Fix rename of GemmaTask to GemmaTaskMixin and GemmaCliTask

PavlidisLab · May 17, 2024 · cdbe165 · cdbe165
1 parent ab6b567
commit cdbe165
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Showing 3 changed files with 24 additions and 7 deletions.
diff --git a/rnaseq_pipeline/webviewer/__init__.py b/rnaseq_pipeline/webviewer/__init__.py
@@ -9,14 +9,17 @@
 
 from rnaseq_pipeline.config import rnaseq_pipeline
 from rnaseq_pipeline.tasks import GenerateReportForExperiment, CountExperiment, ExtractGeoSeriesBatchInfo, SubmitExperimentDataToGemma, SubmitExperimentBatchInfoToGemma
-from rnaseq_pipeline.gemma import GemmaTask
+from rnaseq_pipeline.gemma import GemmaTaskMixin
 
 app = Flask('rnaseq_pipeline.webviewer')
 
 cfg = rnaseq_pipeline()
 
 references = ['hg38_ncbi', 'mm10_ncbi', 'm6_ncbi']
 
+class FakeGemmaTask(GemmaTaskMixin, luigi.Task):
+    pass
+
 @app.errorhandler(400)
 def bad_request(e):
     return render_template('400.html', e=e), 400
@@ -63,13 +66,18 @@ def experiment_batch_info(experiment_id):
 @app.route('/experiment/<experiment_id>/by-reference-id/<reference_id>/quantifications/<mode>')
 def experiment_quantifications(experiment_id, mode, reference_id=None):
     if reference_id is None:
-        gemma_task = GemmaTask(experiment_id)
+        gemma_task = FakeGemmaTask(experiment_id)
         reference_id = gemma_task.reference_id
+        taxon = gemma_task.taxon
+        source = 'gemma'
+    else:
+        taxon = 'human'
+        source = 'local'
     try:
         mode_ix = ['counts', 'fpkm'].index(mode)
     except ValueError:
         abort(400, f'Unknown mode {mode} for quantifications, try either counts or fpkm.')
-    count_experiment_task = CountExperiment(experiment_id, reference_id=reference_id, taxon=None)
+    count_experiment_task = CountExperiment(experiment_id, reference_id=reference_id, taxon=taxon, source=source)
     if not count_experiment_task.complete():
         abort(404, f'No quantifications available for {experiment_id} in {reference_id}.')
     file_path = count_experiment_task.output()[mode_ix].path
@@ -79,9 +87,14 @@ def experiment_quantifications(experiment_id, mode, reference_id=None):
 @app.route('/experiment/<experiment_id>/by-reference-id/<reference_id>/report')
 def experiment_report(experiment_id, reference_id=None):
     if reference_id is None:
-        gemma_task = GemmaTask(experiment_id)
+        gemma_task = FakeGemmaTask(experiment_id)
         reference_id = gemma_task.reference_id
-    generate_report_task = GenerateReportForExperiment(experiment_id, reference_id=reference_id, taxon=None)
+        taxon = gemma_task.taxon
+        source = 'gemma'
+    else:
+        taxon = 'human'
+        source = 'local'
+    generate_report_task = GenerateReportForExperiment(experiment_id, reference_id=reference_id, taxon=taxon, source=source)
     if not generate_report_task.complete():
         abort(404, f'No report available for {experiment_id} in {reference_id}.')
     return send_file(generate_report_task.output().path)

diff --git a/tests/test_gemma.py b/tests/test_gemma.py
@@ -7,7 +7,7 @@ def test_gemma_api():
     gemma_api.samples('GSE110256')
 
 def test_gemma_task():
-    task = GemmaTask(experiment_id='GSE110256')
+    task = GemmaCliTask(experiment_id='GSE110256')
     env = task.program_environment()
     assert 'JAVA_OPTS' in env
     assert 'JAVA_HOME' in env

diff --git a/tests/test_tasks.py b/tests/test_tasks.py
@@ -1,6 +1,8 @@
 import datetime
 import pytest
 
+import luigi
+
 from rnaseq_pipeline.config import rnaseq_pipeline
 from rnaseq_pipeline.tasks import *
 
@@ -42,7 +44,9 @@ def test_align_sample_task():
     assert task.output().path == join(cfg.OUTPUT_DIR, cfg.ALIGNDIR, 'hg38_ncbi', 'GSE', 'GSM.genes.results')
     assert task.walltime == datetime.timedelta(days=1)
 
-def test_gemma_task():
+def test_gemma_task_mixin():
+    class GemmaTask(GemmaTaskMixin, luigi.Task):
+        pass
     gemma_task = GemmaTask('GSE110256')
     assert gemma_task.taxon == 'mouse'
     assert gemma_task.accession == 'GSE110256'