Merge pull request #30 from CompEpigen/dev

Dev

Author: KerstenBreuer

cwlab/__init__.py

@@ -1,7 +1,7 @@
 
 from __future__ import absolute_import
 
-__version__ = "0.3.0"
+__version__ = "0.3.1"
 
 import os
 from flask import Flask

cwlab/utils.py

@@ -430,7 +430,7 @@ def import_wf(
         wf_type = get_workflow_type_from_file_ext(wf_path)
     else:
         assert wf_type in supported_workflow_types, "Provided workflow type \"{wf_type}\" is not supported."
-    if name is None:
+    if name is None or name == "":
         name = os.path.splitext(os.path.basename(wf_path))[0]
     if os.path.splitext(name)[1] in supported_workflow_exts[wf_type]:
         name = os.path.splitext(name)[0]

cwlab/wf_input/make_runs.py

@@ -4,6 +4,7 @@
 import sys
 import re
 from .read_wf import supported_workflow_exts
+from copy import copy
 
 supported_workflow_types = supported_workflow_exts.keys()
 
@@ -18,9 +19,10 @@ def make_CWL_File_or_Directory(path, is_dir=False, secondary_files=[""]):
             if sec_ext[0] == "^":
                 capture_sec_ext = re.search('^(\^+)(.*)', sec_ext)
                 n_exts_to_rm = len(capture_sec_ext.group(1))
+                value_root = copy(path) 
                 for idx in range(0,n_exts_to_rm):
-                    value_root = os.path.splitext(path)[0]
-                sec_file_item_path = path + capture_sec_ext.group(2)
+                  value_root = os.path.splitext(value_root)[0]
+                sec_file_item_path =value_root + capture_sec_ext.group(2)
             else:
                 sec_file_item_path = path + sec_ext
             cwl_sec_file_array.append( {"class": "File", "path": sec_file_item_path } )

cwlab/wf_input/match_types.py

@@ -2,6 +2,7 @@
 import fnmatch
 import sys
 import re
+from copy import copy
 
 def path_exists(path_str, is_dir=False):
     if is_dir:
@@ -61,7 +62,7 @@ def class_file(value_string, secondary_files, validate_paths=True, search_paths=
             if sec_ext[0] == "^":
                 capture_sec_ext = re.search('^(\^+)(.*)', sec_ext)
                 n_exts_to_rm = len(capture_sec_ext.group(1))
-                value_root = path 
+                value_root = copy(path) 
                 for idx in range(0,n_exts_to_rm):
                   value_root = os.path.splitext(value_root)[0]
                 sec_file_item_path =value_root + capture_sec_ext.group(2)

cwlab/wf_input/read_cwl.py

@@ -1,5 +1,6 @@
 import sys, os
 from .read_xls import clean_string
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 def is_basic_type_instance(value):
     return (isinstance(value, int) or 
@@ -113,6 +114,15 @@ def read_config_from_cwl_file(cwl_file):
         if type_ == "File" and "secondaryFiles" in inp_rec:
             if isinstance(inp_rec["secondaryFiles"], str):
                 secondary_files = [ inp_rec["secondaryFiles"] ]
+            elif isinstance(inp_rec["secondaryFiles"], CommentedMap) and \
+                "pattern" in inp_rec["secondaryFiles"].keys():
+                secondary_files = [ inp_rec["secondaryFiles"]["pattern"] ]
+            elif isinstance(inp_rec["secondaryFiles"], CommentedSeq):
+                secondary_files = []
+                for sec_file in inp_rec["secondaryFiles"]:
+                    assert isinstance(sec_file, CommentedMap) and "pattern" in sec_file, \
+                        print_pref + "E: invalid secondaryFiles field for parameter " + name
+                    secondary_files.append(sec_file["pattern"])
             elif isinstance(inp_rec["secondaryFiles"], list):
                 secondary_files = inp_rec["secondaryFiles"]
             else:

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='cwlab',
-    version='0.3.0',    
+    version='0.3.1',    
     description='A platform-agnostic, cloud-ready framework for simplified deployment of the Common Workflow Language using a graphical web interface',
     long_description=open(README).read(),
     long_description_content_type="text/x-rst",
@@ -35,9 +35,9 @@
                       'pyexcel-xlsx',
                       'PyYAML',
                       'pexpect',
-                      'janis-pipelines>=0.7.0'
+                      'janis-pipelines>=0.7.0',
                       'cwltool==1.0.20181201184214; platform_system=="Windows"',
-                      'cwltool>=1.0.20180809224403; platform_system!="Windows"',
+                      'cwltool >=1.0.20180809224403, <=1.0.20191022103248; platform_system!="Windows"',
                       'psutil',
                       'miniwdl>=0.0.5'               
                       ],