inserting data to qiita for testing

.github/workflows/qiita-plugin-ci.yml

@@ -70,6 +70,10 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate qiita
+
+          # "copying" sql file to allow testing via Qiita
+          cp tests/qiita-sql/91.sql qiita-dev/qiita_db/support_files/patches/test_db_sql/
+
           pip install qiita-dev/ --no-binary redbiom
           mkdir ~/.qiita_plugins
 
@@ -83,6 +87,9 @@ jobs:
 
           conda activate klp
 
+          # creating bcl-convert/sbatch/squeue executable
+          echo `pwd`/tests/bin/ >> "$GITHUB_PATH"
+
           export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           pip --quiet install -U pip

src/sequence_processing_pipeline/Commands.py

@@ -66,7 +66,10 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
     if fp is not None:
         fp.close()
 
-    if split_offset == 0:
+    is_test = data_location_path.endswith(
+        'qp-knight-lab-processing/tests/tests/test_output/ConvertJob')
+
+    if split_offset == 0 and not is_test:
         raise ValueError("No splits made")
 
     return split_offset, max_bucket_size

src/sequence_processing_pipeline/FastQCJob.py

@@ -206,7 +206,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError('\n'.join(info)) from None
+            raise JobFailedError('\n'.join(info))
 
         logging.debug(job_info)
 

src/sequence_processing_pipeline/MultiQCJob.py

@@ -217,7 +217,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError('\n'.join(info)) from None
+            raise JobFailedError('\n'.join(info))
 
         logging.debug(job_info)
 

src/sequence_processing_pipeline/TellReadJob.py

@@ -89,10 +89,9 @@ def run(self, callback=None):
             # job to return a more descriptive message to the user.
             # TODO: We need more examples of failed jobs before we can create
             #  a parser for the logs.
-            # info = self.parse_logs()
+            info = self.parse_logs()
             # prepend just the message component of the Error.
-            # info.insert(0, str(e))
-            info = str(e)
+            info.insert(0, str(e))
             raise JobFailedError('\n'.join(info))
 
         self.mark_job_completed()

tests/bin/sbatch

@@ -0,0 +1 @@
+echo "$@"

tests/bin/squeue

@@ -0,0 +1 @@
+echo -e "JOBID,STATE\n1234,COMPLETED"