Make links thicker, reduce timeout trigger time

bayer/templates/objects/compound_structure_viz.html

@@ -4,7 +4,9 @@
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
     <div class="collapse-content">
-      <a href="{{ compound_structure.pes_link }}" class="hover:bg-base-200">{{ compound_structure.pes_link }}</a>
+      <p>
+        <a href="{{ compound_structure.pes_link }}" class="hover:bg-base-200">{{ compound_structure.pes_link }}</a>
+      </p>
     </div>
   </div>
 

bayer/templates/objects/compound_viz.html

@@ -4,7 +4,9 @@
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
     <div class="collapse-content">
-      <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
+      <p>
+        <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
+      </p>
     </div>
   </div>
 

bayer/templates/objects/node_viz.html

@@ -4,7 +4,9 @@
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
     <div class="collapse-content">
-      <a href="{{ node.default_node_label.pes_link }}" class="hover:bg-base-200">{{ node.default_node_label.pes_link }}</a>
+      <p>
+        <a href="{{ node.default_node_label.pes_link }}" class="hover:bg-base-200">{{ node.default_node_label.pes_link }}</a>
+      </p>
     </div>
   </div>
 

epdb/legacy_api.py

@@ -633,9 +633,14 @@ 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_review_status(obj: CompoundStructure):
+    def resolve_pes_link(obj: Compound):
+        return getattr(obj.default_structure, "pes_link", None)
+
+    @staticmethod
+    def resolve_review_status(obj: Compound):
         return "reviewed" if obj.package.reviewed else "unreviewed"
 
     @staticmethod
@@ -709,6 +714,7 @@ 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):
@@ -1695,6 +1701,7 @@ 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):
@@ -1707,24 +1714,10 @@ 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")
@@ -2392,3 +2385,31 @@ 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

@@ -1896,6 +1896,12 @@ 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

@@ -2379,6 +2379,7 @@ 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,
         }
@@ -2452,6 +2453,26 @@ 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

@@ -2482,7 +2482,22 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        return HttpResponseBadRequest()
+        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")
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 

static/js/alpine/pagination.js

@@ -5,6 +5,125 @@
  */
 
 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

@@ -67,6 +67,9 @@ 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);
 
@@ -154,6 +157,10 @@ 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) {
@@ -256,7 +263,7 @@ function draw(pathway, elem) {
     }
 
     // Wait before showing popup (ms)
-    var popupWaitBeforeShow = 1000;
+    var popupWaitBeforeShow = 500;
 
     // Custom popover element
     let popoverTimeout = null;
@@ -647,21 +654,31 @@ function draw(pathway, elem) {
         .on("tick", ticked);
 
     // Kanten zeichnen
-    const link = zoomable.append("g")
+    const linkGroup = zoomable.append("g")
-        .selectAll("path")
+      .selectAll("g")
-        .data(links)
+      .data(links)
-        .enter().append("path")
+      .enter()
-        // Check if target is pseudo and draw marker only if not pseudo
+      .append("g")
-        .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
+      .attr("class", "link-group");
-        .attr("marker-end", d => {
+
-            if (d.target.pseudo) return '';
+    const link = linkGroup
-            if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops
+      .append("path")
-            return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
+      .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-        })
+      .attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow)")
-        .attr("fill", "none")
+      .attr("fill", "none")
-        .on("click", function(event, d) {
+
+      // 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);
@@ -688,6 +705,18 @@ 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

templates/objects/node.html

@@ -55,6 +55,15 @@
       </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

@@ -21,6 +21,7 @@
     .link {
       stroke: #999;
       stroke-opacity: 0.6;
+      stroke-width: 1.5px;
       /* marker-end: url(#arrow); */
     }
 
@@ -177,6 +178,52 @@
                   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">
@@ -497,6 +544,10 @@
   {{ 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
@@ -532,6 +583,67 @@
         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

@@ -24,6 +24,76 @@
         <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

@@ -36,7 +36,7 @@ from epdb.models import (
     Setting,
     SimpleAmbitRule,
     SimpleRDKitRule,
-    SimpleRule,
+    SimpleRule, Group,
 )
 from utilities.chem import FormatConverter
 
@@ -44,7 +44,7 @@ logger = logging.getLogger(__name__)
 Package = s.GET_PACKAGE_MODEL()
 
 if TYPE_CHECKING:
-    from epdb.logic import SPathway
+    from epdb.logic import SPathway, GroupManager
 
 
 class LicenseExportSchema(Schema):
@@ -123,8 +123,8 @@ class PESCompoundExportSchema(RefCompoundExportSchema):
     description: str
     aliases: List[str]
     default_structure: RefCompoundStructureExportSchema
-    structures: List["CompoundStructureExportSchema"]
     structures: List["PESCompoundStructureExportSchema"]
+    scenarios: List[RefScenarioExportSchema]
 
 
 class PESCompoundStructureExportSchema(RefCompoundStructureExportSchema):
@@ -277,7 +277,7 @@ class PackageExportSchema(Schema):
 
     @staticmethod
     def resolve_classification_level(obj):
-        if isinstance(obj, str):
+        if isinstance(obj, dict):
             return obj["classification_level"]
         return obj.Classification(obj.classification_level).name
 
@@ -602,15 +602,20 @@ 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()]
 
-        package = Package.objects.create(
+        print(parsed.classification_level, "->", package_classification_level)
-            uuid=package_uuid,
+
-            name=f"{parsed.name} - Imported at {datetime.now()}",
+        package = Package()
-            description=parsed.description,
+        package.uuid = package_uuid
-            reviewed=False, # Everything will be imported as non reviewed
+        package.name = f"{parsed.name} - Imported at {datetime.now()}"
-            license=package_license,
+        package.description = parsed.description
-            classification_level=package_classification_level,
+        package.reviewed = False
-            data_pool=parsed.data_pool,
+        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)