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Merged
merged 10 commits into from
Mar 10, 2021
Merged

Workflows GUI #3078

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3b934a1
fix #3076
antgonza Feb 19, 2021
fb17bd5
addressing @ElDeveloper comments
antgonza Feb 23, 2021
be9848a
Merge branch 'dev' of github.com:biocore/qiita into workflows-GUI
antgonza Feb 23, 2021
51cc864
adding workflows GUI
antgonza Feb 23, 2021
d7655ae
improve HTML
antgonza Feb 23, 2021
aa82154
db changes and improvements
antgonza Feb 25, 2021
189ffd0
Merge branch 'dev' of github.com:biocore/qiita into workflows-GUI
antgonza Mar 3, 2021
35ed05e
comment out new db changes
antgonza Mar 3, 2021
e0a05c0
rm default_workflows from PluginHandler.get
antgonza Mar 3, 2021
5e608c2
Apply suggestions from code review [skip ci]
antgonza Mar 9, 2021
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fix #3076
  • Loading branch information
@antgonza
antgonza committed Feb 19, 2021
commit 3b934a1bd3b0d421ad0c1d1ec9a6ed18343744a3
10 changes: 10 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 +265,16 @@ 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.assertRaises(RuntimeError) as error:
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'))
self.assertIn('Your file has more columns with values than headers.',
str(error.exception))

def test_get_invalid_sample_names(self):
all_valid = ['2.sample.1', 'foo.bar.baz', 'roses', 'are', 'red',
'v10l3t5', '4r3', '81u3']
Expand Down
30 changes: 20 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 @@ -144,16 +144,26 @@ 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)
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>
<entity schema="qiita" name="analysis" color="D0DEF5" x="224" y="880" />
<entity schema="qiita" name="analysis_filepath" color="C0D4F3" x="400" y="880" />
<entity schema="qiita" name="analysis_portal" color="A8C4EF" x="176" y="768" />
<entity schema="qiita" name="analysis_sample" color="D0DEF5" x="256" y="1072" />
<entity schema="qiita" name="analysis_users" color="D0DEF5" x="48" y="880" />
<entity schema="qiita" name="archive_feature_value" color="B2CDF7" x="1472" y="1552" />
<entity schema="qiita" name="archive_merging_scheme" color="B2CDF7" x="1248" y="1552" />
<entity schema="qiita" name="artifact" color="B2CDF7" x="1200" y="960" />
<entity schema="qiita" name="artifact_filepath" color="B2CDF7" x="1040" y="1040" />
<entity schema="qiita" name="artifact_output_processing_job" color="B2CDF7" x="1760" y="1456" />
<entity schema="qiita" name="artifact_processing_job" color="B2CDF7" x="1744" y="1344" />
<entity schema="qiita" name="artifact_type" color="D0DEF5" x="1408" y="960" />
<entity schema="qiita" name="artifact_type_filepath_type" color="B2CDF7" x="1376" y="816" />
<entity schema="qiita" name="checksum_algorithm" color="B2CDF7" x="736" y="1040" />
<entity schema="qiita" name="column_controlled_vocabularies" color="D0DEF5" x="272" y="1248" />
<entity schema="qiita" name="column_ontology" color="D0DEF5" x="272" y="1504" />
<entity schema="qiita" name="command_output" color="B2CDF7" x="1760" y="1216" />
<entity schema="qiita" name="command_parameter" color="B2CDF7" x="2176" y="1040" />
<entity schema="qiita" name="controlled_vocab" color="D0DEF5" x="48" y="1248" />
<entity schema="qiita" name="controlled_vocab_values" color="D0DEF5" x="48" y="1376" />
<entity schema="qiita" name="data_directory" color="B2CDF7" x="576" y="1008" />
<entity schema="qiita" name="data_type" color="D0DEF5" x="704" y="1200" />
<entity schema="qiita" name="default_parameter_set" color="B2CDF7" x="2416" y="1168" />
<entity schema="qiita" name="default_workflow" color="B2CDF7" x="2656" y="1120" />
<entity schema="qiita" name="default_workflow_edge" color="B2CDF7" x="2640" y="1312" />
<entity schema="qiita" name="default_workflow_edge_connections" color="B2CDF7" x="2384" y="1424" />
<entity schema="qiita" name="default_workflow_node" color="B2CDF7" x="2416" y="1280" />
<entity schema="qiita" name="ebi_run_accession" color="B2CDF7" x="1344" y="1184" />
<entity schema="qiita" name="environmental_package" color="B2CDF7" x="2176" y="224" />
<entity schema="qiita" name="filepath" color="C0D4F3" x="640" y="832" />
<entity schema="qiita" name="filepath_type" color="C0D4F3" x="816" y="784" />
<entity schema="qiita" name="investigation" color="C0D4F3" x="2256" y="352" />
<entity schema="qiita" name="investigation_study" color="C0D4F3" x="2032" y="400" />
<entity schema="qiita" name="logging" color="C0D4F3" x="976" y="1376" />
<entity schema="qiita" name="message" color="A8C4EF" x="1504" y="1360" />
<entity schema="qiita" name="message_user" color="A8C4EF" x="1312" y="1344" />
<entity schema="qiita" name="mixs_field_description" color="D0DEF5" x="256" y="1360" />
<entity schema="qiita" name="oauth_identifiers" color="B7C8E3" x="2352" y="768" />
<entity schema="qiita" name="oauth_software" color="B2CDF7" x="2192" y="768" />
<entity schema="qiita" name="ontology" color="D0DEF5" x="576" y="1488" />
<entity schema="qiita" name="parameter_artifact_type" color="B2CDF7" x="1760" y="1120" />
<entity schema="qiita" name="parent_artifact" color="B2CDF7" x="1040" y="928" />
<entity schema="qiita" name="parent_processing_job" color="B2CDF7" x="2016" y="1472" />
<entity schema="qiita" name="per_study_tags" color="B2CDF7" x="2160" y="496" />
<entity schema="qiita" name="portal_type" color="C0D4F3" x="816" y="640" />
<entity schema="qiita" name="prep_template" color="B2CDF7" x="1232" y="512" />
<entity schema="qiita" name="prep_template_filepath" color="B2CDF7" x="1024" y="512" />
<entity schema="qiita" name="prep_template_processing_job" color="B2CDF7" x="1728" y="1008" />
<entity schema="qiita" name="prep_template_sample" color="D0DEF5" x="1136" y="304" />
<entity schema="qiita" name="prep_y" color="D0DEF5" x="992" y="320" />
<entity schema="qiita" name="processing_job" color="B2CDF7" x="1952" y="1168" />
<entity schema="qiita" name="processing_job_resource_allocation" color="C1D8EE" x="2624" y="1456" />
<entity schema="qiita" name="processing_job_status" color="B2CDF7" x="1760" y="1552" />
<entity schema="qiita" name="processing_job_validator" color="B2CDF7" x="2176" y="1472" />
<entity schema="qiita" name="processing_job_workflow" color="B2CDF7" x="2176" y="1584" />
<entity schema="qiita" name="processing_job_workflow_root" color="B2CDF7" x="2416" y="1584" />
<entity schema="qiita" name="publication" color="B2CDF7" x="2016" y="768" />
<entity schema="qiita" name="qiita_user" color="D0DEF5" x="592" y="384" />
<entity schema="qiita" name="reference" color="C0D4F3" x="2016" y="1584" />
<entity schema="qiita" name="restrictions" color="B2CDF7" x="1536" y="400" />
<entity schema="qiita" name="sample_template_filepath" color="B2CDF7" x="1040" y="656" />
<entity schema="qiita" name="sample_x" color="D0DEF5" x="1536" y="288" />
<entity schema="qiita" name="severity" color="C0D4F3" x="1120" y="1376" />
<entity schema="qiita" name="software" color="B2CDF7" x="2416" y="992" />
<entity schema="qiita" name="software_artifact_type" color="B2CDF7" x="1984" y="1008" />
<entity schema="qiita" name="software_command" color="B2CDF7" x="2176" y="1264" />
<entity schema="qiita" name="software_publication" color="B2CDF7" x="1984" y="864" />
<entity schema="qiita" name="software_type" color="B2CDF7" x="2640" y="992" />
<entity schema="qiita" name="stats_daily" color="B2CDF7" x="2496" y="368" />
<entity schema="qiita" name="study" color="D0DEF5" x="1792" y="288" />
<entity schema="qiita" name="study_artifact" color="B2CDF7" x="1600" y="800" />
<entity schema="qiita" name="study_environmental_package" color="B2CDF7" x="2096" y="80" />
<entity schema="qiita" name="study_person" color="C0D4F3" x="2016" y="176" />
<entity schema="qiita" name="study_portal" color="A8C4EF" x="1856" y="80" />
<entity schema="qiita" name="study_prep_template" color="D0DEF5" x="1504" y="528" />
<entity schema="qiita" name="study_publication" color="B2CDF7" x="1856" y="768" />
<entity schema="qiita" name="study_sample" color="D0DEF5" x="1360" y="288" />
<entity schema="qiita" name="study_tags" color="B2CDF7" x="2304" y="528" />
<entity schema="qiita" name="study_users" color="D0DEF5" x="1776" y="176" />
<entity schema="qiita" name="term" color="D0DEF5" x="736" y="1488" />
<entity schema="qiita" name="timeseries_type" color="C0D4F3" x="2016" y="576" />
<entity schema="qiita" name="user_level" color="D0DEF5" x="432" y="352" />
<entity schema="qiita" name="visibility" color="B2CDF7" x="1040" y="1152" />
<comment><![CDATA[qiita-db]]></comment>
<entity schema="qiita" name="analysis" color="D0DEF5" x="192" y="896" />
<entity schema="qiita" name="analysis_filepath" color="C0D4F3" x="384" y="848" />
<entity schema="qiita" name="analysis_portal" color="A8C4EF" x="224" y="736" />
<entity schema="qiita" name="analysis_sample" color="D0DEF5" x="368" y="976" />
<entity schema="qiita" name="analysis_users" color="D0DEF5" x="80" y="800" />
<entity schema="qiita" name="archive_feature_value" color="B2CDF7" x="1472" y="1472" />
<entity schema="qiita" name="archive_merging_scheme" color="B2CDF7" x="1248" y="1472" />
<entity schema="qiita" name="artifact" color="B2CDF7" x="1200" y="880" />
<entity schema="qiita" name="artifact_filepath" color="B2CDF7" x="1040" y="960" />
<entity schema="qiita" name="artifact_output_processing_job" color="B2CDF7" x="1760" y="1376" />
<entity schema="qiita" name="artifact_processing_job" color="B2CDF7" x="1728" y="1280" />
<entity schema="qiita" name="artifact_type" color="D0DEF5" x="1408" y="880" />
<entity schema="qiita" name="artifact_type_filepath_type" color="B2CDF7" x="1376" y="736" />
<entity schema="qiita" name="checksum_algorithm" color="B2CDF7" x="736" y="960" />
<entity schema="qiita" name="column_controlled_vocabularies" color="D0DEF5" x="272" y="1168" />
<entity schema="qiita" name="column_ontology" color="D0DEF5" x="272" y="1424" />
<entity schema="qiita" name="command_output" color="B2CDF7" x="1728" y="1136" />
<entity schema="qiita" name="command_parameter" color="B2CDF7" x="2192" y="960" />
<entity schema="qiita" name="controlled_vocab" color="D0DEF5" x="48" y="1168" />
<entity schema="qiita" name="controlled_vocab_values" color="D0DEF5" x="48" y="1296" />
<entity schema="qiita" name="data_directory" color="B2CDF7" x="576" y="928" />
<entity schema="qiita" name="data_type" color="D0DEF5" x="704" y="1120" />
<entity schema="qiita" name="default_parameter_set" color="B2CDF7" x="2416" y="1104" />
<entity schema="qiita" name="default_workflow" color="B2CDF7" x="2656" y="1040" />
<entity schema="qiita" name="default_workflow_edge" color="B2CDF7" x="2640" y="1232" />
<entity schema="qiita" name="default_workflow_edge_connections" color="B2CDF7" x="2384" y="1376" />
<entity schema="qiita" name="default_workflow_node" color="B2CDF7" x="2416" y="1232" />
<entity schema="qiita" name="ebi_run_accession" color="B2CDF7" x="1344" y="1104" />
<entity schema="qiita" name="environmental_package" color="B2CDF7" x="2176" y="176" />
<entity schema="qiita" name="filepath" color="C0D4F3" x="640" y="752" />
<entity schema="qiita" name="filepath_type" color="C0D4F3" x="816" y="704" />
<entity schema="qiita" name="investigation" color="C0D4F3" x="2176" y="272" />
<entity schema="qiita" name="investigation_study" color="C0D4F3" x="2000" y="384" />
<entity schema="qiita" name="logging" color="C0D4F3" x="976" y="1296" />
<entity schema="qiita" name="message" color="A8C4EF" x="1504" y="1280" />
<entity schema="qiita" name="message_user" color="A8C4EF" x="1312" y="1264" />
<entity schema="qiita" name="mixs_field_description" color="D0DEF5" x="272" y="1264" />
<entity schema="qiita" name="oauth_identifiers" color="B7C8E3" x="2352" y="688" />
<entity schema="qiita" name="oauth_software" color="B2CDF7" x="2192" y="688" />
<entity schema="qiita" name="ontology" color="D0DEF5" x="576" y="1408" />
<entity schema="qiita" name="parameter_artifact_type" color="B2CDF7" x="1728" y="1040" />
<entity schema="qiita" name="parent_artifact" color="B2CDF7" x="1040" y="848" />
<entity schema="qiita" name="parent_processing_job" color="B2CDF7" x="2016" y="1392" />
<entity schema="qiita" name="per_study_tags" color="B2CDF7" x="2192" y="528" />
<entity schema="qiita" name="portal_type" color="C0D4F3" x="768" y="560" />
<entity schema="qiita" name="prep_template" color="B2CDF7" x="1232" y="464" />
<entity schema="qiita" name="prep_template_filepath" color="B2CDF7" x="1024" y="416" />
<entity schema="qiita" name="prep_template_processing_job" color="B2CDF7" x="1728" y="928" />
<entity schema="qiita" name="prep_template_sample" color="D0DEF5" x="1152" y="304" />
<entity schema="qiita" name="prep_y" color="D0DEF5" x="992" y="304" />
<entity schema="qiita" name="processing_job" color="B2CDF7" x="1968" y="1072" />
<entity schema="qiita" name="processing_job_resource_allocation" color="C1D8EE" x="2656" y="1376" />
<entity schema="qiita" name="processing_job_status" color="B2CDF7" x="1728" y="1504" />
<entity schema="qiita" name="processing_job_validator" color="B2CDF7" x="2192" y="1392" />
<entity schema="qiita" name="processing_job_workflow" color="B2CDF7" x="2192" y="1504" />
<entity schema="qiita" name="processing_job_workflow_root" color="B2CDF7" x="2448" y="1504" />
<entity schema="qiita" name="publication" color="B2CDF7" x="1936" y="688" />
<entity schema="qiita" name="qiita_user" color="D0DEF5" x="704" y="288" />
<entity schema="qiita" name="reference" color="C0D4F3" x="2016" y="1504" />
<entity schema="qiita" name="restrictions" color="B2CDF7" x="1584" y="400" />
<entity schema="qiita" name="sample_template_filepath" color="B2CDF7" x="1008" y="560" />
<entity schema="qiita" name="sample_x" color="D0DEF5" x="1568" y="288" />
<entity schema="qiita" name="severity" color="C0D4F3" x="1120" y="1296" />
<entity schema="qiita" name="software" color="B2CDF7" x="2432" y="896" />
<entity schema="qiita" name="software_artifact_type" color="B2CDF7" x="1984" y="944" />
<entity schema="qiita" name="software_command" color="B2CDF7" x="2192" y="1184" />
<entity schema="qiita" name="software_publication" color="B2CDF7" x="1920" y="784" />
<entity schema="qiita" name="software_type" color="B2CDF7" x="2640" y="912" />
<entity schema="qiita" name="stats_daily" color="B2CDF7" x="2464" y="400" />
<entity schema="qiita" name="study" color="D0DEF5" x="1776" y="208" />
<entity schema="qiita" name="study_artifact" color="B2CDF7" x="1600" y="720" />
<entity schema="qiita" name="study_environmental_package" color="B2CDF7" x="2176" y="80" />
<entity schema="qiita" name="study_person" color="C0D4F3" x="2000" y="224" />
<entity schema="qiita" name="study_portal" color="A8C4EF" x="1920" y="80" />
<entity schema="qiita" name="study_prep_template" color="D0DEF5" x="1536" y="560" />
<entity schema="qiita" name="study_publication" color="B2CDF7" x="1792" y="688" />
<entity schema="qiita" name="study_sample" color="D0DEF5" x="1376" y="288" />
<entity schema="qiita" name="study_tags" color="B2CDF7" x="2176" y="416" />
<entity schema="qiita" name="study_users" color="D0DEF5" x="1776" y="96" />
<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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