Introduce new table parsers to get data files back; temporarily puts …

…dependency back to Git repo to test against (updated PyPI package for isa-rwval will be pushed soon).

lib/galaxy/datatypes/isa.py

@@ -24,7 +24,7 @@
 # Imports isatab after turning off warnings inside logger settings to avoid pandas warning making uploads fail.
 logging.getLogger("isatools.isatab").setLevel(logging.ERROR)
 from isatools import isajson
-from isatools import isatab
+from isatools import isatab_meta
 
 from galaxy import model
 from galaxy import util
@@ -345,15 +345,16 @@ def __init__(self, **kwd):
     def _make_investigation_instance(self, filename):
 
         # Parse ISA-Tab investigation file
-        parser = isatab.InvestigationParser()
+        parser = isatab_meta.InvestigationParser()
+        isa_dir = os.path.dirname(filename)
         fp = utf8_text_file_open(filename)
         parser.parse(fp)
         for study in parser.isa.studies:
-            s_parser = isatab.LazyStudySampleTableParser(parser.isa)
-            s_parser.parse(study.filename)
+            s_parser = isatab_meta.LazyStudySampleTableParser(parser.isa)
+            s_parser.parse(os.path.join(isa_dir, study.filename))
             for assay in study.assays:
-                a_parser = isatab.LazyAssayTableParser(parser.isa)
-                a_parser.parse(assay.filename)
+                a_parser = isatab_meta.LazyAssayTableParser(parser.isa)
+                a_parser.parse(os.path.join(isa_dir, assay.filename))
         isa = parser.isa
 
         return isa

lib/galaxy/dependencies/pinned-requirements.txt

@@ -72,7 +72,7 @@ pulsar-galaxy-lib==0.8.3
 
 # sqlalchemy-migrate and dependencies
 sqlalchemy-migrate==0.11.0
-decorator==4.0.2
+decorator==4.1.0
 Tempita==0.5.3dev
 sqlparse==0.1.16
 pbr==3.1.1
@@ -91,4 +91,3 @@ python-genomespaceclient==0.1.8
 
 # ISA
 git+https://github.com/ISA-tools/isa-rwval.git@develop#egg=isa-rwval
-