Merge branch 'feature/custom-pathways' into 'main'

Custom Pathways and other Features

See merge request jmueller/biowc-pathwaygraph!8

custom_pathway_notes.txt

@@ -0,0 +1,37 @@
+Done:
+- mode: viewing/editing
+    - Create storybook with switch, same as for the hue + upload and download button
+    - Clear PTM & FP Inputlist when switching to edit mode
+- New Context Menu:
+    - Add Node
+        - Popup Form where you can enter:
+            - Type of Node (options: Gene/Protein, Metabolite/Compound, Pathway)
+            - For Gene/Protein:
+                - List of Names (first one will implicitly become default one)
+                - List of Uniprot Accession Numbers
+        -> Create node at position of right-click
+            - Just add to what is parsed from the JSON
+    - Add Edge
+        - Await two clicks 'After clicking confirm, please click on the source, then the target node.'
+        - Increase Border of node after click to feedback selection
+        - Popup Form where you can choose edge type and optionally set a label (e.g. '+p')
+- Export: Create JSON using current positions 
+    - Node: Add Edge to...
+    - Node: Add Edge from...
+    - Edge: Change Edge Type
+    - Edge: Delete Edge
+    - Node: Delete Node -> Need to delete all adjacent edges too -> AND HIGHER ORDER LINKS!
+    - Create Group
+    - Edge: Change Label
+    - Node: Change Node Type
+    - Node: Change Name(s)
+    - Group: Delete Group -> Merge code with Delete Node, it is similar
+    - Group: When addition of group clears another group, delete orphaned edges (you can probably reuse code from delete group, since you're implicitly deleting a group here)
+    - Edge: Add Anchor Edge
+    - When adding edge, highlight selected groups and edges similarly to how nodes are highlighted
+
+
+Todo:
+	BiowcPathwaygraph:
+
+	In PTMNavigator:

demo/index.html

@@ -20,11 +20,13 @@
     render(
       html`
         <biowc-pathwaygraph
-          .graphdataSkeleton = ${ {nodes: StoryFixtures.simplePTMGraphFixture.nodes,
-            links: StoryFixtures.simplePTMGraphFixture.links} }
+          .graphdataSkeleton = ${ {nodes: StoryFixtures.linkTypesFixture.nodes,
+            links: StoryFixtures.linkTypesFixture.links} }
           .ptmInputList = ${StoryFixtures.ptmGraphWithDetailsFixture.ptmInputList}
           .fullProteomeInputList = ${StoryFixtures.proteinExpressionFixture.fullProteomeInputList}
-          .hue= ${'foldchange'}
+          .hue= ${'potency'}
+          .applicationMode = ${'viewing'}
+          .perturbedNodes = ${{up: ['Protein B', 'Protein D'], down:['Protein A', 'Protein C']}}
         >
         </biowc-pathwaygraph>
       `,

package.json

@@ -3,7 +3,7 @@
   "description": "Webcomponent biowc-pathwaygraph following open-wc recommendations",
   "license": "Apache-2.0",
   "author": "biowc-pathwaygraph",
-  "version": "0.0.19",
+  "version": "0.1.0",
   "main": "dist/src/index.js",
   "module": "dist/src/index.js",
   "exports": {