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Generate CWL abstract with gxformat2 #35

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Generate CWL abstract with gxformat2 #35

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9c2c745
convert to cwl abstract with gxformat2
simleo Nov 10, 2020
14eee0a
convert dict to abstract dict
ieguinoa Nov 11, 2020
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2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,5 @@ pyld[requests]==1.0.5
requests==2.22.0
urllib3==1.25.6
arcp==0.2.1
galaxy2cwl
gxformat2
jinja2
11 changes: 6 additions & 5 deletions rocrate/rocrate_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,14 +20,13 @@
import atexit
import os
import tempfile
from contextlib import redirect_stdout
from pathlib import Path

import rocrate.rocrate as roc
from rocrate.model import entity
from rocrate.model.workflow import Workflow
from galaxy2cwl import get_cwl_interface

from gxformat2.yaml import ordered_dump, ordered_load
from gxformat2.abstract import from_dict

def make_workflow_rocrate(workflow_path, wf_type, include_files=[],
fetch_remote=False, cwl=None, diagram=None):
Expand Down Expand Up @@ -86,8 +85,10 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[],
if not cwl:
# create cwl_abstract
with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix=".cwl") as f:
with redirect_stdout(f):
get_cwl_interface.main(['1', workflow_path])
with open(workflow_path) as orig_f:
wf_dict = ordered_load(orig_f)
abstract_dict = from_dict(wf_dict)
ordered_dump(abstract_dict, f)
atexit.register(os.unlink, f.name)
abstract_wf_id = wf_path.with_suffix(".cwl").name
abstract_wf_file = Workflow(wf_crate, f.name, abstract_wf_id)
Expand Down