Merge pull request #6 from jfear/biosample_des

Biosample des
jfear · May 18, 2017 · bc3b21c · bc3b21c
2 parents c4ffa25 + 986d7cf
commit bc3b21c
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Showing 4 changed files with 14 additions and 6 deletions.
diff --git a/sramongo/biosample.py b/sramongo/biosample.py
@@ -23,6 +23,7 @@ def __init__(self, node):
                 'tax_id': ('Description/Organism', 'taxonomy_id'),
                 'tax_name': ('Description/Organism', 'taxonomy_name'),
                 'organism_name': ('Description/Organism/OrganismName', 'text'),
+                'description': ('Description/Comment/Paragraph', 'text'),
                 'institute': ('Owner/Name', 'text'),
                 'access': ('.', 'access'),
                 'biosample_accn': ('.', 'accession'),

diff --git a/sramongo/mongo_schema.py b/sramongo/mongo_schema.py
@@ -857,6 +857,9 @@ class BioSample(EmbeddedDocument):
     title: mongoengine.StringField
         A free text description of the sample.
 
+    description: mongoengine.StringField
+        A free text description of the sample.
+
     tax_id: mongoengine.StringField
         The tax_id that the sample belongs.
 
@@ -900,6 +903,7 @@ class BioSample(EmbeddedDocument):
     sample_id = StringField()
     GEO = StringField()
     title = StringField()
+    description = StringField()
     tax_id = StringField()
     tax_name = StringField()
     organism_name = StringField()

diff --git a/sramongo/sra2mongo.py b/sramongo/sra2mongo.py
@@ -118,10 +118,10 @@ def arguments():
     args = parser.parse_args()
 
     if args.host and (args.dbDir or args.logDir):
-        logger.warn('Both --host and --dbpath/--logDir were provided; going to try using running mongo server.')
+        logger.warning('Both --host and --dbpath/--logDir were provided; going to try using running mongo server.')
 
     if not (args.host or args.dbDir or args.logDir):
-        logger.warn('You must provide either a `--host hostname` with a running database or '
+        logger.warning('You must provide either a `--host hostname` with a running database or '
                 '`--dbpath <path to db> --logDir <path to log>`')
 
     return args
@@ -222,17 +222,17 @@ def fetch_sra(records, cache, runinfo_retmode='text', **kwargs):
 
                 except HTTPError as err:
                     if (500 <= err.code <= 599) & (attempt < 3):
-                        logger.warn("Received error from server %s" % err)
-                        logger.warn("Attempt %i of 3" % attempt)
+                        logger.warning("Received error from server %s" % err)
+                        logger.warning("Attempt %i of 3" % attempt)
                         time.sleep(15)
                     else:
                         logger.error("Received error from server %s" % err)
                         logger.error("Please re-run command latter.")
                         sys.exit(1)
                 except IncompleteRead as err:
                     if attempt < 3:
-                        logger.warn("Received error from server %s" % err)
-                        logger.warn("Attempt %i of 3" % attempt)
+                        logger.warning("Received error from server %s" % err)
+                        logger.warning("Attempt %i of 3" % attempt)
                         time.sleep(15)
                     else:
                         logger.error("Received error from server %s" % err)

diff --git a/sramongo/sra_const.py b/sramongo/sra_const.py
@@ -22,6 +22,7 @@
 
 LIBRARY_STRATEGY = [
     "AMPLICON",
+    "ATAC-seq",
     "Bisulfite-Seq",
     "ChIP-Seq",
     "CLONE",
@@ -32,6 +33,7 @@
     "FAIRE-seq",
     "FINISHING",
     "FL-cDNA",
+    "HI-C",
     "MBD-Seq",
     "MeDIP-Seq",
     "miRNA-Seq",
@@ -151,6 +153,7 @@
     "Illumina HiSeq X Ten",
     "Illumina MiSeq",
     "Illumina MiniSeq",
+    "Illumina NextSeq 500",
     "Ion Torrent PGM",
     "Ion Torrent Proton",
     "NextSeq 500",