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Import Documents: Read metas as the right type #677

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Jul 21, 2021
Merged

Import Documents: Read metas as the right type #677

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6024a65
Import Documents: Read metas as the right type
ajdapretnar Jul 6, 2021
c1d7c8a
Fix tests
ajdapretnar Jul 21, 2021
42405e2
Sanitize Yaml
ajdapretnar Jul 21, 2021
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22 changes: 16 additions & 6 deletions orangecontrib/text/import_documents.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import contextlib
import datetime
import fnmatch
import logging
import os
Expand Down Expand Up @@ -29,8 +30,10 @@

import serverfiles

from Orange.data import DiscreteVariable, Domain, StringVariable
from Orange.data.io import detect_encoding, UrlReader as CoreUrlReader
from Orange.data import DiscreteVariable, Domain, StringVariable, \
guess_data_type
from Orange.data.io import detect_encoding, sanitize_variable,\
UrlReader as CoreUrlReader
from Orange.data.util import get_unique_names
from Orange.util import Registry

Expand Down Expand Up @@ -284,6 +287,8 @@ def _read_meta_data(self):
content = data.content
if isinstance(content, dict):
content = pd.DataFrame(content, index=[0])
# if reader is YamlMetaReader:
# content = content.replace("None", np.nan)
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@VesnaT Should we keep this? Currently, null values in yamls are treated as "None" (strings).

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I'd rather put fixes like this inside the YamlMetaReader.
Besides, I'm not sure the fix works correctly for theStringVariables.

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@VesnaT VesnaT Jul 21, 2021 •
edited
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Something like this could work:

class YamlMetaReader(Reader):
    ext = [".yaml"]

    def read_file(self):
        with open(self.path, "r") as f:
            self.content = yaml.safe_load(f)
            for k in self.content:
                if self.content[k] is None:
                    self.content[k] = ""

meta_dfs.append(content)
else:
errors.append(error)
Expand Down Expand Up @@ -345,13 +350,18 @@ def _add_metadata(self, corpus: Corpus) -> Corpus:
if len(df.index.drop_duplicates()) != len(df.index):
df = df[~df.index.duplicated(keep='first')]
filtered = df.reindex(path_column)
for column in filtered.columns:
for name, column in filtered.iteritems():
data = column.astype(str).values
val_map, vals, var_type = guess_data_type(data)
values, variable = sanitize_variable(val_map, vals, data,
var_type, {},
name=get_unique_names(
corpus.domain, name))
corpus = corpus.add_column(
StringVariable(get_unique_names(corpus.domain, column)),
filtered[column].to_numpy(),
variable,
values,
to_metas=True
)

return corpus

@staticmethod
Expand Down
8 changes: 4 additions & 4 deletions orangecontrib/text/tests/test_import_documents.py
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Expand Up @@ -130,16 +130,16 @@ def test_run_url(self):
importer = ImportDocuments(path, True)
corpus2, _ = importer.run()
self.assertGreater(len(corpus1), 0)
self.assertEqual(corpus1.metas[mask].tolist(),
corpus2.metas[mask].tolist())
np.testing.assert_array_equal(corpus1.metas[mask].tolist(),
corpus2.metas[mask].tolist())

path = "http://file.biolab.si/text-semantics/data" \
"/predlogi-vladi-sample"
importer = ImportDocuments(path, True)
corpus3, _ = importer.run()
self.assertGreater(len(corpus2), 0)
self.assertEqual(corpus1.metas[mask].tolist(),
corpus3.metas[mask].tolist())
np.testing.assert_array_equal(corpus1.metas[mask].tolist(),
corpus3.metas[mask].tolist())

def test_run_url_special_characters(self):
path = "http://file.biolab.si/text-semantics/data/" \
Expand Down