Merge branch 'main' into release

.github/workflows/test_example_scripts.yml

@@ -0,0 +1,50 @@
+name: Test Example Scripts
+
+on:
+  push:
+    branches: [ main, staging ]
+  pull_request:
+    branches: [ main, staging]
+
+jobs:
+  run-scripts:
+    runs-on: 'ubuntu-latest'
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: '3.3'
+
+    - name: Install Ruby dependencies
+      run: gem install httparty
+
+    - name: Run Ruby script
+      run: ruby examples/fetch_variant_links.rb
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.13'
+
+    - name: Install Python dependencies
+      run: pip install requests
+
+    - name: Run Python script
+      run: python examples/fetch_all_variants.py
+
+    - name: Set up R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: '4.4'
+
+    - name: Install system dependencies for R packages
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
+
+    - name: Run R script
+      run: Rscript examples/fetch_acmg_code.R

client/src/app/forms/components/user-profile/user-profile.form.html

@@ -46,6 +46,8 @@
       <nz-select
         [(ngModel)]="this.countryId"
         nzAllowClear
+        [nzDropdownMatchSelectWidth]="false"
+        nzPlaceHolder="Select a Country"
         nzShowSearch>
         <nz-option
           *ngFor="let country of countries$ | ngrxPush"

client/yarn.lock

@@ -5367,9 +5367,9 @@ [email protected]:
     tslib "^2.4.0"
 
 cross-spawn@^7.0.0, cross-spawn@^7.0.2, cross-spawn@^7.0.3:
-  version "7.0.3"
-  resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-7.0.3.tgz#f73a85b9d5d41d045551c177e2882d4ac85728a6"
-  integrity sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==
+  version "7.0.6"
+  resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-7.0.6.tgz#8a58fe78f00dcd70c370451759dfbfaf03e8ee9f"
+  integrity sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==
   dependencies:
     path-key "^3.1.0"
     shebang-command "^2.0.0"

examples/fetch_acmg_code.R

@@ -1,3 +1,4 @@
+install.packages(c("ghql", "jsonlite", "dplyr"), repos="https://cloud.r-project.org")
 library(ghql)
 library(jsonlite)
 library(dplyr)

examples/fetch_all_variants.py

@@ -23,34 +23,28 @@ def run_query(query, variables):
       id
       name
       variantAliases
-      variantBases
-      referenceBases
-      referenceBuild
-      clinvarIds
-      alleleRegistryId
-      ensemblVersion
-      gene {
-        name
+        variantTypes {
         id
-        entrezId
+        soid
+        description
       }
-      hgvsDescriptions
-      primaryCoordinates {
-        start
-        stop
-        chromosome
-        representativeTranscript
+      ... on GeneVariant {
+        coordinates {
+          chromosome
+          start
+          stop
+          referenceBases
+          variantBases
+          representativeTranscript
+          referenceBuild
+        }
       }
-      secondaryCoordinates{
-        start
-        stop
-        chromosome
-        representativeTranscript
+      ... on FactorVariant {
+        name
+        ncitId
       }
-      variantTypes {
-        id
-        soid
-        description
+      ... on FusionVariant {
+        viccCompliantName
       }
     }
   }

examples/fetch_variant_links.rb

@@ -1,4 +1,5 @@
 require 'httparty'
+require 'json'
 
 def call_graphql_api(url:, query:, vars:)
   headers = {

server/Gemfile.lock

@@ -237,7 +237,7 @@ GEM
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.22.0)
+    loofah (2.23.1)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     mail (2.8.1)
@@ -274,17 +274,17 @@ GEM
       net-protocol
     net-ssh (7.2.1)
     nio4r (2.7.3)
-    nokogiri (1.16.7-aarch64-linux)
+    nokogiri (1.16.8-aarch64-linux)
       racc (~> 1.4)
-    nokogiri (1.16.7-arm-linux)
+    nokogiri (1.16.8-arm-linux)
       racc (~> 1.4)
-    nokogiri (1.16.7-arm64-darwin)
+    nokogiri (1.16.8-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86-linux)
+    nokogiri (1.16.8-x86-linux)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-darwin)
+    nokogiri (1.16.8-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-linux)
+    nokogiri (1.16.8-x86_64-linux)
       racc (~> 1.4)
     oauth2 (1.4.11)
       faraday (>= 0.17.3, < 3.0)
@@ -369,9 +369,9 @@ GEM
       activesupport (>= 5.0.0)
       minitest
       nokogiri (>= 1.6)
-    rails-html-sanitizer (1.6.0)
+    rails-html-sanitizer (1.6.1)
       loofah (~> 2.21)
-      nokogiri (~> 1.14)
+      nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
     railties (7.1.4.1)
       actionpack (= 7.1.4.1)
       activesupport (= 7.1.4.1)

server/app/graphql/resolvers/top_level_molecular_profiles.rb

@@ -35,7 +35,9 @@ class Resolvers::TopLevelMolecularProfiles < GraphQL::Schema::Resolver
     )
     ids = results.hits.map { |x| x["_id"] }
 
-    scope.where(molecular_profiles: { id: ids })
+    scope.left_joins(:molecular_profile_aliases).where(molecular_profiles: { id: ids })
+      .or(scope.where('molecular_profile_aliases.name ILIKE :query', {query: "%#{value}%"}))
+      .distinct
   end
 
   option(:gene_id, type: Int, description: "Filter molecular profiles to the CIViC id of the gene(s) involved.") do |scope, value|

server/app/jobs/generate_tsvs.rb

@@ -1,12 +1,14 @@
+require 'csv'
 class GenerateTsvs < ApplicationJob
   def perform
     ensure_downloads_directory_exists
     tsvs_to_generate.each do |e|
       begin
         tmp_file = tmp_file(e.file_name)
-        tmp_file.puts(e.headers.join("\t"))
+        tmp_file.puts CSV.generate_line(e.headers, col_sep: "\t")
         e.objects.find_each do |object|
-          tmp_file.puts(e.row_from_object(object).join("\t"))
+          row = e.row_from_object(object).map {|col| col.is_a?(String) ? col.squish : col }
+          tmp_file.puts CSV.generate_line(row, col_sep: "\t", quote_empty: false)
         end
         tmp_file.close
         public_path = public_file_path(e.file_name)

server/app/lib/importer/disease_ontology_mirror.rb

@@ -88,8 +88,7 @@ def delete_unprocessed_diseases
 
       unprocessed_doids.each do |doid|
         d = Disease.find_by(doid: doid)
-        revisions = Revision.where(field_name: 'disease_id').where(current_value: d.id).or(Revision.where(field_name: 'disease_id').where(suggested_value: d.id))
-        if d.evidence_items.count == 0 && d.assertions.count == 0 && d.source_suggestions.count == 0 && revisions.count == 0
+        if is_disease_with_no_relations?(d)
           d.disease_aliases.clear
           d.delete
         else
@@ -121,7 +120,7 @@ def delete_unprocessed_diseases
         end
       end
       Disease.where(doid: nil).each do |d|
-        if d.evidence_items.count == 0 && d.assertions.count == 0 && d.source_suggestions.count == 0
+        if is_disease_with_no_relations?(d)
           d.disease_aliases.clear
           d.delete
         elsif ['Solid Tumor', 'Ventricular Dysfunction', 'Acute Mountain Sickness', 'Glioma', 'Low Bone Mineral Density'].include? d.name
@@ -135,6 +134,20 @@ def delete_unprocessed_diseases
       end
     end
 
+    def is_disease_with_no_relations?(d)
+       d.evidence_items.count == 0 &&
+       d.assertions.count == 0 &&
+       d.source_suggestions.count == 0 &&
+       revisions_count(d) == 0
+    end
+
+    def revisions_count(disease)
+      Revision.where(field_name: 'disease_id')
+        .where(current_value: disease.id)
+        .or(Revision.where(field_name: 'disease_id').where(suggested_value: disease.id))
+        .count
+    end
+
     def url_from_doid(doid)
       URI.parse("https://disease-ontology.org/api/metadata/DOID:#{doid}/")
     end

server/app/models/materialized_views/source_browse_table_row.rb

@@ -1,4 +1,5 @@
 class MaterializedViews::SourceBrowseTableRow < MaterializedViews::MaterializedView
+  self.primary_key = :id
   has_and_belongs_to_many :clinical_trials, join_table: :clinical_trials_sources, foreign_key: :source_id
 
   enum source_type: ['PubMed', 'ASCO', 'ASH']

server/yarn.lock

@@ -1891,9 +1891,9 @@ cosmiconfig@^7.0.0:
     yaml "^1.10.0"
 
 cross-spawn@^7.0.3:
-  version "7.0.3"
-  resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-7.0.3.tgz#f73a85b9d5d41d045551c177e2882d4ac85728a6"
-  integrity sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==
+  version "7.0.6"
+  resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-7.0.6.tgz#8a58fe78f00dcd70c370451759dfbfaf03e8ee9f"
+  integrity sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==
   dependencies:
     path-key "^3.1.0"
     shebang-command "^2.0.0"