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Fix extra files path type hint #18958

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merged 3 commits into from
Oct 10, 2024
Merged

Fix extra files path type hint #18958

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3cd1e7b
Add type annotation for HasExtraFilesPath.extra_files_path
davelopez Oct 9, 2024
8f6610f
Avoid type mismatch for reusing variables in genetics.py
davelopez Oct 9, 2024
422221d
Refactor header split
davelopez Oct 9, 2024
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13 changes: 6 additions & 7 deletions lib/galaxy/datatypes/genetics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -863,16 +863,15 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
pp = os.path.join(dataset.extra_files_path, pn)
dataset.metadata.pheno_path = pp
try:
with open(pp) as f:
pf = f.readlines() # read the basename.phenodata in the extra_files_path
with open(pp) as file:
pf = file.readlines() # read the basename.phenodata in the extra_files_path
except Exception:
pf = None
if pf:
h = pf[0].strip()
h = h.split("\t") # hope is header
h = [escape(x) for x in h]
dataset.metadata.column_names = h
dataset.metadata.columns = len(h)
header = pf[0].strip()
columns = [escape(x) for x in header.split("\t")] # hope is header
dataset.metadata.column_names = columns
dataset.metadata.columns = len(columns)
dataset.peek = "".join(pf[:5])
else:
dataset.metadata.column_names = []
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2 changes: 1 addition & 1 deletion lib/galaxy/datatypes/protocols.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ def ext(self): ...

class HasExtraFilesPath(Protocol):
@property
def extra_files_path(self): ...
def extra_files_path(self) -> str: ...


class HasFileName(Protocol):
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