Relocate Gemma-specific configuration under [rnaseq_pipeline.gemma]

example.luigi.cfg

@@ -53,11 +53,14 @@ JAVA_HOME=
 JAVA_OPTS=
 GEMMACLI=gemma-cli
 
-GEMMA_BASEURL=https://gemma.msl.ubc.ca
-
 SLACK_WEBHOOK_URL=
 
 [rnaseq_pipeline.gemma]
+cli_bin=gemma-cli
+# values for $JAVA_HOME and $JAVA_OPTS environment variables
+cli_JAVA_HOME=
+cli_JAVA_OPTS=
+baseurl=https://gemma.msl.ubc.ca
 appdata_dir=/space/gemmaData
 human_reference_id=hg38_ncbi
 mouse_reference_id=mm10_ncbi

rnaseq_pipeline/config.py

@@ -18,13 +18,4 @@ class rnaseq_pipeline(luigi.Config):
 
     RSEM_DIR = luigi.Parameter()
 
-    GEMMACLI = luigi.Parameter()
-    JAVA_HOME = luigi.Parameter()
-    JAVA_OPTS = luigi.Parameter()
-
-    GEMMA_BASEURL = luigi.Parameter()
-
     SLACK_WEBHOOK_URL = luigi.OptionalParameter(default=None)
-
-    def asenv(self, attrs):
-        return {attr: getattr(self, attr) for attr in attrs}

rnaseq_pipeline/gemma.py

@@ -12,14 +12,16 @@
 
 class gemma(luigi.Config):
     task_namespace = 'rnaseq_pipeline'
+    baseurl = luigi.Parameter()
     appdata_dir = luigi.Parameter()
+    cli_bin = luigi.Parameter()
+    cli_JAVA_HOME = luigi.Parameter()
+    cli_JAVA_OPTS = luigi.Parameter()
     human_reference_id = luigi.Parameter()
     mouse_reference_id = luigi.Parameter()
     rat_reference_id = luigi.Parameter()
 
-cfg = rnaseq_pipeline()
-
-gemma_cfg = gemma()
+cfg = gemma()
 
 class GemmaApi:
     def __init__(self):
@@ -36,7 +38,7 @@ def _get_password(self):
             return getpass()
 
     def _query_api(self, endpoint):
-        res = self._session.get(join(cfg.GEMMA_BASEURL, 'rest/v2', endpoint))
+        res = self._session.get(join(cfg.baseurl, 'rest/v2', endpoint))
         res.raise_for_status()
         return res.json()['data']
 
@@ -91,7 +93,7 @@ def taxon(self):
     @property
     def reference_id(self):
         try:
-            return {'human': gemma_cfg.human_reference_id, 'mouse': gemma_cfg.mouse_reference_id, 'rat': gemma_cfg.rat_reference_id}[self.taxon]
+            return {'human': cfg.human_reference_id, 'mouse': cfg.mouse_reference_id, 'rat': cfg.rat_reference_id}[self.taxon]
         except KeyError:
             raise ValueError('Unsupported Gemma taxon {}.'.format(self.taxon))
 
@@ -107,11 +109,12 @@ class GemmaCliTask(GemmaTaskMixin, ExternalProgramTask):
 
     def program_environment(self):
         env = super().program_environment()
-        env.update(cfg.asenv(['JAVA_HOME', 'JAVA_OPTS']))
+        env['JAVA_HOME'] = cfg.cli_JAVA_HOME
+        env['JAVA_OPTS'] = cfg.cli_JAVA_OPTS
         return env
 
     def program_args(self):
-        args = [cfg.GEMMACLI,
+        args = [cfg.cli_bin,
                 self.subcommand,
                 '-e', self.experiment_id]
         args.extend(self.subcommand_args())