From cdbe165dd5743d7b5fe41b01f9083b6c39f43490 Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <poirigui@msl.ubc.ca>
Date: Fri, 17 May 2024 12:43:05 -0700
Subject: [PATCH] Fix rename of GemmaTask to GemmaTaskMixin and GemmaCliTask

---
 rnaseq_pipeline/webviewer/__init__.py | 23 ++++++++++++++++++-----
 tests/test_gemma.py                   |  2 +-
 tests/test_tasks.py                   |  6 +++++-
 3 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/rnaseq_pipeline/webviewer/__init__.py b/rnaseq_pipeline/webviewer/__init__.py
index a2701272..fda48d99 100644
--- a/rnaseq_pipeline/webviewer/__init__.py
+++ b/rnaseq_pipeline/webviewer/__init__.py
@@ -9,7 +9,7 @@
 
 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')
 
@@ -17,6 +17,9 @@
 
 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
index 647d8ec7..00e11d0e 100644
--- 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
index b2b2db07..2a11fe0a 100644
--- 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'