get("name", None)

epdb/views.py

@@ -2482,22 +2482,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        new_node_name = request.POST.get("node-name")
-        new_node_description = request.POST.get("node-description")
-
-        if any([new_node_name, new_node_description]):
-            if new_node_name is not None and new_node_name.strip() != "":
-                new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-                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()
-                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")
+        return HttpResponseBadRequest()
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 

static/css/input.css

@@ -39,7 +39,3 @@ select.select[multiple] {
   display: block;
   white-space: normal;
 }
-
-p a {
-  @apply underline;
-}

static/js/alpine/pagination.js

@@ -5,125 +5,6 @@
  */
 
 document.addEventListener('alpine:init', () => {
-
-  const basePagination = (
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId
-  ) => ({
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId,
-
-    get paginatedItems() {
-      return this.items;
-    },
-
-    get showingStart() {
-      if (this.totalItems === 0) return 0;
-      return (this.currentPage - 1) * this.perPage + 1;
-    },
-
-    get showingEnd() {
-      if (this.totalItems === 0) return 0;
-      return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
-    },
-
-    nextPage() {
-      if (this.currentPage < this.totalPages) {
-        this.fetchPage(this.currentPage + 1);
-      }
-    },
-
-    prevPage() {
-      if (this.currentPage > 1) {
-        this.fetchPage(this.currentPage - 1);
-      }
-    },
-
-    goToPage(page) {
-      if (page >= 1 && page <= this.totalPages) {
-        this.fetchPage(page);
-      }
-    },
-
-    get pageNumbers() {
-      const pages = [];
-      const total = this.totalPages;
-      const current = this.currentPage;
-
-      if (total === 0) {
-        return pages;
-      }
-
-      if (total <= 7) {
-        for (let i = 1; i <= total; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-      } else {
-        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
-
-        let rangeStart;
-        let rangeEnd;
-
-        if (current <= 4) {
-          rangeStart = 2;
-          rangeEnd = 5;
-        } else if (current >= total - 3) {
-          rangeStart = total - 4;
-          rangeEnd = total - 1;
-        } else {
-          rangeStart = current - 1;
-          rangeEnd = current + 1;
-        }
-
-        if (rangeStart > 2) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
-        }
-
-        for (let i = rangeStart; i <= rangeEnd; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-
-        if (rangeEnd < total - 1) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
-        }
-
-        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
-      }
-
-      return pages;
-    }
-  });
-
-  Alpine.data('paginatedList',
-    (items, options = {}) => ({
-      ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),),
-
-      init() {
-        this.fetchPage(1);
-      },
-
-      async fetchPage(page) {
-        this.totalItems = this.items.length;
-        this.totalPages = Math.ceil(this.items.length / this.perPage);
-        this.currentPage = page
-
-        const start = page * this.perPage - this.perPage;
-        const end = page * this.perPage;
-        return this.items.slice(start, end);
-      }
-
-    }));
-
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],
     currentPage: 1,

static/js/pw.js

@@ -1,19 +1,13 @@
 console.log("loaded pw.js")
 
-function findPaths(source_idx, links) {
+function findPaths(source_idx, target_idx, links) {
     const resultLinks = new Set();
     const visited = new Set();
     // Helper function for depth-first search
     function dfs(current) {
-
-        if (visited.has(current)) {
+        if (current === target_idx) {
             return;
         }
-
-        if (links.filter(link => link.target.id === current).length === 0) {
-            return;
-        }
-
         visited.add(current);
         links.forEach(link => {
             if (
@@ -29,7 +23,7 @@ function findPaths(source_idx, links) {
     }
     // Start DFS
     dfs(source_idx);
-    return Array.from(resultLinks);
+    return Array.from(resultLinks); // Convert Set to Array for result
 }
 
 function predictFromNode(url) {
@@ -67,9 +61,6 @@ function draw(pathway, elem) {
         const horizontalSpacing = 75; // horizontal space between nodes
         const depthMap = new Map();
 
-        // Avoid leaving unconnected Nodes leaving the viewport
-        nodes.forEach(node => {if (node.depth < 0)  node.depth = 0;});
-
         // Sort nodes by depth first to minimize crossings
         const sortedNodes = [...nodes].sort((a, b) => a.depth - b.depth);
 
@@ -157,10 +148,6 @@ function draw(pathway, elem) {
         });
 
         node.attr("transform", d => `translate(${d.x},${d.y})`);
-
-        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) {
@@ -263,7 +250,7 @@ function draw(pathway, elem) {
     }
 
     // Wait before showing popup (ms)
-    var popupWaitBeforeShow = 500;
+    var popupWaitBeforeShow = 1000;
 
     // Custom popover element
     let popoverTimeout = null;
@@ -654,31 +641,21 @@ function draw(pathway, elem) {
         .on("tick", ticked);
 
     // Kanten zeichnen
-    const linkGroup = zoomable.append("g")
-      .selectAll("g")
-      .data(links)
-      .enter()
-      .append("g")
-      .attr("class", "link-group");
-
-    const link = linkGroup
-      .append("path")
-      .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-      .attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow)")
-      .attr("fill", "none")
-
-      // Check if target is pseudo and draw marker only if not pseudo
-      .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-      .attr("marker-end", d => {
-        if (d.target.pseudo) return '';
-        if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops
-          return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
-        }
-      )
-      .attr("fill", "none")
-      .on("click", function(event, d) {
+    const link = zoomable.append("g")
+        .selectAll("path")
+        .data(links)
+        .enter().append("path")
+        // Check if target is pseudo and draw marker only if not pseudo
+        .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
+        .attr("marker-end", d => {
+            if (d.target.pseudo) return '';
+            if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops
+            return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
+        })
+        .attr("fill", "none")
+        .on("click", function(event, d) {
           const wasHighlighted = d3.select(this).classed("highlighted");
-          d3.selectAll("path").classed("highlighted", false);
+	      d3.selectAll("path").classed("highlighted", false);
           if (!wasHighlighted) {
             const toHighlight = [];
             toHighlight.push(d.el);
@@ -705,18 +682,6 @@ function draw(pathway, elem) {
           }
         });
 
-    const linkText = linkGroup
-      .append("text")
-      .attr("class", "link-label")
-      .attr("text-anchor", "middle")
-      .attr("dy", -6)
-      .style("font-size", "4px")
-      .style("pointer-events", "none")
-      .style("display", "none")
-      .text(d => d.name)
-      .attr("x", d => (d.source.x + d.target.x) / 2)
-      .attr("y", d => (d.source.y + d.target.y) / 2);
-
     // add element to links array
     link.each(function (d) {
         d.el = this;  // attach the DOM element to the data object
@@ -742,7 +707,7 @@ function draw(pathway, elem) {
 
           if (!wasHighlighted) {
             d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-            const inEdges = findPaths(d.id, links);
+            const inEdges = findPaths(d.id, 3, links);
             const outEdges = []
             // Colorize out edges green
             for (const l of links) {
@@ -840,14 +805,14 @@ function draw(pathway, elem) {
 
 function serializeSVG(svgElement) {
 
-    svgElement.querySelectorAll("path.link").forEach(line => {
+    svgElement.querySelectorAll("line.link").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);
         line.setAttribute("fill", style.fill);
     });
 
-    svgElement.querySelectorAll("path.link_no_arrow").forEach(line => {
+    svgElement.querySelectorAll("line.link_no_arrow").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);

templates/objects/node.html

@@ -55,15 +55,6 @@
       </div>
     </div>
 
-    <!-- Description -->
-    {% if node.description and node.description != "no description" %}
-      <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
-        <div class="collapse-title text-xl font-medium">Description</div>
-        <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

@@ -21,7 +21,6 @@
     .link {
       stroke: #999;
       stroke-opacity: 0.6;
-      stroke-width: 1.5px;
       /* marker-end: url(#arrow); */
     }
 
@@ -178,52 +177,6 @@
                   tabindex="0"
                   class="dropdown-content menu bg-base-100 rounded-box z-50 w-60 p-2"
                 >
-                  <li>
-                    <a id="compound-names-toggle-button" class="cursor-pointer">
-                      <svg
-                          id="compound-names-icon"
-                          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-eye"
-                        >
-                          <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" />
-                        </svg>
-                      Compound Names
-                    </a>
-                  </li>
-                  <li>
-                    <a id="reaction-names-toggle-button" class="cursor-pointer">
-                      <svg
-                          id="reaction-names-icon"
-                          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-eye"
-                        >
-                          <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" />
-                        </svg>
-                      Reaction Names
-                    </a>
-                  </li>
                   {% if pathway.setting.model.app_domain %}
                     <li>
                       <a id="app-domain-toggle-button" class="cursor-pointer">
@@ -249,7 +202,6 @@
                       </a>
                     </li>
                   {% endif %}
-                  {% if 1 == 0 %}
                   <li>
                     <a id="timeseries-toggle-button" class="cursor-pointer">
                       <svg
@@ -300,7 +252,6 @@
                       Show Predicted Properties
                     </a>
                   </li>
-                  {% endif %}
                 </ul>
               </div>
             </div>
@@ -544,10 +495,6 @@
   {{ pathway.d3_json|json_script:"pathway" }}
 
   <script>
-    // Global switch for compound names view
-    var compoundNamesViewEnabled = false;
-    // Gloabl switch for reaction names view
-    var reactionNamesViewEnabled = false;
     // Global switch for app domain view
     var appDomainViewEnabled = false;
     // Global switch for timeseries view
@@ -583,67 +530,6 @@
         descContent.innerHTML = newDesc;
       }
 
-      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)
-                  .attr("text-anchor", "middle")
-                  .attr("y", -20)
-                  .style("font-size", "4px");
-              }
-            });
-          } 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"/>';
-
-            nodes.forEach((x) => {
-              d3.select(x.el)
-                .select("text")
-                .remove()
-            })
-          }
-        });
-      }
-
-      const reactionNamesBtn = document.getElementById("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);
-
-          } 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");
-
-          }
-        });
-      }
-
       // App domain toggle
       const appDomainBtn = document.getElementById("app-domain-toggle-button");
       if (appDomainBtn) {

templates/objects/setting_template.html

@@ -24,76 +24,6 @@
         <td>Setting Name</td>
         <td>{{ setting_to_render.name }}</td>
       </tr>
-      <tr>
-        <td>Setting URL</td>
-        <td>
-          <a href="{{ setting_to_render.url }}" class="link link-primary">{{ setting_to_render.url }}</a>
-          <div
-            x-data="{
-              value: '{{ setting_to_render.url }}',
-              copied: false,
-
-              async copy() {
-                await navigator.clipboard.writeText(this.value)
-                this.copied = true
-
-                setTimeout(() => {
-                  this.copied = false
-                }, 1500)
-              }
-            }"
-            class="join"
-          >
-          <button
-            type="button"
-            class="btn btn-ghost"
-            :data-tip="copied ? 'Copied!' : 'Copy'"
-            @click="copy"
-            aria-label="Copy to clipboard"
-          >
-            <svg
-              x-show="!copied"
-              xmlns="http://www.w3.org/2000/svg"
-              class="h-4 w-4"
-              fill="none"
-              viewBox="0 0 24 24"
-              stroke="currentColor"
-              stroke-width="2"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                d="M8 16H6a2 2 0 01-2-2V6a2 2 0 012-2h8a2 2 0 012 2v2"
-              />
-              <rect
-                width="12"
-                height="12"
-                x="8"
-                y="8"
-                rx="2"
-                ry="2"
-              />
-            </svg>
-
-            <svg
-              x-show="copied"
-              xmlns="http://www.w3.org/2000/svg"
-              class="h-4 w-4"
-              fill="none"
-              viewBox="0 0 24 24"
-              stroke="currentColor"
-              stroke-width="2"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                d="M5 13l4 4L19 7"
-              />
-            </svg>
-            </button>
-          </div>
-        </td>
-      </tr>
       {% if setting_to_render.description %}
         <tr>
           <td>Setting Description</td>

utilities/misc.py

@@ -11,10 +11,8 @@ 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
+from pydantic import HttpUrl
 
-from bayer.models import PESCompound, PESStructure
-from epdb.exceptions import PackageImportException
 from epdb.models import (
     AdditionalInformation,
     Compound,
@@ -36,7 +34,7 @@ from epdb.models import (
     Setting,
     SimpleAmbitRule,
     SimpleRDKitRule,
-    SimpleRule, Group,
+    SimpleRule,
 )
 from utilities.chem import FormatConverter
 
@@ -44,7 +42,7 @@ logger = logging.getLogger(__name__)
 Package = s.GET_PACKAGE_MODEL()
 
 if TYPE_CHECKING:
-    from epdb.logic import SPathway, GroupManager
+    from epdb.logic import SPathway
 
 
 class LicenseExportSchema(Schema):
@@ -66,9 +64,6 @@ class RefExportSchema(Schema):
         return str(value)
 
 
-class RefGroupExportSchema(RefExportSchema): ...
-
-
 class RefCompoundExportSchema(RefExportSchema): ...
 
 
@@ -93,9 +88,6 @@ class RefPathwayExportSchema(RefExportSchema): ...
 class RefScenarioExportSchema(RefExportSchema): ...
 
 
-class RefEnzymeExportSchema(RefExportSchema): ...
-
-
 ############
 # Compound #
 ############
@@ -118,26 +110,6 @@ class CompoundStructureExportSchema(RefCompoundStructureExportSchema):
     scenarios: List[RefScenarioExportSchema]
 
 
-class PESCompoundExportSchema(RefCompoundExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    default_structure: RefCompoundStructureExportSchema
-    structures: List["PESCompoundStructureExportSchema"]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class PESCompoundStructureExportSchema(RefCompoundStructureExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    smiles: str
-    molfile: Optional[str]
-    normalized_structure: bool
-    scenarios: List[RefScenarioExportSchema]
-    pes_link: HttpUrl
-
-
 ############
 # Reaction #
 ############
@@ -156,28 +128,7 @@ class ReactionExportSchema(RefReactionExportSchema):
 #########
 # Rules #
 #########
-class EnzymeExportSchema(RefEnzymeExportSchema):
-    ec_number: str
-    classification_level: int
-    linking_method: str
-    reaction_evidence: List[RefReactionExportSchema]
-    edge_evidence: List[RefEdgeExportSchema]
-
-
-class EnzymeRuleExportSchema(RefRuleExportSchema):
-    enzymes: List[EnzymeExportSchema] | None = None
-
-    @staticmethod
-    def resolve_enzymes(obj):
-        if isinstance(obj, dict):
-            res = []
-            for e in obj.get("enzymes", []):
-                res.append(EnzymeExportSchema.model_validate(e))
-            return res
-        return obj.enzymelink_set.all()
-
-
-class RuleExportSchema(EnzymeRuleExportSchema):
+class RuleExportSchema(RefRuleExportSchema):
     name: str
     description: str
     aliases: List[str]
@@ -187,7 +138,7 @@ class RuleExportSchema(EnzymeRuleExportSchema):
     scenarios: List[RefScenarioExportSchema]
 
 
-class ParallelRuleExportSchema(EnzymeRuleExportSchema):
+class ParallelRuleExportSchema(RefRuleExportSchema):
     name: str
     description: str
     aliases: List[str]
@@ -259,10 +210,8 @@ class PackageExportSchema(Schema):
     description: str
     uuid: str
     reviewed: bool
-    license: LicenseExportSchema | None = None
-    classification_level: str = "Internal"
-    data_pool: RefGroupExportSchema | None = None
-    compounds: List[CompoundExportSchema | PESCompoundExportSchema]
+    license: LicenseExportSchema | None
+    compounds: List[CompoundExportSchema]
     reactions: List[ReactionExportSchema]
     simple_rules: List[RuleExportSchema]
     composite_rules: List[ParallelRuleExportSchema]
@@ -275,31 +224,6 @@ class PackageExportSchema(Schema):
         value = obj.get("uuid") if isinstance(obj, dict) else obj.uuid
         return str(value)
 
-    @staticmethod
-    def resolve_classification_level(obj):
-        if isinstance(obj, dict):
-            return obj["classification_level"]
-        return obj.Classification(obj.classification_level).name
-
-
-    @staticmethod
-    def resolve_compounds(obj):
-        res = []
-        if isinstance(obj, dict):
-            for c in obj.get("compounds", []):
-                is_pes = any([cs.get("pes_link", None) is not None for cs in c.get("structures", [])])
-                if is_pes:
-                    res.append(PESCompoundExportSchema.model_validate(c))
-                else:
-                    res.append(CompoundExportSchema.model_validate(c))
-        else:
-            for c in obj.compounds.all():
-                if isinstance(c, PESCompound):
-                    res.append(PESCompoundExportSchema.from_orm(c))
-                else:
-                    res.append(CompoundExportSchema.from_orm(c))
-        return res
-
     @staticmethod
     def resolve_simple_rules(obj):
         if isinstance(obj, dict):
@@ -353,281 +277,51 @@ class PackageExporter:
 
 
 class PackageImporter:
+    """
+    Imports package data from JSON export.
+    Handles object creation, relationship mapping, and dependency resolution.
+    """
 
-    def __init__(self, package: Dict[str, Any], preserve_uuids: bool = False):
+    def __init__(
+        self,
+        package: Dict[str, Any],
+        preserve_uuids: bool = False,
+        add_import_timestamp=True,
+        trust_reviewed=False,
+    ):
+        """
+        Initialize the importer.
+
+        Args:
+            preserve_uuids: If True, preserve original UUIDs. If False, generate new ones.
+        """
         self.preserve_uuids = preserve_uuids
+        self.add_import_timestamp = add_import_timestamp
+        self.trust_reviewed = trust_reviewed
+        self.uuid_mapping = {}
+        self.object_cache = {}
         self._raw_package = package
-        self._cache = {}
+
+    def _get_or_generate_uuid(self, original_uuid: str) -> str:
+        """Get mapped UUID or generate new one if not preserving UUIDs."""
+        if self.preserve_uuids:
+            return original_uuid
+
+        if original_uuid not in self.uuid_mapping:
+            self.uuid_mapping[original_uuid] = str(uuid.uuid4())
+
+        return self.uuid_mapping[original_uuid]
+
+    def _cache_object(self, model_name: str, uuid_str: str, obj):
+        """Cache a created object for later reference."""
+        self.object_cache[(model_name, uuid_str)] = obj
+
+    def _get_cached_object(self, model_name: str, uuid_str: str):
+        """Get a cached object by model name and UUID."""
+        return self.object_cache.get((model_name, uuid_str))
 
     def do_import(self) -> Package:
-        return self._import_package_from_json()
-
-    def _import_compounds(
-            self,
-            package: Package,
-            compounds: List[CompoundExportSchema | PESCompoundExportSchema],
-    ):
-        for c in compounds:
-
-            if isinstance(c, PESCompoundExportSchema):
-                c_cls = PESCompound
-            else:
-                c_cls = Compound
-
-            new_c = c_cls()
-            new_c.uuid = str(uuid.uuid4()) if not self.preserve_uuids else c.uuid
-            new_c.package = package
-            new_c.name = c.name
-            new_c.description = c.description
-            new_c.aliases = c.aliases
-            new_c.save()
-
-            self._cache[c.uuid] = new_c
-
-            for cs in c.structures:
-
-                if isinstance(cs, PESCompoundStructureExportSchema):
-                    cs_cls = PESStructure
-                else:
-                    cs_cls = CompoundStructure
-
-                new_cs = cs_cls()
-                new_cs.uuid = str(uuid.uuid4()) if not self.preserve_uuids else cs.uuid
-                new_cs.compound = new_c
-                new_cs.name = cs.name
-                new_cs.description = cs.description
-                new_cs.aliases = cs.aliases
-                new_cs.smiles = cs.smiles
-                new_cs.molfile = cs.molfile
-
-                if cs_cls == PESStructure:
-                    new_cs.pes_link = cs.pes_link
-
-                new_cs.normalized_structure = cs.normalized_structure
-                new_cs.save()
-
-                self._cache[cs.uuid] = new_cs
-
-            # Now we can assigne the default_structure to the compound
-            new_c.default_structure = self._cache[c.default_structure.uuid]
-            new_c.save()
-
-    def _import_simple_rules(
-            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
-            new_r.package = package
-            new_r.name = r.name
-            new_r.description = r.description
-            new_r.aliases = r.aliases
-            new_r.smirks = r.smirks
-            new_r.reactant_filter_smarts = r.reactant_filter_smarts
-            new_r.product_filter_smarts = r.product_filter_smarts
-            new_r.save()
-
-            self._cache[r.uuid] = new_r
-
-    def _import_composite_rules(
-        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
-            new_r.package = package
-            new_r.name = r.name
-            new_r.description = r.description
-            new_r.aliases = r.aliases
-            new_r.save()
-
-            for sr in r.simple_rules:
-                new_r.simple_rules.add(self._cache[sr.uuid])
-
-            self._cache[r.uuid] = new_r
-
-    def _import_reactions(
-            self,
-            package: Package,
-            reactions: List[ReactionExportSchema],
-    ):
-        for r in reactions:
-            new_r = Reaction()
-            new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
-            new_r.package = package
-            new_r.name = r.name
-            new_r.description = r.description
-            new_r.aliases = r.aliases
-            new_r.multi_step = r.multi_step
-            new_r.medline_references = r.medline_references
-            new_r.save()
-
-            for educt in r.educts:
-                new_r.educts.add(self._cache[educt.uuid])
-
-            for product in r.products:
-                new_r.products.add(self._cache[product.uuid])
-
-            for rule in r.rules:
-                new_r.rules.add(self._cache[rule.uuid])
-
-            self._cache[r.uuid] = new_r
-
-    def _import_pathways(
-            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
-            new_pw.package = package
-            new_pw.name = pw.name
-            new_pw.description = pw.description
-            new_pw.aliases = pw.aliases
-            new_pw.predicted = pw.predicted
-            new_pw.save()
-
-            self._cache[pw.uuid] = new_pw
-
-            for n in pw.nodes:
-                new_n = Node()
-                new_n.uuid = str(uuid.uuid4()) if not self.preserve_uuids else n.uuid
-                new_n.pathway = new_pw
-                new_n.name = n.name
-                new_n.description = n.description
-                new_n.aliases = n.aliases
-                new_n.default_node_label = self._cache[n.default_node_label.uuid]
-                new_n.depth = n.depth
-                new_n.stereo_removed = n.stereo_removed
-                new_n.save()
-
-                for nl in n.node_labels:
-                    new_n.node_labels.add(self._cache[nl.uuid])
-
-                self._cache[n.uuid] = new_n
-
-            for e in pw.edges:
-                new_e = Edge()
-                new_e.uuid = str(uuid.uuid4()) if not self.preserve_uuids else e.uuid
-                new_e.pathway = new_pw
-                new_e.name = e.name
-                new_e.description = e.description
-                new_e.aliases = e.aliases
-                new_e.edge_label = self._cache[e.edge_label.uuid]
-                new_e.save()
-
-                for sn in e.start_nodes:
-                    new_e.start_nodes.add(self._cache[sn.uuid])
-
-                for en in e.end_nodes:
-                    new_e.end_nodes.add(self._cache[en.uuid])
-
-                self._cache[e.uuid] = new_e
-
-    def _import_scenarios(
-            self,
-            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.package = package
-            new_s.name = s.name
-            new_s.description = s.description
-            new_s.scenario_date = s.scenario_date
-            new_s.scenario_type = s.scenario_type
-            new_s.save()
-
-            self._cache[s.uuid] = new_s
-
-    def _import_additional_information(
-            self,
-            package: Package,
-            additional_information: List[AdditionalInformationExportSchema]
-    ):
-        for ai in additional_information:
-            new_ai = AdditionalInformation()
-            new_ai.uuid = str(uuid.uuid4()) if not self.preserve_uuids else ai.uuid
-            new_ai.package = package
-            new_ai.type = ai.type
-            new_ai.data = ai.data
-
-            if ai.scenario:
-                new_ai.scenario = self._cache[ai.scenario.uuid]
-
-            if ai.attach_object:
-                new_ai.content_object = self._cache[ai.attach_object.uuid]
-
-            new_ai.save()
-
-            self._cache[ai.uuid] = new_ai
-
-    def _link_scenarios_after_import(self, data: PackageExportSchema):
-        collections = [
-            data.compounds,
-            data.simple_rules,
-            data.composite_rules,
-            data.reactions,
-            data.pathways,
-            [n for pw in data.pathways for n in pw.nodes],
-            [e for pw in data.pathways for e in pw.edges],
-        ]
-
-        for coll in collections:
-            for elem in coll:
-                elem_obj = self._cache[elem.uuid]
-                for s in elem.scenarios:
-                    elem_obj.scenarios.add(self._cache[s.uuid])
-
-
-    def _import_package_from_json(
-            self,
-    ) -> Package:
-        try:
-            parsed = PackageExportSchema.model_validate(self._raw_package)
-        except ValidationError as e:
-            logger.error(f"Error validating package data: {e}")
-            raise PackageImportException("Deserialization failed")
-
-        package_uuid = str(uuid.uuid4())
-        if self.preserve_uuids:
-            package_uuid = parsed.uuid
-
-        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()}"
-        package.description = parsed.description
-        package.reviewed = False
-        package.license = package_license
-        package.classification_level = package_classification_level
-
-        if package_classification_level == Package.Classification.SECRET:
-            package.data_pool = Group.objects.get(uuid=parsed.data_pool.uuid)
-
-        package.save()
-
-        # Import Elements
-        self._import_compounds(package, parsed.compounds)
-        self._import_simple_rules(package, parsed.simple_rules)
-        self._import_composite_rules(package, parsed.composite_rules)
-        self._import_reactions(package, parsed.reactions)
-        self._import_pathways(package, parsed.pathways)
-        self._import_scenarios(package, parsed.scenarios)
-        self._import_additional_information(package, parsed.additional_information)
-        self._link_scenarios_after_import(parsed)
-
-        return package
+        return self._import_package_from_json(self._raw_package)
 
     @staticmethod
     def sign(data: Dict[str, Any], key: str) -> Dict[str, Any]:
@@ -645,6 +339,510 @@ class PackageImporter:
         expected = hmac.new(key.encode(), json_str.encode(), hashlib.sha256).digest()
         return hmac.compare_digest(signature, expected)
 
+    @transaction.atomic
+    def _import_package_from_json(self, package_data: Dict[str, Any]) -> Package:
+        """
+        Import a complete package from JSON data.
+
+        Args:
+            package_data: Dictionary containing the package export data
+
+        Returns:
+            The created Package instance
+        """
+        print(f"Starting import of package: {package_data['name']}")
+
+        # Create the main package
+        package = self._create_package(package_data)
+
+        # Import in dependency order
+        self._import_compounds(package, package_data.get("compounds", []))
+        self._import_structures(package, package_data.get("structures", []))
+        self._import_rules(package, package_data.get("rules", {}))
+        self._import_reactions(package, package_data.get("reactions", []))
+        self._import_pathways(package, package_data.get("pathways", []))
+        self._import_nodes(package, package_data.get("nodes", []))
+        self._import_edges(package, package_data.get("edges", []))
+        self._import_scenarios(package, package_data.get("scenarios", []))
+
+        if package_data.get("models"):
+            self._import_models(package, package_data["models"])
+
+        # Set default structures for compounds (after all structures are created)
+        self._set_default_structures(package_data.get("compounds", []))
+
+        print(f"Package import completed: {package.name}")
+        return package
+
+    def _create_package(self, package_data: Dict[str, Any]) -> Package:
+        """Create the main package object."""
+        package_uuid = self._get_or_generate_uuid(package_data["uuid"])
+
+        # Handle license
+        license_obj = None
+        if package_data.get("license"):
+            license_data = package_data["license"]
+            license_obj, _ = License.objects.get_or_create(
+                name=license_data["name"],
+                defaults={
+                    "cc_string": license_data.get("cc_string", ""),
+                    "link": license_data.get("link", ""),
+                    "image_link": license_data.get("image_link", ""),
+                },
+            )
+
+        new_name = package_data.get("name")
+        if self.add_import_timestamp:
+            new_name = f"{new_name} - Imported at {datetime.now()}"
+
+        new_reviewed = False
+        if self.trust_reviewed:
+            new_reviewed = package_data.get("reviewed", False)
+
+        package = Package.objects.create(
+            uuid=package_uuid,
+            name=new_name,
+            description=package_data["description"],
+            kv=package_data.get("kv", {}),
+            reviewed=new_reviewed,
+            license=license_obj,
+        )
+
+        self._cache_object("Package", package_data["uuid"], package)
+        print(f"Created package: {package.name}")
+        return package
+
+    def _import_compounds(self, package: Package, compounds_data: List[Dict[str, Any]]):
+        """Import compounds."""
+        print(f"Importing {len(compounds_data)} compounds...")
+
+        for compound_data in compounds_data:
+            compound_uuid = self._get_or_generate_uuid(compound_data["uuid"])
+
+            compound = Compound.objects.create(
+                uuid=compound_uuid,
+                package=package,
+                name=compound_data["name"],
+                description=compound_data["description"],
+                kv=compound_data.get("kv", {}),
+                # default_structure will be set later
+            )
+
+            # Set aliases if present
+            if compound_data.get("aliases"):
+                compound.aliases = compound_data["aliases"]
+                compound.save()
+
+            self._cache_object("Compound", compound_data["uuid"], compound)
+
+            # Handle external identifiers
+            self._create_external_identifiers(
+                compound, compound_data.get("external_identifiers", [])
+            )
+
+    def _import_structures(self, package: Package, structures_data: List[Dict[str, Any]]):
+        """Import compound structures."""
+        print(f"Importing {len(structures_data)} compound structures...")
+
+        for structure_data in structures_data:
+            structure_uuid = self._get_or_generate_uuid(structure_data["uuid"])
+            compound_uuid = structure_data["compound"]["uuid"]
+            compound = self._get_cached_object("Compound", compound_uuid)
+
+            if not compound:
+                print(f"Warning: Compound with UUID {compound_uuid} not found for structure")
+                continue
+
+            structure = CompoundStructure.objects.create(
+                uuid=structure_uuid,
+                compound=compound,
+                name=structure_data["name"],
+                description=structure_data["description"],
+                kv=structure_data.get("kv", {}),
+                smiles=structure_data["smiles"],
+                canonical_smiles=structure_data["canonical_smiles"],
+                inchikey=structure_data["inchikey"],
+                normalized_structure=structure_data.get("normalized_structure", False),
+            )
+
+            # Set aliases if present
+            if structure_data.get("aliases"):
+                structure.aliases = structure_data["aliases"]
+                structure.save()
+
+            self._cache_object("CompoundStructure", structure_data["uuid"], structure)
+
+            # Handle external identifiers
+            self._create_external_identifiers(
+                structure, structure_data.get("external_identifiers", [])
+            )
+
+    def _import_rules(self, package: Package, rules_data: Dict[str, Any]):
+        """Import all types of rules."""
+        print("Importing rules...")
+
+        # Import simple rules first
+        simple_rules_data = rules_data.get("simple_rules", [])
+        print(f"Importing {len(simple_rules_data)} simple rules...")
+
+        for rule_data in simple_rules_data:
+            self._create_simple_rule(package, rule_data)
+
+        # Import parallel rules
+        parallel_rules_data = rules_data.get("parallel_rules", [])
+        print(f"Importing {len(parallel_rules_data)} parallel rules...")
+
+        for rule_data in parallel_rules_data:
+            self._create_parallel_rule(package, rule_data)
+
+    def _create_simple_rule(self, package: Package, rule_data: Dict[str, Any]):
+        """Create a simple rule (SimpleAmbitRule or SimpleRDKitRule)."""
+        rule_uuid = self._get_or_generate_uuid(rule_data["uuid"])
+        rule_type = rule_data.get("rule_type", "SimpleRule")
+
+        common_fields = {
+            "uuid": rule_uuid,
+            "package": package,
+            "name": rule_data["name"],
+            "description": rule_data["description"],
+            "kv": rule_data.get("kv", {}),
+        }
+
+        if rule_type == "SimpleAmbitRule":
+            rule = SimpleAmbitRule.objects.create(
+                **common_fields,
+                smirks=rule_data.get("smirks", ""),
+                reactant_filter_smarts=rule_data.get("reactant_filter_smarts", ""),
+                product_filter_smarts=rule_data.get("product_filter_smarts", ""),
+            )
+        elif rule_type == "SimpleRDKitRule":
+            rule = SimpleRDKitRule.objects.create(
+                **common_fields, reaction_smarts=rule_data.get("reaction_smarts", "")
+            )
+        else:
+            rule = SimpleRule.objects.create(**common_fields)
+
+        # Set aliases if present
+        if rule_data.get("aliases"):
+            rule.aliases = rule_data["aliases"]
+            rule.save()
+
+        self._cache_object("SimpleRule", rule_data["uuid"], rule)
+        return rule
+
+    def _create_parallel_rule(self, package: Package, rule_data: Dict[str, Any]):
+        """Create a parallel rule."""
+        rule_uuid = self._get_or_generate_uuid(rule_data["uuid"])
+
+        rule = ParallelRule.objects.create(
+            uuid=rule_uuid,
+            package=package,
+            name=rule_data["name"],
+            description=rule_data["description"],
+            kv=rule_data.get("kv", {}),
+        )
+
+        # Set aliases if present
+        if rule_data.get("aliases"):
+            rule.aliases = rule_data["aliases"]
+            rule.save()
+
+        # Add simple rules
+        for simple_rule_ref in rule_data.get("simple_rules", []):
+            simple_rule = self._get_cached_object("SimpleRule", simple_rule_ref["uuid"])
+            if simple_rule:
+                rule.simple_rules.add(simple_rule)
+
+        self._cache_object("ParallelRule", rule_data["uuid"], rule)
+        return rule
+
+    def _import_reactions(self, package: Package, reactions_data: List[Dict[str, Any]]):
+        """Import reactions."""
+        print(f"Importing {len(reactions_data)} reactions...")
+
+        for reaction_data in reactions_data:
+            reaction_uuid = self._get_or_generate_uuid(reaction_data["uuid"])
+
+            reaction = Reaction.objects.create(
+                uuid=reaction_uuid,
+                package=package,
+                name=reaction_data["name"],
+                description=reaction_data["description"],
+                kv=reaction_data.get("kv", {}),
+                multi_step=reaction_data.get("multi_step", False),
+                medline_references=reaction_data.get("medline_references", []),
+            )
+
+            # Set aliases if present
+            if reaction_data.get("aliases"):
+                reaction.aliases = reaction_data["aliases"]
+                reaction.save()
+
+            # Add educts and products
+            for educt_ref in reaction_data.get("educts", []):
+                compound = self._get_cached_object("CompoundStructure", educt_ref["uuid"])
+                if compound:
+                    reaction.educts.add(compound)
+
+            for product_ref in reaction_data.get("products", []):
+                compound = self._get_cached_object("CompoundStructure", product_ref["uuid"])
+                if compound:
+                    reaction.products.add(compound)
+
+            # Add rules
+            for rule_ref in reaction_data.get("rules", []):
+                # Try to find rule in different caches
+                rule = self._get_cached_object(
+                    "SimpleRule", rule_ref["uuid"]
+                ) or self._get_cached_object("ParallelRule", rule_ref["uuid"])
+                if rule:
+                    reaction.rules.add(rule)
+
+            self._cache_object("Reaction", reaction_data["uuid"], reaction)
+
+            # Handle external identifiers
+            self._create_external_identifiers(
+                reaction, reaction_data.get("external_identifiers", [])
+            )
+
+    def _import_pathways(self, package: Package, pathways_data: List[Dict[str, Any]]):
+        """Import pathways."""
+        print(f"Importing {len(pathways_data)} pathways...")
+
+        for pathway_data in pathways_data:
+            pathway_uuid = self._get_or_generate_uuid(pathway_data["uuid"])
+
+            pathway = Pathway.objects.create(
+                uuid=pathway_uuid,
+                package=package,
+                name=pathway_data["name"],
+                description=pathway_data["description"],
+                kv=pathway_data.get("kv", {}),
+                # setting will be handled separately if needed
+            )
+
+            # Set aliases if present
+            if pathway_data.get("aliases"):
+                pathway.aliases = pathway_data["aliases"]
+                pathway.save()
+
+            self._cache_object("Pathway", pathway_data["uuid"], pathway)
+
+    def _import_nodes(self, package: Package, nodes_data: List[Dict[str, Any]]):
+        """Import pathway nodes."""
+        print(f"Importing {len(nodes_data)} nodes...")
+
+        for node_data in nodes_data:
+            node_uuid = self._get_or_generate_uuid(node_data["uuid"])
+            pathway_uuid = node_data["pathway"]["uuid"]
+            pathway = self._get_cached_object("Pathway", pathway_uuid)
+
+            if not pathway:
+                print(f"Warning: Pathway with UUID {pathway_uuid} not found for node")
+                continue
+
+            # For now, we'll set default_node_label to None and handle it later
+            # as it requires compound structures to be fully imported
+            node = Node.objects.create(
+                uuid=node_uuid,
+                pathway=pathway,
+                name=node_data["name"],
+                description=node_data["description"],
+                kv=node_data.get("kv", {}),
+                depth=node_data.get("depth", 0),
+                default_node_label=self._get_cached_object(
+                    "CompoundStructure", node_data["default_node_label"]["uuid"]
+                ),
+            )
+
+            # Set aliases if present
+            if node_data.get("aliases"):
+                node.aliases = node_data["aliases"]
+                node.save()
+
+            self._cache_object("Node", node_data["uuid"], node)
+            # Store node_data for later processing of relationships
+            node._import_data = node_data
+
+    def _import_edges(self, package: Package, edges_data: List[Dict[str, Any]]):
+        """Import pathway edges."""
+        print(f"Importing {len(edges_data)} edges...")
+
+        for edge_data in edges_data:
+            edge_uuid = self._get_or_generate_uuid(edge_data["uuid"])
+            pathway_uuid = edge_data["pathway"]["uuid"]
+            pathway = self._get_cached_object("Pathway", pathway_uuid)
+
+            if not pathway:
+                print(f"Warning: Pathway with UUID {pathway_uuid} not found for edge")
+                continue
+
+            # For now, we'll set edge_label to None and handle it later
+            edge = Edge.objects.create(
+                uuid=edge_uuid,
+                pathway=pathway,
+                name=edge_data["name"],
+                description=edge_data["description"],
+                kv=edge_data.get("kv", {}),
+                edge_label=self._get_cached_object("Reaction", edge_data["edge_label"]["uuid"]),
+            )
+
+            # Set aliases if present
+            if edge_data.get("aliases"):
+                edge.aliases = edge_data["aliases"]
+                edge.save()
+
+            # Add start and end nodes
+            for start_node_ref in edge_data.get("start_nodes", []):
+                node = self._get_cached_object("Node", start_node_ref["uuid"])
+                if node:
+                    edge.start_nodes.add(node)
+
+            for end_node_ref in edge_data.get("end_nodes", []):
+                node = self._get_cached_object("Node", end_node_ref["uuid"])
+                if node:
+                    edge.end_nodes.add(node)
+
+            self._cache_object("Edge", edge_data["uuid"], edge)
+
+    def _import_scenarios(self, package: Package, scenarios_data: List[Dict[str, Any]]):
+        """Import scenarios."""
+        print(f"Importing {len(scenarios_data)} scenarios...")
+
+        # First pass: create scenarios without parent relationships
+        for scenario_data in scenarios_data:
+            scenario_uuid = self._get_or_generate_uuid(scenario_data["uuid"])
+
+            scenario_date = None
+            if scenario_data.get("scenario_date"):
+                scenario_date = scenario_data["scenario_date"]
+
+            scenario = Scenario.objects.create(
+                uuid=scenario_uuid,
+                package=package,
+                name=scenario_data["name"],
+                description=scenario_data["description"],
+                kv=scenario_data.get("kv", {}),
+                scenario_date=scenario_date,
+                scenario_type=scenario_data.get("scenario_type"),
+                additional_information=scenario_data.get("additional_information", {}),
+            )
+
+            self._cache_object("Scenario", scenario_data["uuid"], scenario)
+            # Store scenario_data for later processing of parent relationships
+            scenario._import_data = scenario_data
+
+        # Second pass: set parent relationships
+        for scenario_data in scenarios_data:
+            if scenario_data.get("parent"):
+                scenario = self._get_cached_object("Scenario", scenario_data["uuid"])
+                parent = self._get_cached_object("Scenario", scenario_data["parent"]["uuid"])
+                if scenario and parent:
+                    scenario.parent = parent
+                    scenario.save()
+
+    def _import_models(self, package: Package, models_data: List[Dict[str, Any]]):
+        """Import EPModels."""
+        print(f"Importing {len(models_data)} models...")
+
+        for model_data in models_data:
+            model_uuid = self._get_or_generate_uuid(model_data["uuid"])
+            model_type = model_data.get("model_type", "EPModel")
+
+            common_fields = {
+                "uuid": model_uuid,
+                "package": package,
+                "name": model_data["name"],
+                "description": model_data["description"],
+                "kv": model_data.get("kv", {}),
+            }
+
+            # Add PackageBasedModel fields if present
+            if "threshold" in model_data:
+                common_fields.update(
+                    {
+                        "threshold": model_data.get("threshold"),
+                        "eval_results": model_data.get("eval_results", {}),
+                        "model_status": model_data.get("model_status", "INITIAL"),
+                    }
+                )
+
+            # Create the appropriate model type
+            if model_type == "RuleBasedRelativeReasoning":
+                model = RuleBasedRelativeReasoning.objects.create(
+                    **common_fields,
+                    min_count=model_data.get("min_count", 1),
+                    max_count=model_data.get("max_count", 10),
+                )
+            elif model_type == "MLRelativeReasoning":
+                model = MLRelativeReasoning.objects.create(**common_fields)
+            elif model_type == "EnviFormer":
+                model = EnviFormer.objects.create(**common_fields)
+            else:
+                model = EPModel.objects.create(**common_fields)
+
+            # Set aliases if present
+            if model_data.get("aliases"):
+                model.aliases = model_data["aliases"]
+                model.save()
+
+            # Add package relationships for PackageBasedModel
+            if hasattr(model, "rule_packages"):
+                for pkg_ref in model_data.get("rule_packages", []):
+                    pkg = self._get_cached_object("Package", pkg_ref["uuid"])
+                    if pkg:
+                        model.rule_packages.add(pkg)
+
+                for pkg_ref in model_data.get("data_packages", []):
+                    pkg = self._get_cached_object("Package", pkg_ref["uuid"])
+                    if pkg:
+                        model.data_packages.add(pkg)
+
+                for pkg_ref in model_data.get("eval_packages", []):
+                    pkg = self._get_cached_object("Package", pkg_ref["uuid"])
+                    if pkg:
+                        model.eval_packages.add(pkg)
+
+            self._cache_object("EPModel", model_data["uuid"], model)
+
+    def _set_default_structures(self, compounds_data: List[Dict[str, Any]]):
+        """Set default structures for compounds after all structures are created."""
+        print("Setting default structures for compounds...")
+
+        for compound_data in compounds_data:
+            if compound_data.get("default_structure"):
+                compound = self._get_cached_object("Compound", compound_data["uuid"])
+                structure = self._get_cached_object(
+                    "CompoundStructure", compound_data["default_structure"]["uuid"]
+                )
+                if compound and structure:
+                    compound.default_structure = structure
+                    compound.save()
+
+    def _create_external_identifiers(self, obj, identifiers_data: List[Dict[str, Any]]):
+        """Create external identifiers for an object."""
+        for identifier_data in identifiers_data:
+            # Get or create the external database
+            db_data = identifier_data["database"]
+            database, _ = ExternalDatabase.objects.get_or_create(
+                name=db_data["name"],
+                defaults={
+                    "base_url": db_data.get("base_url", ""),
+                    "full_name": db_data.get("name", ""),
+                    "description": "",
+                    "is_active": True,
+                },
+            )
+
+            # Create the external identifier
+            ExternalIdentifier.objects.create(
+                content_object=obj,
+                database=database,
+                identifier_value=identifier_data["identifier_value"],
+                url=identifier_data.get("url", ""),
+                is_primary=identifier_data.get("is_primary", False),
+            )
+
 
 class PathwayUtils:
     def __init__(self, pathway: "Pathway"):