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DIG-1663: Implement curator ingest in katsu and batch ingest #666
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We shouldn't merge this until CanDIG/katsu#238 is approved and merged, will need to update the katsu submodule too |
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Please remove the commits to lib/candigv2-ingest and lib/katsu as they are already merged. This will help us avoid any conflicts.
I also have a couple of comments that are out of scope for this PR:
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I don't think they are out of scope, if we want to change them we can incorporate it into this PR
Do you have a suggestion for how to split them up?
I don't really understand what you mean by this, can you give an example? |
Yes, it's out of scope for now, but we can create a ticket to address it during the redesign. Line 120, it set admin to default user def add_program_authorization(dataset: str, curators: list = [ENV['CANDIG_SITE_ADMIN_USER']],
team_members: list = [ENV['CANDIG_SITE_ADMIN_USER']]): |
* fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth
…nstructions (#667) * updating submodules * Update pip * Update Makefile * Update requirements.txt * remove update setuptools * setuptools first * Update requirements.txt * Update example.env * Update Makefile * manually update setuptools * remove setuptools * Update example.env * remove setuptools * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com>
* fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth
…nstructions (#667) * updating submodules * Update pip * Update Makefile * Update requirements.txt * remove update setuptools * setuptools first * Update requirements.txt * Update example.env * Update Makefile * manually update setuptools * remove setuptools * Update example.env * remove setuptools * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com>
…inated (#668) * updating submodules * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth * CanDIG/candigv2-ingest merging: DIG-1658: Update commandline ingest instructions (#667) * updating submodules * Update pip * Update Makefile * Update requirements.txt * remove update setuptools * setuptools first * Update requirements.txt * Update example.env * Update Makefile * manually update setuptools * remove setuptools * Update example.env * remove setuptools * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com> --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com>
* fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth
…nstructions (#667) * updating submodules * Update pip * Update Makefile * Update requirements.txt * remove update setuptools * setuptools first * Update requirements.txt * Update example.env * Update Makefile * manually update setuptools * remove setuptools * Update example.env * remove setuptools * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com>
…inated (#668) * updating submodules * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth * CanDIG/candigv2-ingest merging: DIG-1658: Update commandline ingest instructions (#667) * updating submodules * Update pip * Update Makefile * Update requirements.txt * remove update setuptools * setuptools first * Update requirements.txt * Update example.env * Update Makefile * manually update setuptools * remove setuptools * Update example.env * remove setuptools * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com> --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com>
… bugs, and styling changes (#670) * updating submodules * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth * CanDIG/candigv2-ingest merging: DIG-1658: Update commandline ingest instructions (#667) * updating submodules * Update pip * Update Makefile * Update requirements.txt * remove update setuptools * setuptools first * Update requirements.txt * Update example.env * Update Makefile * manually update setuptools * remove setuptools * Update example.env * remove setuptools * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com> * CanDIG/candigv2-query merging: Bugfix: sidebar cohort style pipeDeliminated (#668) * updating submodules * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth * CanDIG/candigv2-ingest merging: DIG-1658: Update commandline ingest instructions (#667) * updating submodules * Update pip * Update Makefile * Update requirements.txt * remove update setuptools * setuptools first * Update requirements.txt * Update example.env * Update Makefile * manually update setuptools * remove setuptools * Update example.env * remove setuptools * updating submodules (#669) Co-authored-by: github-actions <github-actions@github.com> * DIG-1663: Implement curator ingest in katsu and batch ingest (#666) * fix clean up * update tests * add 200 * add comment * update pip * revert pip * try pip update * fix typo * fix command * fix command properly * add #egg * test names * fix typos * update pip * revert reqs * fix req * fix req2 * remove setup upgrade * remove setuptools upgrade * delete auth * update katsu * update setuptools * update ingest * remove default site admin program auth --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com> --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com> --------- Co-authored-by: github-actions <github-actions@github.com> Co-authored-by: Marion <mshadbolt@users.noreply.github.com>
Incorporates changes in katsu and ingest to allow program curators to ingest into katsu
Also includes upgrading pip to version 24 because the github action build started failing and this seemed to fix it