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fix array error in tsv parsing #112

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Merged
MichaelLukowski merged 1 commit into from
Jun 29, 2023
Merged

fix array error in tsv parsing #112

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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[tool.poetry]
name = "pypfb"
version = "0.5.23"
version = "0.5.24"
description = "Python SDK for PFB format"
authors = ["CTDS UChicago <[email protected]>"]
license = "Apache-2.0"
Expand Down
21 changes: 14 additions & 7 deletions src/pfb/importers/tsv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,9 @@ def from_tsv(ctx, path, schema, program, project):
with PFBReader(schema) as reader:
writer.copy_schema(reader)

writer.write(_from_tsv(writer.metadata, writer.schema, path, program, project))
writer.write(
_from_tsv(writer.metadata, writer.schema, path, program, project)
)
except Exception:
click.secho("Failed!", fg="red", bold=True, err=True)
raise
Expand Down Expand Up @@ -88,7 +90,12 @@ def convert_types(val, field_type):
return None
return str(val)
elif field_type == "float":
if val is None or val.strip() == "" or val.strip() == "null" or val.strip() == "Null":
if (
val is None
or val.strip() == ""
or val.strip() == "null"
or val.strip() == "Null"
):
return None
return float(val)
elif field_type == "integer" or field_type == "long":
Expand All @@ -102,6 +109,7 @@ def convert_types(val, field_type):
# finally if the type doesn't match any case then we return the supplied value
return val


def get_type_from_schema(schema, node, field):
nodes = None
for n in schema:
Expand Down Expand Up @@ -130,7 +138,6 @@ def get_type_from_schema(schema, node, field):
return field_type



def _convert_tsv(node_name, tsv_record, program, project, link_dests):
relations = []
try:
Expand All @@ -154,12 +161,13 @@ def _convert_tsv(node_name, tsv_record, program, project, link_dests):
"dst_name": link_dests[node_name][v],
}
)

# array typing being passed off as string
if (
type(tsv_record[item]) == str
and "[" in tsv_record[item]
and "]" in tsv_record[item]
and len(tsv_record[item]) > 0
and tsv_record[item][0] == "["
and tsv_record[item][-1] == "]"
):
arrayStrip = tsv_record[item].strip("[']")
vals[item] = arrayStrip.split(",")
Expand All @@ -169,7 +177,6 @@ def _convert_tsv(node_name, tsv_record, program, project, link_dests):
{"dst_id": tsv_record[item], "dst_name": item.split(".")[0]}
)
to_del.append(item)


for i in to_del:
if i in vals:
Expand Down