fix #3076 #3077
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fix #3076 #3077
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Codecov Report
@@ Coverage Diff @@
## dev #3077 +/- ##
=======================================
Coverage 95.02% 95.03%
=======================================
Files 74 74
Lines 14279 14311 +32
=======================================
+ Hits 13569 13600 +31
- Misses 710 711 +1
Continue to review full report at Codecov.
|
ElDeveloper
suggested changes
Feb 22, 2021
Comment on lines
269
to
276
| 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)) |
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Any reason not to use assertRaisesRegex?
Suggested change
| 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)) | |
| 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')) |
| '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) |
There was a problem hiding this comment.
Can you add this to the docstring?
|
I'll address your suggestions soon. The changes are cause I downloaded the latest version of the DBSchema software and generated the html with the latest version so it's clearer; in other words, nothing really changed just the files to the latest version. |
|
Makes sense, thanks! |
|
Thanks @antgonza |
antgonza
added a commit
that referenced
this pull request
Mar 19, 2021
* adding creation and modification timestamps to prep_templates (#3066) * adding creation and modification timestamps to prep_templates * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * fix #3068 (#3069) * minor improvements (#3067) * minor improvements * fix test * adding @wasade suggestion * minor fixes (#3073) * fix #3072 (#3074) * fix #3072 * flake8 * fix #3076 (#3077) * fix #3076 * addressing @ElDeveloper comments * fix #3070 (#3075) * fix #3070 * Apply suggestions from code review Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * flake8 Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * fix-3064 (#3080) * Create qiita-ci.yml * add passwd to psql * nginx + redis * redis via conda * redis-server - -> redis-server -- * daemonize -> daemonize * conda libevent * apt-get libevent-dev * adding multiple sections * rm travis_retry * add missing activagte * onfig_test.cfg * rm indent * add 1 indent * pgport * add drop * change db name * redis version * redis -> redbiom version * split tests * source .profile * adding ssh command * mkdir ~/.ssh/ * only ssh * pushing to retrigger * add run * split ssh conf/run * 60367309 * add bash * fix ident * rm ssh cmd * strict=no * localhost * mod permissions * user ssh * rm keys * echos * start ssh service * ssh -vvv * split setup/test * localhost -> 127 * localhost -> 127 * rm ssh setup * -o StrictHostKeyChecking=no * change key creation * echo sshd_config * readd ssh config * cp sshd_config and then move * rm echos * extra qiita folder * ls test_data * rm qiita folder * use key in .ssh * more ssh params * tee -> > * chmod * fullpath * ls key * rm localhost * params * rsa -> rsa-sha2-256 * rm root login * readd -o StrictHostKeyChecking=no * minimizing params * permissions * cleaning up * comments => echo * -o StrictHostKeyChecking=no * export REDBIOM_HOST=http://127.0.0.1:7379 * localhost -> 127.0.0.1 * add runner * cover package * cleaning env vars * renaming jobs * redbiom host * add env vars via export * changing echo * add env COVER_PACKAGE * rm user sftp * just qiita_db * open_sftp -> SFTPClient * +1 worker * only SCPClient * ssh.SCPClient -> SCPClient * return sftp/ssh back * just qiita_db * rm sftp * add all tests * BASE_URL = https://127.0.0.1:8383 * bash -c * start_biom * start_biom 127 * populate QIITA_SERVER_CERT * nginx 127 * adding ports to conf * lowering ports * service qiita * 8383 postgres * curl test * mkdir nginx * moving tests around * moving curl up * echos for curl * sleep 10 * 127.0.0.1 -> localhost * returning some localhost to 127... * qiita_pet! * final clean up * kill qiita first * addreesing @ElDeveloper comments * checkout repo for flake8 * split cover_package * Workflows GUI (#3078) * fix #3076 * addressing @ElDeveloper comments * adding workflows GUI * improve HTML * db changes and improvements * comment out new db changes * rm default_workflows from PluginHandler.get * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * fix #3081 (#3082) * fix #3081 * generate_analysis_list_per_study to speed up retrival * minor modifications * split sql * addressing @ElDeveloper comments * add Command.processing_jobs (#3085) * add Command.processing_jobs * Update qiita_db/software.py [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * Improve workflows (#3083) * fix #3076 * addressing @ElDeveloper comments * adding workflows GUI * improve HTML * db changes and improvements * comment out new db changes * rm default_workflows from PluginHandler.get * improving workflows after deployment * fix error * clean up * minor fixes * improving html * comments from @justinshaffer * addressing @ElDeveloper comments * 2021.03 (#3084) * 2021.03 * add Command.processing_jobs to changelog * codecov * codecov required * codecov token Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu>
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Extra from fixing the above issue, this is also updating to the latests version of DbSchema the qdb/html files.