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merged 2 commits into from
Feb 23, 2021
Merged

fix #3076 #3077

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3b934a1
fix #3076
antgonza Feb 19, 2021
fb17bd5
addressing @ElDeveloper comments
antgonza Feb 23, 2021
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9 changes: 9 additions & 0 deletions qiita_db/metadata_template/test/test_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -265,6 +265,15 @@ def test_load_template_to_dataframe_with_nulls(self):
exp.index.name = 'sample_name'
assert_frame_equal(obs, exp, check_like=True)

def test_load_template_to_dataframe_better_tokenizing_error_msg(self):
with self.assertRaisesRegex(RuntimeError, 'Your file has more columns '
'with values than headers'):
qdb.metadata_template.util.load_template_to_dataframe(
StringIO('sample_name\tcollection_timestamp\n'
'2.Sample1\t2014-05-29 12:24:51\t\n'
'2.Sample2\taaa\n'
'xxx\tadfa\t\t\n'))

def test_get_invalid_sample_names(self):
all_valid = ['2.sample.1', 'foo.bar.baz', 'roses', 'are', 'red',
'v10l3t5', '4r3', '81u3']
Expand Down
34 changes: 24 additions & 10 deletions qiita_db/metadata_template/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,10 @@ def load_template_to_dataframe(fn, index='sample_name'):
the database

Everything in the DataFrame will be read and managed as string

While reading the file via pandas, it's possible that it will raise a
'tokenizing' pd.errors.ParserError which is confusing for users; thus,
rewriting the error with an explanation of what it means and how to fix.
"""
# Load in file lines
holdfile = None
Expand Down Expand Up @@ -144,16 +148,26 @@ def load_template_to_dataframe(fn, index='sample_name'):
# comment:
# using the tab character as "comment" we remove rows that are
# constituted only by delimiters i. e. empty rows.
template = pd.read_csv(
StringIO(''.join(holdfile)),
sep='\t',
dtype=str,
encoding='utf-8',
infer_datetime_format=False,
keep_default_na=False,
index_col=False,
comment='\t',
converters={index: lambda x: str(x).strip()})
try:
template = pd.read_csv(
StringIO(''.join(holdfile)),
sep='\t',
dtype=str,
encoding='utf-8',
infer_datetime_format=False,
keep_default_na=False,
index_col=False,
comment='\t',
converters={index: lambda x: str(x).strip()})
except pd.errors.ParserError as e:
if 'tokenizing' in str(e):
msg = ('Your file has more columns with values than headers. To '
'fix, make sure to delete any extra rows or columns; they '
'might look empty because they have spaces. Then upload '
'and try again.')
raise RuntimeError(msg)
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Can you add this to the docstring?

else:
raise e
# remove newlines and tabs from fields
template.replace(to_replace='[\t\n\r\x0b\x0c]+', value='',
regex=True, inplace=True)
Expand Down
174 changes: 87 additions & 87 deletions qiita_db/support_files/qiita-db.dbs
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Original file line number Diff line number Diff line change
Expand Up @@ -939,10 +939,10 @@
<column name="deprecated" type="boolean" jt="-7" >
<defo><![CDATA[FALSE]]></defo>
</column>
<column name="creation_timestamp" type="timestamp" jt="-9" >
<column name="creation_timestamp" type="timestamp" jt="93" >
<defo><![CDATA[FALSE]]></defo>
</column>
<column name="modification_timestamp" type="timestamp" jt="-11" >
<column name="modification_timestamp" type="timestamp" jt="93" >
<defo><![CDATA[FALSE]]></defo>
</column>
<index name="pk_prep_template" unique="PRIMARY_KEY" >
Expand Down Expand Up @@ -1686,90 +1686,90 @@ Controlled Vocabulary]]></comment>
</schema>
<connector name="PostgreSQL" database="PostgreSQL" host="localhost" port="5432" instance="qiita_test" user="ccowart" />
<layout name="qiita" id="Layout669806" confirmed="y" show_relation="columns" >
<comment><![CDATA[qiita]]></comment>
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<comment><![CDATA[qiita-db]]></comment>
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<entity schema="qiita" name="term" color="D0DEF5" x="736" y="1408" />
<entity schema="qiita" name="timeseries_type" color="C0D4F3" x="2000" y="496" />
<entity schema="qiita" name="user_level" color="D0DEF5" x="560" y="272" />
<entity schema="qiita" name="visibility" color="B2CDF7" x="1040" y="1072" />
<group name="Group_analyses" color="C4E0F9" >
<comment><![CDATA[analysis tables]]></comment>
<entity schema="qiita" name="analysis" />
Expand Down Expand Up @@ -1895,4 +1895,4 @@ ALTER TABLE oauth_software ADD CONSTRAINT fk_oauth_software FOREIGN KEY ( client
]]></string>
</script>
</layout>
</project>
</project>
3,148 changes: 1,556 additions & 1,592 deletions qiita_db/support_files/qiita-db.html
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