From 0765dcbde6a3a792cba7c59f8fd8ab446272bc59 Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <poirigui@msl.ubc.ca>
Date: Fri, 17 May 2024 10:47:10 -0700
Subject: [PATCH] Copy MultiQC report to its final destination

---
 rnaseq_pipeline/gemma.py | 13 +++++++------
 rnaseq_pipeline/tasks.py | 23 ++++++++++++++++-------
 2 files changed, 23 insertions(+), 13 deletions(-)

diff --git a/rnaseq_pipeline/gemma.py b/rnaseq_pipeline/gemma.py
index 4bb5de9d..12ec7ccf 100644
--- a/rnaseq_pipeline/gemma.py
+++ b/rnaseq_pipeline/gemma.py
@@ -51,14 +51,9 @@ def samples(self, experiment_id):
     def platforms(self, experiment_id):
         return self._query_api(join('datasets', experiment_id, 'platforms'))
 
-class GemmaTask(ExternalProgramTask):
-    """
-    Base class for tasks that wraps Gemma CLI.
-    """
+class GemmaTaskMixin:
     experiment_id = luigi.Parameter()
 
-    subcommand = None
-
     def __init__(self, *kwargs, **kwds):
         super().__init__(*kwargs, **kwds)
         self._gemma_api = GemmaApi()
@@ -103,6 +98,12 @@ def reference_id(self):
     def platform_short_name(self):
         return f'Generic_{self.taxon}_ncbiIds'
 
+class GemmaCliTask(GemmaTaskMixin, ExternalProgramTask):
+    """
+    Base class for tasks that wraps Gemma CLI.
+    """
+    subcommand = None
+
     def program_environment(self):
         env = super().program_environment()
         env.update(cfg.asenv(['JAVA_HOME', 'JAVA_OPTS']))
diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py
index 4f672343..c587ae43 100755
--- a/rnaseq_pipeline/tasks.py
+++ b/rnaseq_pipeline/tasks.py
@@ -2,8 +2,9 @@
 import logging
 import os
 from glob import glob
-from os.path import abspath, join
+from os.path import abspath, join, dirname
 import uuid
+from shutil import copytree
 
 import luigi
 import luigi.task
@@ -12,6 +13,7 @@
 from bioluigi.scheduled_external_program import ScheduledExternalProgramTask
 from bioluigi.tasks import fastqc, multiqc
 from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, TaskWithOutputMixin, DynamicWrapperTask
+from luigi.contrib.external_program import ExternalProgramTask
 from luigi.task import flatten, flatten_output, WrapperTask
 from luigi.util import requires
 
@@ -23,7 +25,7 @@
 from .sources.sra import DownloadSraProject, DownloadSraExperiment, ExtractSraProjectBatchInfo
 from .targets import GemmaDatasetPlatform, GemmaDatasetHasBatch, RsemReference
 from .utils import no_retry, IlluminaFastqHeader, RerunnableTaskMixin, remove_task_output
-from .gemma import GemmaTask, gemma
+from .gemma import GemmaTaskMixin, GemmaCliTask, gemma
 
 logger = logging.getLogger('luigi-interface')
 
@@ -331,7 +333,7 @@ def run(self):
             join(cfg.OUTPUT_DIR, cfg.DATAQCDIR, self.experiment_id),
             join(cfg.OUTPUT_DIR, cfg.ALIGNDIR, self.reference_id, self.experiment_id)]
         self.output().makedirs()
-        yield multiqc.GenerateReport(search_dirs, os.path.dirname(self.output().path), force=self.rerun)
+        yield multiqc.GenerateReport(search_dirs, dirname(self.output().path), force=self.rerun)
 
     def output(self):
         return luigi.LocalTarget(join(cfg.OUTPUT_DIR, 'report', self.reference_id, self.experiment_id, 'multiqc_report.html'))
@@ -363,7 +365,7 @@ def output(self):
         return [luigi.LocalTarget(join(destdir, f'{self.experiment_id}_counts.{self.scope}')),
                 luigi.LocalTarget(join(destdir, f'{self.experiment_id}_fpkm.{self.scope}'))]
 
-class SubmitExperimentBatchInfoToGemma(RerunnableTaskMixin, GemmaTask):
+class SubmitExperimentBatchInfoToGemma(RerunnableTaskMixin, GemmaCliTask):
     """
     Submit the batch information of an experiment to Gemma.
     """
@@ -389,7 +391,7 @@ def output(self):
         return GemmaDatasetHasBatch(self.experiment_id)
 
 @no_retry
-class SubmitExperimentDataToGemma(RerunnableTaskMixin, GemmaTask):
+class SubmitExperimentDataToGemma(RerunnableTaskMixin, GemmaCliTask):
     """
     Submit an experiment to Gemma.
 
@@ -420,19 +422,26 @@ def subcommand_args(self):
     def output(self):
         return GemmaDatasetPlatform(self.experiment_id, self.platform_short_name)
 
-class SubmitExperimentReportToGemma(WrapperTask, GemmaTask):
+class SubmitExperimentReportToGemma(GemmaTaskMixin, luigi.Task):
     """
     Submit an experiment QC report to Gemma.
 
     TODO: This is not yet fully implemented, so only a report is being generated.
     """
+    experiment_id = luigi.Parameter()
+
     def requires(self):
         return GenerateReportForExperiment(self.experiment_id,
                                            taxon=self.taxon,
                                            reference_id=self.reference_id,
                                            source='gemma')
+
     def run(self):
-        pass # do nothing
+        self.output().makedirs()
+        copytree(dirname(self.input().path), dirname(self.output().path), dirs_exist_ok=True)
+
+    def output(self):
+       return luigi.LocalTarget(f'/space/gemmaData/metadata/{self.experiment_id}/MultiQCReports/multiqc_report.html')
 
 @requires(SubmitExperimentDataToGemma, SubmitExperimentBatchInfoToGemma, SubmitExperimentReportToGemma)
 class SubmitExperimentToGemma(TaskWithOutputMixin, WrapperTask):