Merge branch 'develop'

CHANGELOG.md

@@ -1,18 +1,70 @@
 # CHANGELOG
 
+## Version 5.3.0
+
+### Functionality
+
+- Add filters to the sample selection component
+
+## Version 5.2.0
+
+### Functionality
+
+- Add exporting of report in Markdown format
+- Add browser access to restarting the API
+- Display tooltip for clipboard and download buttons in export menu
+
+### Other
+
+- Filter functionality made dynamic so that new filter groups can be added as needed
+- Improve sturdiness against invalid input
+- Filter a-link references on 'do-not-route' before sending to the router
+
+### Deployment changes
+
+- Requires extra translations for each filter type in `deployments.json`
+
+## Version 5.1.0
+
+### Functionality
+
+- URL Queries: ComPass accepts URL queries and runs the complete analysis automatically. For instance, the following URI:
+
+  ```
+  http://localhost:3000/disease?autorun&signature=HSPA1A+DNAJB1+DDIT4+-TSEN2&numTableHead=10
+  ```
+
+  will run the Disease workflow using the signature `HSPA1A DNAJB1 DDIT4` and will show 10 entries for the top table.
+
+- Export: Add buttons to export data and plots to a file or copy it to the clipboard. A popup window is available with all the possible export features on the right bottom of the screen.
+
+- Correlation workflow has filters.
+
+- Sample tables can be sorted by clicking the columns header
+
+### Other
+
+- Ghost mode has been improved, it no longer requires explicit timings in the scenarios
+- Moved scss files from `src/js` to `src/sass`, so any alternative versions of e.g. `_variables.scss` or `_main.custom.scss` should now be placed in the new folder
+
 ## Version 5.0.2
 
 - Fix mistake in sample selection column truncation code
 
-## Version 5.0.0-alpha4
+## Version 5.0.1
+
+- The head and tail tables use pictures to display the treatment type
+- Adapt the behaviour for the autocomplete when there is only one option to choose from and if the entered value matches the single autocomplete value
+
+## Version 5.0.0
 
-## Functionality
+### Functionality
 
 - A new 'Genetic' workflow is created useful for searching for genetic perturbations.
 - Inverting the filter selection can be done using the `ALT` (Option on Mac) modifier key instead of the `a` key
 - Filter values are populated dynamically based on the data available through the API
 
-## Other
+### Other
 
 - The dependency stack has been cleaned and (partly) updated
 - Cycle dependencies have been updated to the latest versions except for `@cycle/state`.

deployments.json

@@ -7,9 +7,6 @@
     "services": {
       "filter": {
         "values": {
-          "dose": ["sample_entry"],
-          "cell": ["sample_entry"],
-          "trtType": ["sample_entry"]
         }
       },
       "common": {
@@ -22,22 +19,41 @@
         },
         "ghost": {
           "compound": {
-            "treatment": "BRD-K93645900",
-            "index": 0,
-            "sample": ["A375_6H_BRD_K93645900_10"],
-            "signature": "-CRCP"
+            "params": {
+              "typer": 500,
+              "treatment": "BRD-K93645900",
+              "samples": "A375_6H_BRD_K93645900_10",
+              "trtType": "trt_cp"
+            }
           },
           "ligand": {
-            "treatment": "ANGPT1",
-            "index": 0,
-            "sample": ["HCC515_4H_CMAP_CYT_SRP3007_50"],
-            "signature": "FBXO11 SLC35 F5BAG4 RIF1"
+            "params": {
+              "typer": 500,
+              "treatment": "ANGPT1",
+              "samples": "HCC515_4H_CMAP_CYT_SRP3007_50",
+              "trtType": "trt_cp"
+            }
           },
           "genetic": {
-            "treatment": "PARP2",
-            "index": 0,
-            "sample": ["DER001_HCC515_96H_X1_F1B6_DUO52HI53LO:B03"],
-            "signature": "-COPS7A -KEAP1 -CCNB1 -HMG20B -ELOVL6 -DERA LPL -PLEKHJ1 -TPI1 ST3GAL5 -HAT1 -MLF2 -FOXG1 -STRAP -MRPL4 -EDN1 -PON2 KMT2A FRMD4A -C16orf58"
+            "params": {
+              "typer": 500,
+              "treatment": "PARP2",
+              "samples": "DER001_HCC515_96H_X1_F1B6_DUO52HI53LO",
+              "trtType": "trt_cp"
+            }
+          },
+          "disease": {
+            "params": {
+              "typer": 100,
+              "signature": "HSPA1A DNAJB1 DDIT4 -TSEN2"
+            }
+          },
+          "correlation": {
+            "params": {
+              "typer": 100,
+              "signature1": "HSPA1A DNAJB1 DDIT4 -TSEN2",
+              "signature2": "DNAJB1 DDIT4 -TSEN2"
+            }
           }
         },
         "modelTranslations": [
@@ -50,6 +66,21 @@
             "ui": "Secondary ID",
             "model": "jnjb",
             "comment": ""
+          },
+          {
+            "ui": "Cell",
+            "model": "cell",
+            "comment": "Filter group name"
+          },
+          {
+            "ui": "Dose",
+            "model": "dose",
+            "comment": "Filter group name"
+          },
+          {
+            "ui": "Type",
+            "model": "trtType",
+            "comment": "Filter group name"
           }
         ]
       },
@@ -59,6 +90,10 @@
       "api": {
         "url": "http://localhost:8090/jobs?context=luciusapi&appName=luciusapi&sync=true&timeout=30"
       },
+      "init": {
+        "url": "http://localhost:8090/",
+        "contextOptions": "context-factory=spark.jobserver.context.SessionContextFactory&spark.scheduler.mode=FAIR&spark.jobserver.context-creation-timeout=60&spark.memory.fraction=0.7&spark.dynamicAllocation.enabled=false&spark.executor.instances=6&spark.executor.cores=4&spark.executor.memory=4g&spark.yarn.executor.memoryOverhead=2g&spark.yarn.am.memory=4G&spark.driver.memory=4G"
+      },
       "sourire": {
         "url": "http://localhost:9999/molecule/"
       },

index.html

@@ -3,7 +3,7 @@
 
 <head>
     <meta charset="UTF-8">
-    <title>ComPass v4</title>
+    <title>ComPass v5</title>
     <link rel="shortcut icon" href="favicon.ico">
     <link href="https://fonts.googleapis.com/css?family=Roboto:400" rel="stylesheet">
     <link href="https://fonts.googleapis.com/css?family=Open+Sans+Condensed:300" rel="stylesheet">

package.json

@@ -1,6 +1,6 @@
 {
     "name": "LuciusWeb",
-    "version": "5.0.2",
+    "version": "5.3.0",
     "description": "Web interface for ComPass aka Lucius",
     "repository": {
         "type": "git",

src/js/components/BinnedPlots/BinnedPlots.js

@@ -41,7 +41,7 @@ const isEmptyState = (state) => {
 
 // For this component, when is a API result empty?
 const isEmptyData = (data) => {
-    return data.length == 0
+    return data == undefined || data.length == 0
 }
 
 const makeVega = (elementID) => {

src/js/components/BinnedPlots/CorrelationPlot.js

@@ -34,7 +34,7 @@ const isEmptyState = (state) => {
 
 // For this component, when is a API result empty?
 const isEmptyData = (data) => {
-    return data.length == 0
+    return data == undefined || data.length == 0
 }
 
 const makeVega = (elementID) => {

src/js/components/CorrelationForm.js

@@ -8,6 +8,7 @@ import { ENTER_KEYCODE } from '../utils/keycodes.js'
 import { SignatureCheck, checkLens1, checkLens2 } from '../components/SignatureCheck'
 import dropRepeats from 'xstream/extra/dropRepeats'
 import { loggerFactory } from '../utils/logger'
+import { typer } from '../utils/searchUtils'
 
 const stateTemplate = {
     form: {
@@ -21,8 +22,29 @@ const stateTemplate = {
 
 // Granular access to global state and parts of settings
 const formLens = {
-    get: state => ({ core: state.form, settings: { form: state.settings.form, api: state.settings.api } }),
-    set: (state, childState) => ({ ...state, form: childState.core })
+    get: state => ({
+        core: state.form, 
+        settings: { 
+            form: state.settings.form, 
+            api: state.settings.api 
+        },
+        search1: state.routerInformation.params?.signature1,
+        search2: state.routerInformation.params?.signature2,
+        searchAutoRun: state.routerInformation.params?.autorun,
+        searchTyper: state.routerInformation.params?.typer,
+    }),
+    set: (state, childState) => ({
+        ...state,
+        form: childState.core,
+        routerInformation: {
+            ...state.routerInformation,
+            pageState: {
+              ...state.routerInformation.pageState,
+              signature1: childState.core.query1,
+              signature2: childState.core.query2,
+            }
+          }
+    })
 };
 
 function CorrelationForm(sources) {
@@ -79,15 +101,20 @@ function CorrelationForm(sources) {
         });
 
     // Update in query, or simply ENTER
+    const typer1$ = typer(state$, 'search1', 'searchTyper')
     const newQuery1$ = xs.merge(
         sources.DOM.select('.Query1').events('input').map(ev => ev.target.value),
         // Ghost 
-        state$.map(state => state.core.query1).compose(dropRepeats())
+        state$.map(state => state.core.query1).compose(dropRepeats()),
+        typer1$,
     )
+
+    const typer2$ = typer(state$, 'search2', 'searchTyper')
     const newQuery2$ = xs.merge(
         sources.DOM.select('.Query2').events('input').map(ev => ev.target.value),
         // Ghost 
-        state$.map(state => state.core.query2).compose(dropRepeats())
+        state$.map(state => state.core.query2).compose(dropRepeats()),
+        typer2$,
     )
 
     // Updated state is propagated and picked up by the necessary components
@@ -187,12 +214,25 @@ function CorrelationForm(sources) {
     const childReducer1$ = signatureCheck1.onion
     const childReducer2$ = signatureCheck2.onion
 
+    // Auto start query
+    // Only run once, even if query is changed and then reverted to original value
+    const searchAutoRun$ = state$
+    .filter(
+        (state) => state.searchAutoRun == "" || state.searchAutoRun == "yes"
+    )
+    .filter((state) => state.search1 == state.core.query1 && state.search2 == state.core.query2)
+    .filter((state) => state.core.validated1 == true && state.core.validated2 == true)
+    .mapTo(true)
+    .compose(dropRepeats(equals))
+
+
     // When GO clicked or enter -> send updated 'value' to sink
     // Maybe catch when no valid query?
     const query$ = xs.merge(
         update$,
         // Ghost mode
-        sources.onion.state$.map(state => state.core.ghost).filter(ghost => ghost).compose(dropRepeats())
+        sources.onion.state$.map(state => state.core.ghost).filter(ghost => ghost).compose(dropRepeats()),
+        searchAutoRun$,
     )
         .compose(sampleCombine(state$))
         .map(([update, state]) => ({query1: state.core.query1, query2: state.core.query2}))