CI attempt

Author: cmdcolin

.github/workflows/python-apollo.yml

@@ -24,27 +24,22 @@ jobs:
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
-        with:
-          node-version: 18
-
-      - name: Install yarn
-        run: npm install -g yarn
+      - name: Build Apollo
+        run: ./gradlew classes
 
       - name: Start Apollo
         run: |
-          ./gradlew installJBrowseWebOnly compileGwt bootRun > apollo.log 2>&1 &
+          ./gradlew bootRun > apollo.log 2>&1 &
 
           # Wait for health endpoint
-          for i in $(seq 1 180); do
-            response=$(curl -s 'http://localhost:8080/apollo/health/index' 2>/dev/null)
+          for i in $(seq 1 300); do
+            response=$(curl -s 'http://localhost:8080/apollo/health/index' 2>/dev/null || true)
             if echo "$response" | grep -q '"status":"ready"'; then
               echo "Apollo is ready (${i}s)"
               break
             fi
-            if [ $i -eq 180 ]; then
-              echo "FAIL: Apollo not ready after 180 seconds"
+            if [ $i -eq 300 ]; then
+              echo "FAIL: Apollo not ready after 300 seconds"
               cat apollo.log
               exit 1
             fi
@@ -66,17 +61,16 @@ jobs:
       - name: Install python-apollo
         run: |
           cd python-apollo
-          pip install apollo
+          pip install apollo pytest
 
       - name: Bootstrap test data
         run: |
           cd python-apollo
           export ARROW_GLOBAL_CONFIG_PATH=$(pwd)/test-data/local-apollo2-arrow.yml
-          arrow users get_users
           ./bootstrap_apollo.sh --nodocker
 
       - name: Run tests
         run: |
           cd python-apollo
           export ARROW_GLOBAL_CONFIG_PATH=$(pwd)/test-data/local-apollo2-arrow.yml
-          python -m pytest || python setup.py nosetests
+          python -m pytest

grails-app/controllers/org/bbop/apollo/InlineAuthInterceptor.groovy

@@ -17,12 +17,19 @@ class InlineAuthInterceptor {
             return true
         }
 
+        String username = null
+        String password = null
+
         if (request.JSON?.username && request.JSON?.password) {
-            permissionService.authenticateWithToken(
-                request.JSON.username as String,
-                request.JSON.password as String,
-                request
-            )
+            username = request.JSON.username as String
+            password = request.JSON.password as String
+        } else if (params.username && params.password) {
+            username = params.username as String
+            password = params.password as String
+        }
+
+        if (username && password) {
+            permissionService.authenticateWithToken(username, password, request)
         }
 
         return true

grails-app/services/org/bbop/apollo/PreferenceService.groovy

@@ -138,6 +138,9 @@ class PreferenceService {
 
     Organism getOrganismForTokenInDB(String token) {
         log.debug "token for org ${token}"
+        if (!token) {
+            return null
+        }
         if (token.isLong()) {
             log.debug "is long "
             return Organism.findById(token as Long)

grails-app/services/org/bbop/apollo/SequenceService.groovy

@@ -44,7 +44,8 @@ class SequenceService {
      */
     String getResiduesFromFeature(Feature feature) {
         String returnResidues = ""
-        def orderedFeatureLocations = feature.featureLocations.sort { it.fmin }
+        List<FeatureLocation> orderedFeatureLocations = new ArrayList<>(feature.featureLocations)
+        orderedFeatureLocations.sort(Comparator.comparingInt { FeatureLocation fl -> fl.fmin })
         for (FeatureLocation featureLocation in orderedFeatureLocations) {
             String residues = getResidueFromFeatureLocation(featureLocation)
             if (featureLocation.strand == Strand.NEGATIVE.value) {
@@ -325,7 +326,7 @@ class SequenceService {
 
           def sequences = Sequence.findAllByOrganism(organism)
           def seqsMap = [:]
-          sequences.each { sequence ->
+          for (Sequence sequence in sequences) {
               seqsMap[sequence.name] = sequence.length
           }
 
@@ -339,7 +340,7 @@ class SequenceService {
           // otherwise if we remove all of the sequences annotations will need to be removed as well
 //          Sequence.deleteAll(Sequence.findAllByOrganism(organism))
 
-            refSeqs.each { refSeq ->
+            for (def refSeq in refSeqs) {
                 int length;
                 if (refSeq.length) {
                     length = refSeq.length
@@ -362,25 +363,13 @@ class SequenceService {
                   Sequence sequence = Sequence.findByNameAndOrganism(refSeq.name,organism)
                   if (!sequence) {
                       log.error "Sequence not found for name '${refSeq.name}' and organism '${organism.commonName}'"
-                      return
+                      continue
                   }
                   sequence.length = length
                   sequence.seqChunkSize = refSeq.seqChunkSize
                   sequence.start = refSeq.start
                   sequence.end = refSeq.end
-//                  sequence.name = refSeq.name
                   sequence.save(failOnError: true,insert:false)
-//                    def preferences = Preference.executeQuery("select p from UserOrganismPreference  p join p.sequence s where s = :sequence",[sequence:seqsMap[refSeq.name]])
-//                    Preference.deleteAll(preferences)
-//                    Sequence.delete(seqsMap[refSeq.name])
-//                    Sequence sequence = new Sequence(
-//                            organism: organism
-//                            , length: length
-//                            , seqChunkSize: refSeq.seqChunkSize
-//                            , start: refSeq.start
-//                            , end: refSeq.end
-//                            , name: refSeq.name
-//                    ).save(failOnError: true)
                     log.debug "uddated sequence ${sequence}"
                 }
                 else {
@@ -411,7 +400,7 @@ class SequenceService {
                 log.info "an indexed fasta size ${index.size()}"
                 def knownSequences = Sequence.findAllByOrganism(organism)
                 def seqsMap = [:]
-                knownSequences.each { sequence ->
+                for (Sequence sequence in knownSequences) {
                     seqsMap[sequence.name] = sequence.length
                 }
                 // reading the index

src/test/groovy/org/bbop/apollo/ProxyControllerSpec.groovy

@@ -12,9 +12,9 @@ class ProxyControllerSpec extends Specification implements ControllerUnitTest<Pr
     }
 
     def setup() {
-        controller.permissionService = [
-                checkPermissions: { PermissionEnum perm -> true }
-        ]
+        controller.permissionService = Stub(PermissionService) {
+            checkPermissions(_) >> true
+        }
     }
 
     void "Test the index action returns the correct model"() {