Comments (4)
Trying to figure out what is happening but it never enters the
def convert_obj(fp, obj):
if "Collection" in as_list(obj.type):
main_entity = obj.get("mainEntity")
if not main_entity:
....
from runcrate.
Maybe.... iets because this particular one is not a CWL workflow but a direct CWL CommandLineTool execution...?
from runcrate.
I think the issue is in
@staticmethod
def _set_alternate_name(prov_param, action_p, parent=None):
basename = getattr(prov_param, "basename", None)
if not basename:
return
if not parent:
action_p["alternateName"] = basename
return
if "alternateName" in parent:
action_p["alternateName"] = (Path(parent["alternateName"]) / basename).as_posix()
else:
# Lets try
action_p["alternateNameTest"] = basename
logging.error("Alternate name not captured")
As alternateName is not in parent
![Screenshot 2023-05-26 at 11 28 32](https://private-user-images.githubusercontent.com/4471699/241179417-bf10721c-e748-45a3-a151-30c934349e9b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.RAiQbn-72Ch1FEEyPtTJegct2P3O5o8iUZH4lHp2Otk)
from runcrate.
{
"@id": "6935c345f5c98b8f78aa6e230ee3163a22c40fd7/76e01c1c849df0cd7601f63b8700508648b99ec4/f38f9214aef6d512d4986ffe475c11673043ce76",
"@type": "File",
"alternateName": "combined/andromeda/allSpectra.UVPD.Unknown.secpep.sil0.apar",
"sha1": "f38f9214aef6d512d4986ffe475c11673043ce76"
},
Latest cwltool did the trick
from runcrate.
Related Issues (20)
- Error from runcrate-analysis, scenario 2_a HOT 1
- Error from runcrate-analysis, scenario 4_a HOT 1
- CWLProv conversion: include creation datetime, size, checksum, format
- CWLProv conversion: add profile conformance HOT 1
- Handle distinct directories with same content
- Convert CWLProv to RO - TypeError: unhashable type: 'list'
- KeyError: <cwl_utils.parser.cwl_v1_2.CommandInputEnumSchema object at 0x10aa191e0> ?
- AttributeError: 'NoneType' object has no attribute 'rsplit' HOT 6
- Option to make data files more user friendly HOT 2
- Bag validation failed: data/.DS_Store exists on filesystem but is not in the manifest HOT 1
- Bug in cwltool results in packed.cwl but no individual cwl files HOT 2
- schema_salad.exceptions.ValidationException tried... HOT 1
- KeyError: 'fastqc.cwl' while cwl file is in the provenance folder HOT 4
- AttributeError: 'CommandLineTool' object has no attribute 'rsplit' HOT 1
- Run: option to download remote inputs
- Error from runcrate convert HOT 2
- Data locations using manifest file HOT 1
- Basedir for data files HOT 1
- Support for ExpressionTool in convert HOT 1
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from runcrate.