fix: batch job ID and label prior to submission

.github/workflows/ci_mocked_api.yaml

@@ -83,13 +83,22 @@ jobs:
       - name: 'Use gcloud CLI'
         run: 'gcloud info'
 
-      # - id: 'auth'
-      #   uses: 'google-github-actions/auth@v1'
-      #   with:
-      #     credentials_json: '${{ secrets.GCP_SA_KEY }}'
+      - name: Setup minio
+        uses: comfuture/minio-action@v1
+        with:
+          access_key: minio
+          secret_key: minio123
+          port: 9000
+
+      - name: Install MinIO Client CLI
+        run: |
+          curl -O https://dl.min.io/client/mc/release/linux-amd64/mc
+          chmod +x mc
+          sudo mv mc /usr/local/bin/
 
-      # - name: 'Set up GCloud SDK'
-      #   uses: 'google-github-actions/setup-gcloud@v1'
+      - name: Configure MinIO client
+        run: |
+          mc alias set minio http://localhost:9000 minio minio123
 
       - name: Run pytest
         run: |

pyproject.toml

@@ -4,7 +4,8 @@ version = "0.5.0"
 description = ""
 authors = [
     "Vanessa Sochat <[email protected]>",
-    "Johannes Koester <[email protected]>"
+    "Johannes Koester <[email protected]>",
+    "Tadas Bareikis <[email protected]>"
 ]
 readme = "README.md"
 license = "MIT"

snakemake_executor_plugin_googlebatch/executor.py

@@ -56,7 +56,7 @@ def get_labels(self, job):
         """
         Derive default labels for the job (and add custom)
         """
-        labels = {"snakemake-job": job.name}
+        labels = {"snakemake-job": self.fix_job_name(job.name)}
         for contender in self.get_param(job, "labels").split(","):
             if not contender:
                 continue
@@ -93,7 +93,7 @@ def generate_jobid(self, job):
         Generate a random jobid
         """
         uid = str(uuid.uuid4())
-        return job.name.replace("_", "-") + "-" + uid[0:6]
+        return self.fix_job_name(job.name) + "-" + uid[0:6]
 
     def get_container(self, job, entrypoint=None, commands=None):
         """
@@ -180,6 +180,13 @@ def get_command_writer(self, job):
             resources=job.resources,
         )
 
+    def fix_job_name(self, name):
+        """
+        Replace illegal symbols and fix the job name length to adhere to
+        the Google Batch API job ID and label naming restrictions
+        """
+        return name.replace("_", "-").replace(".", "")[:50]
+
     def run_job(self, job: JobExecutorInterface):
         """
         Run the Google Batch job.