Improve GLS location validation

nextflow-io · Jan 27, 2020 · 5b89ab5 · 5b89ab5
1 parent 8db8d8a
commit 5b89ab5
Show file tree

Hide file tree

Showing 4 changed files with 60 additions and 17 deletions.
diff --git a/...les/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesConfig.groovy b/...les/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesConfig.groovy
@@ -138,24 +138,20 @@ class GoogleLifeSciencesConfig {
 
     static String fallbackToRegionOrZone(List<String> regions, List<String> zones) {
         if( regions ) {
-            if( regions.size()>1 ) {
-                log.warn "Google LifeSciences location is missing -- Defaulting to region: ${regions[0]}"
-            }
-            return regions[0]
+            return bestLocationForRegion(regions[0])
         }
         if( zones ) {
             def norm = zones
                     .collect { int p = zones[0].lastIndexOf('-'); p!=-1 ? it.substring(0,p) : it }
                     .unique()
-            if( norm.size()>1 ) {
-                log.warn "Google LifeSciences location is missing -- Defaulting to zone: ${norm[0]}"
-            }
-
-            return norm[0]
+            return bestLocationForRegion(norm[0])
         }
-        throw new AbortOperationException("Missing Google region or location information")
+        throw new AbortOperationException("Missing Google region or zone information")
     }
 
+    static String bestLocationForRegion(String region) {
+        region.startsWith('europe-') ? 'europe-west2' : 'us-central1'
+    }
 
     static String getProjectIdFromCreds(String credsFilePath) {
         if( !credsFilePath )

diff --git a/...s/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesExecutor.groovy b/...s/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesExecutor.groovy
@@ -87,6 +87,8 @@ class GoogleLifeSciencesExecutor extends Executor {
 
         log.debug "Google Life Science config=$config"
         helper = initClient()
+        // validate specified location
+        helper.checkValidLocation()
     }
 
     protected GoogleLifeSciencesHelper initClient() {

diff --git a/...les/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy b/...les/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy
@@ -51,10 +51,14 @@ import nextflow.util.Escape
 @CompileStatic
 class GoogleLifeSciencesHelper {
 
+    /*
+     * Avail location see https://cloud.google.com/life-sciences/docs/concepts/locations
+     */
+    public static final List<String> DEFAULT_LOCATIONS  = ['us-central1','europe-west2']
+
     public static final String SSH_DAEMON_NAME = 'ssh-daemon'
     public static final String DEFAULT_APP_NAME = "Nextflow/GLS"
     public static final String SCOPE_CLOUD_PLATFORM = "https://www.googleapis.com/auth/cloud-platform"
-    public static final List<String> ENV_VAR_TO_INCLUDE = ["NXF_DEBUG"]
 
     CloudLifeSciences client
     GoogleCredentials credentials
@@ -306,4 +310,24 @@ class GoogleLifeSciencesHelper {
         result += "{ cd $localTaskDir; bash ${TaskRun.CMD_RUN} nxf_unstage; } >> $localTaskDir/${TaskRun.CMD_LOG} 2>&1"
         return result
     }
+
+    void checkValidLocation() {
+        if( config.location in DEFAULT_LOCATIONS ) {
+            // that's fine, just return
+            return
+        }
+        // check the current list of location to make sure the specified one really exists
+        final availLocations = client
+                .projects()
+                .locations()
+                .list("projects/$config.project")
+                .execute()
+                .getLocations()
+                *.getLocationId()
+        if( config.location in availLocations ) {
+            return
+        }
+        // show a warning message
+        log.warn "The specified Google Life Sciences location is not available: \"$config.location\" -- Please choose open of the following ${availLocations.join(',')}"
+    }
 }
diff --git a/...nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesConfigTest.groovy b/...nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesConfigTest.groovy
@@ -15,6 +15,8 @@
  */
 package nextflow.cloud.google.lifesciences
 
+import spock.lang.Unroll
+
 import nextflow.exception.AbortOperationException
 import nextflow.util.MemoryUnit
 import spock.lang.Specification
@@ -75,13 +77,13 @@ class GoogleLifeSciencesConfigTest extends Specification {
         def map = [google:
                            [
                                    project: 'bar',
-                                   zone: 'eu-west1-a',
+                                   zone: 'europe-west1-a',
                                    lifeSciences: [preemptible: false, disableRemoteBinDir: false]
                            ]]
         def config = GoogleLifeSciencesConfig.fromSession0(map)
         then:
         config.project == 'bar'
-        config.location == 'eu-west1'
+        config.location == 'europe-west2'
         !config.preemptible
         !config.disableBinDir
 
@@ -90,13 +92,13 @@ class GoogleLifeSciencesConfigTest extends Specification {
         map = [google:
                            [
                                    project: 'bar',
-                                   zone: 'eu-west1-a',
+                                   zone: 'europe-west1-a',
                                    lifeSciences: [preemptible: true, disableRemoteBinDir: true]
                            ]]
         config = GoogleLifeSciencesConfig.fromSession0(map)
         then:
         config.project == 'bar'
-        config.location == 'eu-west1'
+        config.location == 'europe-west2'
         config.preemptible
         config.disableBinDir
     }
@@ -112,7 +114,7 @@ class GoogleLifeSciencesConfigTest extends Specification {
         config.project == 'foo'
         config.regions == ['us-central']
         config.zones == []
-        config.location == 'us-central'
+        config.location == 'us-central1'
     }
 
     def 'should config location from zone' () {
@@ -126,7 +128,7 @@ class GoogleLifeSciencesConfigTest extends Specification {
         config.project == 'foo'
         config.regions == []
         config.zones == ['us-east4-a','us-east4-c']
-        config.location == 'us-east4'
+        config.location == 'us-central1'
     }
 
     def 'should report missing region' () {
@@ -195,4 +197,23 @@ class GoogleLifeSciencesConfigTest extends Specification {
         then:
         config.copyImage == 'foo'
     }
+
+    @Unroll
+    def 'should return location from region'( ){
+        given:
+        def config = new GoogleLifeSciencesConfig()
+
+        expect:
+        config.bestLocationForRegion(REGION) == LOCATION
+
+        where:
+        REGION          | LOCATION
+        'europe-west1'  | 'europe-west2'
+        'europe-west2'  | 'europe-west2'
+        'europe-any'    | 'europe-west2'
+        'us-central1'   | 'us-central1'
+        'us-any'        | 'us-central1'
+        'foo'           | 'us-central1'
+    }
+
 }