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updating #119

Merged
merged 10 commits into from
Nov 14, 2022
Merged

updating #119

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7719a26
fix broken file names
HadleyKing Oct 14, 2022
6af0647
Added ngs_id_script.py and template docs
Jgergely11 Oct 14, 2022
ae25547
Added ngs_id_script.py and template dataset
Jgergely11 Oct 14, 2022
0d1b402
Bump numpy from 1.21.4 to 1.22.0
dependabot[bot] Oct 16, 2022
260b325
ngs from API (#115)
Jgergely11 Nov 2, 2022
a41d9dd
Update galaxy_converter.py
HadleyKing Nov 8, 2022
54328dc
ARGOSDB API argosdb_api_query
HadleyKing Oct 27, 2022
8c45d52
saving changes
HadleyKing Nov 11, 2022
0c7becb
make argosdb_api_query.py script
HadleyKing Nov 14, 2022
cd36d68
Merge branch 'multi'
HadleyKing Nov 14, 2022
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Update galaxy_converter.py
  • Loading branch information
@HadleyKing
HadleyKing committed Nov 8, 2022
commit a41d9ddebd2c3cb554a9b1162187fe433f89e09b
15 changes: 10 additions & 5 deletions lib/galaxy_converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from urllib.parse import urlparse
from dateutil.parser import parse, ParserError

__version__ = "1.0.0"
__version__ = "1.1.0"
__status__ = "Production"

def usr_args():
Expand Down Expand Up @@ -130,7 +130,7 @@ def convert_bco(bco):
for index, item in enumerate(bco_dict['execution_domain']['script']):
if isinstance(item, dict) is False:
bco_dict['execution_domain']['script'][index]={'uri':{'uri':item}}
if bco_dict['execution_domain']['script_access_type']:
if 'script_access_type' in bco_dict['execution_domain']:
del bco_dict['execution_domain']['script_access_type']
for index, item in enumerate(
bco_dict['execution_domain']['external_data_endpoints']
Expand Down Expand Up @@ -178,13 +178,18 @@ def convert_bco(bco):
except ParserError:
del prereq['uri']['access_time']

for input_obj in bco_dict['io_domain']['input_subdomain']:
for index, input_obj in enumerate(bco_dict['io_domain']['input_subdomain']):
if isinstance(input_obj['uri'], str):
bco_dict['io_domain']['input_subdomain'][index] = {'uri': input_obj}
uri_obj = bco_dict['io_domain']['input_subdomain'][index]
try:
input_obj['uri']['access_time'] = timezone_aware(
input_obj['uri']['access_time']
uri_obj['uri']['access_time'] = timezone_aware(
uri_obj['uri']['access_time']
)
except ParserError:
del input_obj['uri']['access_time']
if not isinstance(uri_obj['uri']['filename'], str):
bco_dict['io_domain']['input_subdomain'][index]['uri']['filename'] = ''

for output_obj in bco_dict['io_domain']['output_subdomain']:
try:
Expand Down