fix #2622 #2646

antgonza · 2018-08-23T15:29:45Z

Screenshots:

Menu

Software Display

codecov-io · 2018-08-24T17:40:25Z

Codecov Report

Merging #2646 into dev will increase coverage by <.01%.
The diff coverage is 98.21%.

@@            Coverage Diff             @@
##              dev    #2646      +/-   ##
==========================================
+ Coverage   94.34%   94.35%   +<.01%     
==========================================
  Files         164      166       +2     
  Lines       19416    19457      +41     
==========================================
+ Hits        18318    18358      +40     
- Misses       1098     1099       +1

Impacted Files	Coverage Δ
qiita_pet/handlers/software.py	`100% <100%> (ø)`
qiita_pet/webserver.py	`100% <100%> (ø)`	⬆️
qiita_db/software.py	`98% <100%> (ø)`	⬆️
qiita_db/test/test_software.py	`99.81% <100%> (ø)`	⬆️
qiita_pet/test/test_software.py	`93.33% <93.33%> (ø)`

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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ElDeveloper

Looks good, just a couple of changes in the code.

As for some feedback on the UI, I think the inner table (the one with the plugin commands) is a little bit redundant. I would make it a single column and put the icons on the left of each command's name for example:

👍 Split libraries FASTQ
👍 Split libraries
👍 Pick closed-reference OTUs

I would also move the "outer Active" column to the left.

ElDeveloper · 2018-08-28T23:14:38Z

qiita_pet/handlers/software.py

+class SoftwareHandler(BaseHandler):
+    def check_access(self):
+        if self.current_user.level not in {'admin', 'dev'}:
+            raise HTTPError(405, reason="User %s doesn't have sufficient "


Minor, but this should be a 403 error.

k, replacing everywhere ...

ElDeveloper · 2018-08-28T23:15:30Z

qiita_pet/handlers/software.py

+        if self.current_user.level not in {'admin', 'dev'}:
+            raise HTTPError(405, reason="User %s doesn't have sufficient "
+                            "privileges to view error page" %
+                            self.current_user)


This should be self.current_user.email (I think), otherwise the message will format the default Python repr i.e. <qiita_db.user.User object at 0x10cceb150>.

ElDeveloper · 2018-08-28T23:23:28Z

qiita_pet/templates/software.html

+    </table>
+  {% else %}
+      <div id="jumbotron" class="jumbotron">
+          <h1><span class="glyphicon glyphicon-thumbs-down"></span> There is no plugin software in this system </h1>


What about: There are no plugins in this system.

antgonza · 2018-08-28T23:35:04Z

I think the information is important because a plugin can be active while a command can be not active ... cause we disable it or something went wrong ... so I rather keep it ...

ElDeveloper · 2018-08-28T23:37:59Z

My bad, I meant to say that you should keep that information, just not as its own column. The table can become a single column if you put two the status and the name in the same column. That's what I was trying to refer to with my example above (I was just referring to the inner tables).

antgonza · 2018-08-28T23:46:02Z

Now, it looks like this:

ElDeveloper · 2018-08-29T00:50:18Z

Awesome, looks great! Tests seem to be failing though.

codecov-io · 2018-08-29T12:42:13Z

Codecov Report

Merging #2646 into dev will increase coverage by <.01%.
The diff coverage is 98.33%.

@@            Coverage Diff             @@
##              dev    #2646      +/-   ##
==========================================
+ Coverage   94.34%   94.35%   +<.01%     
==========================================
  Files         164      166       +2     
  Lines       19416    19457      +41     
==========================================
+ Hits        18318    18358      +40     
- Misses       1098     1099       +1

Impacted Files	Coverage Δ
qiita_pet/handlers/software.py	`100% <100%> (ø)`
qiita_pet/handlers/logger_handlers.py	`69.56% <100%> (ø)`	⬆️
qiita_pet/test/test_logger.py	`92.3% <100%> (ø)`	⬆️
qiita_db/software.py	`98% <100%> (ø)`	⬆️
qiita_pet/webserver.py	`100% <100%> (ø)`	⬆️
qiita_db/test/test_software.py	`99.81% <100%> (ø)`	⬆️
qiita_pet/test/test_software.py	`93.33% <93.33%> (ø)`

Continue to review full report at Codecov.

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ElDeveloper · 2018-08-29T18:06:21Z

Thanks @antgonza

@ElDeveloper

* fix #1067 * addressing @ElDeveloper comments * fix #2512 * fix #1999 (#2514) * fix #1999 * fix template error * rm maintenance conditional * some improvements * fix #1053 * addressing @ElDeveloper comments * adding secret * WIP: EBI-ENA test (#2516) * fix Keemei (#2510) * rename preprocessed_data_id artifact-id * prints to debug * Keemei fix (#2517) * fix Keemei * delete keemei * keemei delete * rewrite_fastq=True * rmtree * add : * testing EBI * add secure * travis tests * @ElDeveloper key! * Fix typo * fix secure * rm single quote * Fix 2321 (#2522) * fix Keemei (#2510) * fix #2321 * fixing get studies * fix qiita_db * addressing @ElDeveloper comments * fixing error with skipIf * Illumina models 0318 (#2532) * fix Keemei (#2510) * updating illumina models * adding secure * Update index.rst (#2533) * fix Keemei (#2510) * Keemei fix (#2517) * fix Keemei * delete keemei * keemei delete * Update index.rst * Plugin API Doc (#2534) * fix Keemei (#2510) * plugin-api * improve format * Fix 1810 (#2523) * fix Keemei (#2510) * fix #2321 * fixing get studies * fix qiita_db * fix #1810 * adding self.ascp_pass * fix flake8 * flake8 * DOC: Cleanup of JavaScript libraries and licenses (#2536) * DOC: Cleanup of JavaScript libraries and licenses There were a few JavaScript files that were not used anywhere and we were missing a handful of license files. I've cleaned up all of that (and for consistency made all the "licence" into "license"). Fixes #2535 * DOC: Document all the JS files * BUG: Add natural sorting for data tables * adding initial download/redbiom info * adding docs * addressing @ElDeveloper comments * Fix aid str workflow (#2537) * fix Keemei (#2510) * fix int/str errors with workflows * adding a patch to fix all ints parameters * all -> any patch 64 * fix #2519 * fix #2524 * fix #2531 * fix #2529 * split qiita-cron-job into multiple commands * rm leftover docs * Update downloading.rst * fix_reference_order (#2547) * addressing @stephanieorch comments * addressing @ElDeveloper comments * Fix 2492 (#2544) * fix Keemei (#2510) * fix #2492 * flake8 * Redbiom -> redbiom @wasade * addressing @wasade comments * Update .travis.yml * Fix 2505 (#2545) * fix Keemei (#2510) * fix #2505 * fix errors * '' -> 'not provided' * Fix 2530 (#2546) * fix #2530 * fix errors * missed 1 error * more erros * fix-secure * improve available files display * fix flake8 * fix #2580 (#2584) * fix #2581 (#2583) * fixed analysis page figure (#2578) * fixed analysis page figure * removed "missing:" from null values * fix #2570 (#2586) * fix #2590 * improve sample summary speed (#2591) * fix #2562 (#2588) * fix #2562 * address @ElDeveloper comments * Update sampleTemplateVue.js * Fix 2565 (#2587) * fix #2565 * rm extra if in make-public * fix #2574 (#2585) * fix #2574 * fix error * fix ebi submission error * fix ebi assertin * adding qiimp via iframes (#2582) * adding qiimp via iframes * addressing @ElDeveloper comments * addressing #AmandaBirmingham comment * fix-test * allow to hide job via GUI (#2593) * allow to hide job via GUI * address @ElDeveloper comment * Fix upload and faq page (#2594) * fixed uplaod and faq page * fixed uplaod and faq page * fixed code and uplaod explanations * fixed code and uplaod explanations * Update upload.html * fix error * fixing bugs found during initial review * fix bug in delete column sample template (#2597) * Add qiimp xlsx (#2599) * fix-secure * improve available files display * initial code for accepting xlsx qiimp files * adding more tests and valid python 2.7 code for openpyxl * adding empty test to load_template_to_dataframe * addressing @ElDeveloper comment * rm qiimp link * Rm qiimp link (#2603) * fix-secure * improve available files display * rm qiimp link * fix #2606 * select all/none from upload * fix #2610 (#2616) * fix #2602 * fix #2601 (#2617) * fix #2601 * sphere->circle * circle_name -> var circle_name * adding ChangeLog message * TRAVIS_PULL_REQUEST -> TRAVIS_BRANCH * addressing @adswafford comment * add ignore parent for command merging scheme (#2619) * add ignore parent for command merging scheme * fix error * adding get_validator_jobs (#2620) * adding get_validator_jobs * fix error with val_job * addressing @ElDeveloper comments * fixes #2629 changed button text from Select None to Unselect All * fixes #2629 changed button text from Select None to Unselect All (#2631) * Labman minimal changes (#2633) * adding SampleInfoDBHandler * adding UserInfoDBHandlerTests * fix error * addressing @ElDeveloper comments * adding ssh backend support * rm QiitaStudySearch (#2638) * rm QiitaStudySearch * rm import search * fixing error * added paramiko * Fix 2635 (#2639) * rm QiitaStudySearch * rm import search * fixing error * fix #2635 * returning private status to preps in test_generate_study_list * addressing @ElDeveloper comments * fix #2627 (#2640) * install scp package for python * adds UsersListDBHandler (#2636) * adds UsersListDBHandler * addressing @ElDeveloper comments * rm leftover lines * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * fix #2632 (#2643) * fix #2632 * fixing error * fix #2608 * fix #2600 * start of edits to the upload page for SCP gui * fix #2622 (#2646) * fix #2622 * fix error * addressing @ElDeveloper comments * fix errors * Fix 2623 (#2644) * fix #2632 * fixing error * initial GUI changes * fix #2623 * sid only once * fix errors * addressing @ElDeveloper comments * fix error * @ElDeveloper comment sample_name -> sample_names * Add specimen_id attribute to the study object (#2649) * Add specimen identifier to the study table * Add specimen_id_column to study object This also adds tests and updates the DBS file, and patch (which was broken before). * ENH: Add unique_columns method to template objects * Remove maxDiff * ENH: Send response data back to the client * Make study's specimen_id_column nullable * Generalize study_tags_patch_request to be study-wide * Add Study patch handler And update tests, etc * Update UI with the new patch handlers * Add missing attribute * ENH: Add prepopulate of the UI * ENH: Add checks to prevent deletion of a specimen_id column * DOC: Delete comment * TST: Fix broken tests * PERF: Don't precompute unique columns * ENH: Add help and make specimen column deselectable * ENH: Sort column names * BUG: Fix column width for update button * DOC: Remove reference to labman * fix #2651 and partial #2652 * Fixes #2398 Strips UTF-8 characters from study titles UTF-8 characters that are not also printable ASCII characters are stripped from new study titles, as well as existing studies flagged 'public'. This is because study titles are passed as metadata to new analyses, and some analysis packages may not work well with them. * Resolving conflict with another new patch file. * Rename file * 67.py renamed to 66.py. minor edit to edit_study.html * Update study title only if UTF-8 characters were removed. * addressing @ElDeveloper comments * fix _get_valid_files * glob.glob -> glob * fix error * fix error * bringing back download_remote * improving tests * rm docstrings as requested by @ElDeveloper * fixing tests - remote_files->local_files * Scp (#2660) * fixes #2629 changed button text from Select None to Unselect All * adding ssh backend support * added paramiko * install scp package for python * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * addressing @ElDeveloper comments * fix _get_valid_files * glob.glob -> glob * fix error * fix error * bringing back download_remote * improving tests * rm docstrings as requested by @ElDeveloper * fixing tests - remote_files->local_files * Fixes #1802 (#2659) Password validation extended to allow only printable ASCII characters A custom validator was written to check whether a password string contains any UTF-8 characters that are not also printable ASCII characters and return false. if true. * init scp-gui * finishing scp-gui * Fixes #2398 (#2658) * Fixes #2398 Strips UTF-8 characters from study titles UTF-8 characters that are not also printable ASCII characters are stripped from new study titles, as well as existing studies flagged 'public'. This is because study titles are passed as metadata to new analyses, and some analysis packages may not work well with them. * Resolving conflict with another new patch file. * Rename file * 67.py renamed to 66.py. minor edit to edit_study.html * Update study title only if UTF-8 characters were removed. * UTF-8 stripper now processes all study-types. Code wrapped in a for loop and iterates through a list of known Study status-types; seems a little cleaner than union-ing multiple result sets. * 66.py now passes flake8 tests. * Plugin outdate version (#2664) * adding GUI changes for deprecated artifacts * fixing some tests * pull upstream dev * addressing @ElDeveloper comments * fixing errors * fixing more errors * update europeanbioinformaticsinstitute * improve ebi submission * Qsub scripts (#2667) * ADD: qsub scripts in use on qiita.ucsd.edu: * STY: flake8 * flake8 * adding changelog for this release * adding plugin updates * Dev 2553 (#2668) * minor spelling change * Migrating to per-template forbidden-words list Removed validate_invalid_column_names() from util.py, as its behavior was very specific to the needs of MetadataTemplate._clean_validate_template(). Decomposed validate_invalid_column_names() into separate methods, each validating separate concerns (invalid characters, pgsql reserved words, forbidden words). MetadataTemplate, and each Template sub-class will contain their own list of forbidden words. Currently, forbidden list is explicitly passed down call-stack; will clean-up as appropriate. * Removed explicit passing of forbidden words. Classes and tests now rely on member variable _forbidden_words to define the list of forbidden words for that Template. * Basic tests recreated for new helper methods _identify_forbidden_words_in_column_names, _identify_pgsql_reserved_words_in_column_names, and _identify_column_names_with_invalid_characters now have test cases. * Fixes #2553 Supports per-template forbidden words Support for per-template forbidden word lists. Unit tests supporting changes in util.py, base_metadata_template, etc. added. * Removed Python3 import-conditional Import import-conditional inherited from util.py * Removed docstrings for new tests. Removed docstrings for new tests. Replaced second import of quitta_db constant with a module-wide variable. * Removed PY3 from import * Modified docstring for clean_validate_template Silent dropping of 'qiita_study_id' and 'qiita_prep_id' added in docstring. * Updated comment * Modified unit-tests MetadataTemplate list of forbidden words changed to {}. Migrated forbidden_words unittest from test_base_metadata_template.py to test_sample_template.py, to give it a defined list of words to test against. Removed previously commented-out tests. * Changed _forbidden_words to be empty set {} * Removed comment * Flake8-compliant comments * SampleTemplate category names changed Category names changed from forbidden words (primer, barcode, run_prefix) to alternatives. * Added unittest to confirm silent drops Unittest confirms silent dropping of qiita_prep_id and qiita_study_id from parameter value for clean_validate_template(). * Fix Tests A few tests should be testing with assertEquals, rather than assertTrue. * Modified test to use assertEquals Test modified to use assertEquals, over assertTrue. * Replaced AssertTrue w/AssertEquals * Test modified to use assertEquals needed minor flake8 * assertItemsEqual assertion fix * fix artifact listing * checking for upload_folder * Change priority of password validation messages 'No UTF-8 characters' and 'Passwords do not match' no prioritized over password-length message. * fix scp instructions * addressing @tkosciol comment

@ElDeveloper

* fix #1067 * addressing @ElDeveloper comments * fix #2512 * fix #1999 (#2514) * fix #1999 * fix template error * rm maintenance conditional * some improvements * fix #1053 * addressing @ElDeveloper comments * adding secret * WIP: EBI-ENA test (#2516) * fix Keemei (#2510) * rename preprocessed_data_id artifact-id * prints to debug * Keemei fix (#2517) * fix Keemei * delete keemei * keemei delete * rewrite_fastq=True * rmtree * add : * testing EBI * add secure * travis tests * @ElDeveloper key! * Fix typo * fix secure * rm single quote * Fix 2321 (#2522) * fix Keemei (#2510) * fix #2321 * fixing get studies * fix qiita_db * addressing @ElDeveloper comments * fixing error with skipIf * Illumina models 0318 (#2532) * fix Keemei (#2510) * updating illumina models * adding secure * Update index.rst (#2533) * fix Keemei (#2510) * Keemei fix (#2517) * fix Keemei * delete keemei * keemei delete * Update index.rst * Plugin API Doc (#2534) * fix Keemei (#2510) * plugin-api * improve format * Fix 1810 (#2523) * fix Keemei (#2510) * fix #2321 * fixing get studies * fix qiita_db * fix #1810 * adding self.ascp_pass * fix flake8 * flake8 * DOC: Cleanup of JavaScript libraries and licenses (#2536) * DOC: Cleanup of JavaScript libraries and licenses There were a few JavaScript files that were not used anywhere and we were missing a handful of license files. I've cleaned up all of that (and for consistency made all the "licence" into "license"). Fixes #2535 * DOC: Document all the JS files * BUG: Add natural sorting for data tables * adding initial download/redbiom info * adding docs * addressing @ElDeveloper comments * Fix aid str workflow (#2537) * fix Keemei (#2510) * fix int/str errors with workflows * adding a patch to fix all ints parameters * all -> any patch 64 * fix #2519 * fix #2524 * fix #2531 * fix #2529 * split qiita-cron-job into multiple commands * rm leftover docs * Update downloading.rst * fix_reference_order (#2547) * addressing @stephanieorch comments * addressing @ElDeveloper comments * Fix 2492 (#2544) * fix Keemei (#2510) * fix #2492 * flake8 * Redbiom -> redbiom @wasade * addressing @wasade comments * Update .travis.yml * Fix 2505 (#2545) * fix Keemei (#2510) * fix #2505 * fix errors * '' -> 'not provided' * Fix 2530 (#2546) * fix #2530 * fix errors * missed 1 error * more erros * fix-secure * improve available files display * fix flake8 * fix #2580 (#2584) * fix #2581 (#2583) * fixed analysis page figure (#2578) * fixed analysis page figure * removed "missing:" from null values * fix #2570 (#2586) * fix #2590 * improve sample summary speed (#2591) * fix #2562 (#2588) * fix #2562 * address @ElDeveloper comments * Update sampleTemplateVue.js * Fix 2565 (#2587) * fix #2565 * rm extra if in make-public * fix #2574 (#2585) * fix #2574 * fix error * fix ebi submission error * fix ebi assertin * adding qiimp via iframes (#2582) * adding qiimp via iframes * addressing @ElDeveloper comments * addressing #AmandaBirmingham comment * fix-test * allow to hide job via GUI (#2593) * allow to hide job via GUI * address @ElDeveloper comment * Fix upload and faq page (#2594) * fixed uplaod and faq page * fixed uplaod and faq page * fixed code and uplaod explanations * fixed code and uplaod explanations * Update upload.html * fix error * fixing bugs found during initial review * fix bug in delete column sample template (#2597) * Add qiimp xlsx (#2599) * fix-secure * improve available files display * initial code for accepting xlsx qiimp files * adding more tests and valid python 2.7 code for openpyxl * adding empty test to load_template_to_dataframe * addressing @ElDeveloper comment * rm qiimp link * Rm qiimp link (#2603) * fix-secure * improve available files display * rm qiimp link * fix #2606 * select all/none from upload * fix #2610 (#2616) * fix #2602 * fix #2601 (#2617) * fix #2601 * sphere->circle * circle_name -> var circle_name * adding ChangeLog message * TRAVIS_PULL_REQUEST -> TRAVIS_BRANCH * addressing @adswafford comment * add ignore parent for command merging scheme (#2619) * add ignore parent for command merging scheme * fix error * adding get_validator_jobs (#2620) * adding get_validator_jobs * fix error with val_job * addressing @ElDeveloper comments * fixes #2629 changed button text from Select None to Unselect All (#2631) * Labman minimal changes (#2633) * adding SampleInfoDBHandler * adding UserInfoDBHandlerTests * fix error * addressing @ElDeveloper comments * rm QiitaStudySearch (#2638) * rm QiitaStudySearch * rm import search * fixing error * Fix 2635 (#2639) * rm QiitaStudySearch * rm import search * fixing error * fix #2635 * returning private status to preps in test_generate_study_list * addressing @ElDeveloper comments * fix #2627 (#2640) * adds UsersListDBHandler (#2636) * adds UsersListDBHandler * addressing @ElDeveloper comments * rm leftover lines * fix #2632 (#2643) * fix #2632 * fixing error * fix #2608 * fix #2600 * fix #2622 (#2646) * fix #2622 * fix error * addressing @ElDeveloper comments * fix errors * Fix 2623 (#2644) * fix #2632 * fixing error * initial GUI changes * fix #2623 * sid only once * fix errors * addressing @ElDeveloper comments * fix error * @ElDeveloper comment sample_name -> sample_names * Add specimen_id attribute to the study object (#2649) * Add specimen identifier to the study table * Add specimen_id_column to study object This also adds tests and updates the DBS file, and patch (which was broken before). * ENH: Add unique_columns method to template objects * Remove maxDiff * ENH: Send response data back to the client * Make study's specimen_id_column nullable * Generalize study_tags_patch_request to be study-wide * Add Study patch handler And update tests, etc * Update UI with the new patch handlers * Add missing attribute * ENH: Add prepopulate of the UI * ENH: Add checks to prevent deletion of a specimen_id column * DOC: Delete comment * TST: Fix broken tests * PERF: Don't precompute unique columns * ENH: Add help and make specimen column deselectable * ENH: Sort column names * BUG: Fix column width for update button * DOC: Remove reference to labman * fix #2651 and partial #2652 * Fixes #2398 Strips UTF-8 characters from study titles UTF-8 characters that are not also printable ASCII characters are stripped from new study titles, as well as existing studies flagged 'public'. This is because study titles are passed as metadata to new analyses, and some analysis packages may not work well with them. * Resolving conflict with another new patch file. * Rename file * 67.py renamed to 66.py. minor edit to edit_study.html * Update study title only if UTF-8 characters were removed. * Scp (#2660) * fixes #2629 changed button text from Select None to Unselect All * adding ssh backend support * added paramiko * install scp package for python * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * testing scp directly in travis * addressing @ElDeveloper comments * fix _get_valid_files * glob.glob -> glob * fix error * fix error * bringing back download_remote * improving tests * rm docstrings as requested by @ElDeveloper * fixing tests - remote_files->local_files * UTF-8 stripper now processes all study-types. Code wrapped in a for loop and iterates through a list of known Study status-types; seems a little cleaner than union-ing multiple result sets. * 66.py now passes flake8 tests. * Additional Processing Command functionality Software.Command extended to support additional metadata regarding extra processing that may be required to merge BIOMs. * Additional Processing Command functionality Software.Command extended to support additional metadata regarding extra processing that may be required to merge BIOMs. * Fixed bug Added conditional check, where it was missing * Pass flake8 Last-minute comment did not meet flake8's approval. * Fix _method in Click _methods renamed to Qmethods * Specified Click 6.7 as a dependency * Misc cleanup Comments modified as requested. 'Q-functions' in qiita-recover-jobs have been reverted to begin with '_'. * Modified qiita-db.dbs Modified qiita-db.dbs to include additional column defined in software_command table. * Added comment metadata to new column. * Refined tests * Replaced Qtest w/_test * Reverted functions beginning w/Q to '_'.

antgonza added 2 commits August 23, 2018 09:27

fix qiita-spots#2622

fa41dff

fix error

048371a

antgonza requested a review from ElDeveloper August 28, 2018 18:23

ElDeveloper suggested changes Aug 28, 2018

View reviewed changes

Merge branch 'dev' of https://github.com/biocore/qiita into fix-2622

862611b

addressing @ElDeveloper comments

18a51a8

ElDeveloper approved these changes Aug 29, 2018

View reviewed changes

fix errors

504f2fd

ElDeveloper merged commit 000c423 into qiita-spots:dev Aug 29, 2018

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fix #2622 #2646

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