Fix a few issues in BatchLogging.groovy

1. Adds the projectId to BatchLogging's LoggingOptions so the logs
will be fetched from the correct project. Previously I got a lot of
"that resource might not exist" responses from the log read requests.
I'm not sure if there's something special about my environment that
causes me to need the projectId in the options, but I think it
couldn't hurt to have the projectId in general.

2. Removes the old paseOutput function, which relied on the STDERR and
STDOUT prefixes in the payload of the log entries. Batch no longer adds
those prefixes so that parsing doesn't work. Now we can distinguish
stderr from stdout by looking at the logEntry's severity.

3. Catches any exception thrown by the log reading code. It could be a
permissions issuee like I was seeing, or a thread pool issuee as in
nextflow-io#3166. Either way,
something going wrong while trying to read task logs should probably
not stop the whole workflow.

With these changes, the nf-core/methylseq workflow can be run with
the google-batch executor.

plugins/nf-google/src/main/nextflow/cloud/google/batch/logging/BatchLogging.groovy

@@ -23,18 +23,15 @@ import com.google.cloud.logging.Logging
 import com.google.cloud.logging.LoggingOptions
 import groovy.transform.Memoized
 import groovy.transform.PackageScope
+import groovy.util.logging.Slf4j
 import nextflow.cloud.google.batch.client.BatchConfig
 /**
  * Batch logging client
  * 
  * @author Paolo Di Tommaso <[email protected]>
  */
+@Slf4j
 class BatchLogging {
-
-    private static final String STDOUT = 'STDOUT:  '
-    private static final String STDERR = 'STDERR:  '
-
-    private String mode = STDOUT
     private LoggingOptions opts
     private String projectId
 
@@ -45,8 +42,8 @@ class BatchLogging {
 
     BatchLogging(BatchConfig config) {
         final creds = config.googleOpts.credentials
-        this.opts = LoggingOptions .newBuilder() .setCredentials(creds) .build()
         this.projectId = config.googleOpts.projectId
+        this.opts = LoggingOptions .newBuilder() .setCredentials(creds) .setProjectId(this.projectId) .build()
     }
 
     String stdout(String jobId) {
@@ -57,45 +54,30 @@ class BatchLogging {
         return fetchLogs(jobId)[1]
     }
 
-    @PackageScope String currentMode() { mode }
-
     @Memoized(maxCacheSize = 1000)
     @PackageScope List<String> fetchLogs(String uid) {
+        final stdout = new StringBuilder()
+        final stderr = new StringBuilder()
         try(Logging logging = opts.getService()) {
             // use logging here
             final filter = "resource.type=generic_task AND logName=projects/${projectId}/logs/batch_task_logs AND labels.job_uid=$uid"
             final entries = logging.listLogEntries(
                     Logging.EntryListOption.filter(filter),
                     Logging.EntryListOption.pageSize(1000) )
 
-            final stdout = new StringBuilder()
-            final stderr = new StringBuilder()
             final page = entries.getValues()
             for (LogEntry logEntry : page.iterator()) {
                 final output = logEntry.payload.data.toString()
-                parseOutput(output, stdout, stderr)
+                if (logEntry.severity == "ERROR") {
+                    stderr.append(output)
+                } else {
+                    stdout.append(output)
+                }
             }
-
-            return [ stdout.toString(), stderr.toString() ]
-        }
-    }
-
-    protected void parseOutput(String output, StringBuilder stdout, StringBuilder stderr) {
-        // check stderr
-        def p = output.indexOf(STDERR)
-        if( p>=0 ) {
-            mode = STDERR
-            output = output.substring(p+STDERR.size())
-        }
-        else if( (p = output.indexOf(STDOUT))>=0 )  {
-            mode = STDOUT
-            output = output.substring(p+STDOUT.size())
+        } catch (Exception e) {
+            log.debug "[GOOGLE BATCH] Cannot read logs for job: `$uid` | ${e.message}"
         }
-        // now append the result
-        if( mode==STDOUT )
-            stdout.append(output)
-        else
-            stderr.append(output)
+        return [ stdout.toString(), stderr.toString() ]
     }
 
 }