Scp #2660

antgonza · 2018-09-05T01:22:10Z

No description provided.

codecov-io · 2018-09-05T13:16:03Z

Codecov Report

Merging #2660 into dev will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #2660   +/-   ##
=======================================
  Coverage   94.38%   94.38%           
=======================================
  Files         166      166           
  Lines       19563    19563           
=======================================
  Hits        18465    18465           
  Misses       1098     1098

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ElDeveloper · 2018-09-05T13:56:13Z

qiita_ware/commands.py

+    scheme = p_url.scheme
+    # note that scp/sftp's code seems similar but the local_path/localpath
+    # variable is different within the for loop
+    if scheme == 'scp':


From my previous review

I think this can be broken down to be a bit simpler, for example:

if scheme == 'scp': client = SCPClient(ssh.get_transport()) elif scheme == 'sftp': client = ssh.open_sftp() for f in file_paths: download = partial(client.get, local_path=join(destination, basename(f))) download(f)

Also it should throw an exception if the scheme is not supported.

Sorry, forgot to mention this.

The split is not really possible because, as the note above says, scp and sftp use a different variable local_path vs localpath; and couldn't figure out how to make it play nice with your above coment - note that most of the pushes were due errors on these lines.

The exception is gonna be thrown a few lines above, when: ssh = _ssh_session(p_url, private_key)

I see, thanks for pointing that out. Subtle differences in the api 😑

ElDeveloper · 2018-09-05T13:57:51Z

qiita_ware/private_plugin.py

+        url = job.parameters.values['url']
+        private_key = job.parameters.values['private_key']
+        try:
+            list_remote(url, private_key)


From my previous review:

What is happening to the output of this function, it seems like it is not being utilized anywhere and that this job does nothing(?)

... also forgot to add a message ... this will store the information in redis so the GUI can retrieve it ... I'm working on this PR and should be ready pretty soon.

I see, so the redis support will be added in the next PR?

yup, yup ...

ElDeveloper · 2018-09-05T14:01:17Z

qiita_ware/test/test_commands.py

+        self.assertEqual(remote_filename_list, self.exp_files)
+
+    def test_download_sftp(self):
+        """Tests remote file listing using private key and sftp"""


Although this was my previous comment:

should be Tests remote file downloading ...

I think we stopped adding docstrings to test cases so I would suggest removing them altogether.

ElDeveloper

Just a few comments that weren't addressed from my previous review.

ElDeveloper · 2018-09-05T14:19:18Z

qiita_ware/commands.py

+        sftp = ssh.open_sftp()
+        for f in file_paths:
+            download = partial(
+                sftp.get, localpath=join(destination, basename(f)))


This for loop is missing a download call right? Since the tests are passing I assume this is not being tested?

great catch! There are tests but turns out that I remove the wrong line when simplifying the code ... fixing ...

ElDeveloper · 2018-09-05T16:24:12Z

Thanks!

antgonza · 2018-09-05T16:26:45Z

Thanks!!

@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 '_'.

ryanusahk and others added 14 commits July 24, 2018 10:59

fixes #2629 changed button text from Select None to Unselect All

af36c83

adding ssh backend support

067cb45

Merge branch 'dev' of http://github.com/biocore/qiita into scp

780f51b

added paramiko

363ad9c

install scp package for python

e2df641

testing scp directly in travis

0e79a43

testing scp directly in travis

82b2ae2

testing scp directly in travis

9b51ba8

testing scp directly in travis

65279e8

testing scp directly in travis

29a4409

testing scp directly in travis

dcf6088

Merge branch 'dev' of http://github.com/biocore/qiita into scp

6642710

upstream master

f2d6699

addressing @ElDeveloper comments

cbbf088

antgonza mentioned this pull request Sep 5, 2018

Adding SCP support #2642

Closed

antgonza added 6 commits September 4, 2018 19:41

fix _get_valid_files

70dd0a0

glob.glob -> glob

f7a66dd

fix error

6c58c43

fix error

71aef4f

bringing back download_remote

7b4cb69

improving tests

5d605d0

ElDeveloper reviewed Sep 5, 2018

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ElDeveloper approved these changes Sep 5, 2018

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rm docstrings as requested by @ElDeveloper

b8607aa

ElDeveloper reviewed Sep 5, 2018

View reviewed changes

fixing tests - remote_files->local_files

558b1c3

ElDeveloper merged commit c723359 into dev Sep 5, 2018

antgonza deleted the scp branch September 5, 2018 17:19

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Scp #2660

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antgonza Sep 5, 2018 •

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