* 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 '_'.

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admin display to see active plugins and commands #2622

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