Test commit check changes

.github/workflows/all-commits-in-master.yml → .github/workflows/release-branch-checks.yml

@@ -1,22 +1,22 @@
-name: all-commits-in-master
+name: Release branch checks
 
 on:
   pull_request:
     branches: [ "customdc_stable" ]
 
 jobs:
-  check_commits:
+  verify_all_commits_are_already_in_master:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # Fetch all history for accurate comparison
           fetch-depth: 0
           # Check out the PR branch
           ref: ${{ github.event.pull_request.head.ref }}
           repository: ${{ github.event.pull_request.head.repo.full_name }}
 
-      - name: Check if commits exist in master
+      - name: Verify that all commits are already in the master branch
         run: |
           git remote add dc https://github.com/datacommonsorg/website.git
           git fetch dc
@@ -26,8 +26,14 @@ jobs:
           MISSING_COMMITS=$(git log --pretty="%H - %s" $MASTER_BRANCH..HEAD --)
 
           if [[ -n "$MISSING_COMMITS" ]]; then
+            echo ""
             echo "ERROR: The following commits are not present in $MASTER_BRANCH:"
+            echo ""
             echo "$MISSING_COMMITS"
+            echo ""
+            echo "PRs to release branches should only contain commits that are already in master."
+            echo "To fix this PR, reset its branch locally to a commit at or behind https://github.com/datacommonsorg/website/commits/master/ and then force-push it."
+            echo "Note that a release branch PR should be based on master and not the previous version of the release branch, which contains merge commits."
             exit 1
           fi
 

deploy/nl/catalog.yaml

@@ -78,7 +78,7 @@ indexes:
   bio_ft:
     store_type: MEMORY
     source_path: ../../tools/nl/embeddings/input/bio
-    embeddings_path: gs://datcom-nl-models/bio_ft_2024_06_24_23_40_05/embeddings.csv
+    embeddings_path: gs://datcom-nl-models/bio_ft_2024_11_05_09_59_39/embeddings.csv
     model: ft-final-v20230717230459-all-MiniLM-L6-v2
     healthcheck_query: "Gene"
   base_uae_lance:

run_cdc_tests.sh

@@ -20,4 +20,4 @@ set -e
 source .env/bin/activate
 export FLASK_ENV=webdriver
 
-python3 -m pytest --reruns 2 server/webdriver/cdc_tests/
+python3 -m pytest -n 5 --reruns 2 server/webdriver/cdc_tests/

server/config/nl_page/prop_titles.json

@@ -1,19 +1,35 @@
 {
-  "<-referenceSNPClusterID{typeOf:GeneticVariantGeneAssociation}->geneSymbol": {
+  "<-variantID{typeOf:GeneGeneticVariantAssociation}->geneID": {
     "displayName": "associated gene",
     "titleFormat": "The associated genes for {entity} are"
   }, 
-  "<-geneSymbol{typeOf:GeneticVariantGeneAssociation}->referenceSNPClusterID": {
+  "<-geneID{typeOf:GeneGeneticVariantAssociation}->variantID": {
     "displayName": "associated genetic variant",
     "titleFormat": "The associated genetic variants for {entity} are"
   }, 
-  "<-diseaseOntologyID{typeOf:DiseaseGeneAssociation}->geneID": {
+  "<-diseaseID{typeOf:DiseaseGeneAssociation}->geneID": {
     "displayName": "associated gene",
     "titleFormat": "The associated genes for {entity} are"
   }, 
-  "<-geneID{typeOf:DiseaseGeneAssociation}->diseaseOntologyID": {
+  "<-geneID{typeOf:DiseaseGeneAssociation}->diseaseID": {
     "displayName": "associated disease",
     "titleFormat": "The associated diseases for {entity} are"
+  }, 
+  "<-diseaseID{typeOf:DiseaseGeneticVariantAssociation}->geneticVariantID": {
+    "displayName": "associated genetic variant",
+    "titleFormat": "The associated genetic variants for {entity} are"
+  }, 
+  "<-geneticVariantID{typeOf:DiseaseGeneticVariantAssociation}->diseaseID": {
+    "displayName": "associated disease",
+    "titleFormat": "The associated diseases for {entity} are"
+  },
+  "<-compoundID{typeOf:ChemicalCompoundGeneticVariantAssociation}->variantID": {
+    "displayName": "associated genetic variant",
+    "titleFormat": "The associated genetic variants for {entity} are"
+  }, 
+  "<-variantID{typeOf:ChemicalCompoundGeneticVariantAssociation}->compoundID": {
+    "displayName": "associated chemical compound",
+    "titleFormat": "The associated chemical compounds for {entity} are"
   },
   "->mRNA": {
     "displayName": "mRNA"

server/integration_tests/explore_test.py

@@ -119,13 +119,23 @@ def handle_response(self,
     # TODO: Proper fix should be to make NL server more deterministic
     if 'variables' in resp:
       resp_var_to_score = {}
+      dbg['sv_matching']['CosineScore'] = _format_scores(
+          dbg['sv_matching']['CosineScore'])
       for i, sv in enumerate(dbg['sv_matching']['SV']):
-        score = dbg['sv_matching']['CosineScore'][i]
-        resp_var_to_score[sv] = float("{:.6f}".format(score))
+        resp_var_to_score[sv] = dbg['sv_matching']['CosineScore'][i]
       sorted_variables = sorted(resp['variables'],
                                 key=lambda x: (-resp_var_to_score.get(x, 0), x))
       resp['variables'] = sorted_variables
 
+    # Truncate CosineScores to 6 decimals to reduce noisy diffs.
+    for candidate in dbg['sv_matching']['MultiSV'].get('Candidates', []):
+      for part in candidate.get('Parts', []):
+        if multisv_scores := part.get('CosineScore', []):
+          part['CosineScore'] = _format_scores(multisv_scores)
+
+    if props_scores := dbg['props_matching'].get('CosineScore', []):
+      dbg['props_matching']['CosineScore'] = _format_scores(props_scores)
+
     resp['debug'] = {}
     resp['context'] = {}
     for category in resp.get('config', {}).get('categories', []):
@@ -793,3 +803,8 @@ def _del_field(d: dict, path: str):
         del tmp[p]
       else:
         tmp = tmp[p]
+
+
+# Helper function to consistently format float scores.
+def _format_scores(scores):
+  return [float("{:.6f}".format(score)) for score in scores]

server/integration_tests/test_data/demo2_cities_feb2023/query_7/chart_config.json

@@ -204,39 +204,6 @@
               }
             ],
             "title": "Population"
-          },
-          {
-            "columns": [
-              {
-                "tiles": [
-                  {
-                    "barTileSpec": {
-                      "maxPlaces": 15,
-                      "maxVariables": 15,
-                      "sort": "DESCENDING"
-                    },
-                    "comparisonPlaces": [
-                      "country/DZA",
-                      "country/MAR",
-                      "country/LBY",
-                      "country/TUN",
-                      "country/MLI",
-                      "country/ERI",
-                      "country/SEN",
-                      "country/GMB",
-                      "country/MWI",
-                      "country/SSD"
-                    ],
-                    "statVarKey": [
-                      "WHO/CM_02_multiple_place_bar_block"
-                    ],
-                    "title": "Number of Infant Deaths (${date})",
-                    "type": "BAR"
-                  }
-                ]
-              }
-            ],
-            "title": "Number of Infant Deaths"
           }
         ],
         "statVarSpec": {
@@ -260,10 +227,6 @@
             "name": "Rate of Population Growth",
             "statVar": "GrowthRate_Count_Person"
           },
-          "WHO/CM_02_multiple_place_bar_block": {
-            "name": "Number Of Infant Deaths",
-            "statVar": "WHO/CM_02"
-          },
           "sdg/SP_DYN_ADKL.AGE--Y10T14__SEX--F_multiple_place_bar_block": {
             "name": "Adolescent birth rate [10 to 14 years old, Female]",
             "statVar": "sdg/SP_DYN_ADKL.AGE--Y10T14__SEX--F"

server/integration_tests/test_data/detection_api_bio/whatisthephylumofvolvox/debug_info.json

@@ -10,29 +10,29 @@
   "query_with_places_removed": "what is the phylum of",
   "sv_matching": {
     "CosineScore": [
-      0.35510897636413574,
-      0.3460872769355774,
-      0.3452577292919159,
-      0.344845712184906,
-      0.34113651514053345,
-      0.3384983241558075,
-      0.3349902033805847,
-      0.3316609561443329,
-      0.3260059356689453,
-      0.32424432039260864,
-      0.3206062316894531,
-      0.31426557898521423,
-      0.3127653896808624,
-      0.31262922286987305,
-      0.31250447034835815,
-      0.31177398562431335,
-      0.31033921241760254,
-      0.31007489562034607,
-      0.30988338589668274,
-      0.3080539405345917,
-      0.30745869874954224,
-      0.30719631910324097,
-      0.3039420247077942
+      0.355109,
+      0.346087,
+      0.345258,
+      0.344846,
+      0.341137,
+      0.338498,
+      0.33499,
+      0.331661,
+      0.326006,
+      0.324244,
+      0.320606,
+      0.314266,
+      0.312765,
+      0.312629,
+      0.312504,
+      0.311774,
+      0.310339,
+      0.310075,
+      0.309883,
+      0.308054,
+      0.307459,
+      0.307196,
+      0.303942
     ],
     "MultiSV": {},
     "Query": "what is the phylum of",
@@ -64,39 +64,42 @@
   },
   "props_matching": {
     "CosineScore": [
-      0.9999998807907104,
-      0.4752839505672455,
-      0.36154165863990784,
-      0.34200993180274963,
-      0.3293309211730957,
-      0.31845176219940186,
-      0.31466981768608093,
-      0.3083951473236084,
-      0.3079407513141632,
-      0.30463001132011414,
-      0.28270864486694336,
-      0.28187549114227295,
-      0.2808278203010559,
-      0.2804529666900635,
-      0.27429836988449097,
-      0.27150505781173706,
-      0.2707182466983795,
-      0.26954683661460876,
-      0.2599008083343506,
-      0.2599008083343506,
-      0.24827907979488373,
-      0.24662044644355774,
-      0.24632112681865692,
-      0.24616354703903198,
-      0.24212250113487244,
-      0.23135541379451752,
-      0.2296244502067566,
-      0.22773587703704834
+      1.0,
+      0.475284,
+      0.361542,
+      0.345431,
+      0.345431,
+      0.34201,
+      0.329331,
+      0.318452,
+      0.31467,
+      0.308395,
+      0.307941,
+      0.30463,
+      0.282709,
+      0.281875,
+      0.280828,
+      0.280453,
+      0.274298,
+      0.271505,
+      0.270718,
+      0.269547,
+      0.259901,
+      0.259901,
+      0.248279,
+      0.24662,
+      0.246321,
+      0.246164,
+      0.242123,
+      0.231355,
+      0.229624
     ],
     "PROP": [
       "phylum",
       "chemblID",
       "geneID",
+      "<-compoundID{typeOf:ChemicalCompoundGeneticVariantAssociation}->variantID",
+      "<-variantID{typeOf:ChemicalCompoundGeneticVariantAssociation}->compoundID",
       "virusGenus",
       "typeOfGene",
       "fullName",
@@ -112,16 +115,15 @@
       "virusHost",
       "strandOrientation",
       "ncbiDNASequenceName",
-      "<-geneSymbol{typeOf:GeneticVariantGeneAssociation}->referenceSNPClusterID",
-      "<-referenceSNPClusterID{typeOf:GeneticVariantGeneAssociation}->geneSymbol",
+      "<-geneID{typeOf:GeneGeneticVariantAssociation}->variantID",
+      "<-variantID{typeOf:GeneGeneticVariantAssociation}->geneID",
       "ncbiProteinAccessionNumber",
       "alleleType",
       "hg38GenomicLocation",
       "ofVirusSpecies",
       "hg19GenomicLocation",
       "ncbiTaxonID",
-      "antigenType",
-      "alleleOrigin"
+      "antigenType"
     ]
   },
   "query_detection_debug_logs": {