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Migrate oauth to GitHub app #155

Merged
merged 63 commits into from
May 19, 2020
Merged

Migrate oauth to GitHub app #155

merged 63 commits into from
May 19, 2020

Commits on Apr 10, 2020

  1. New env vars and private files for GitHub apps.

    @jimallman
    jimallman committed Apr 10, 2020
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Commits on Apr 11, 2020

  1. Populate the installation IDs for GitHub apps

    @jimallman
    jimallman committed Apr 11, 2020
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Commits on Apr 12, 2020

  1. comment out failing steps

    @snacktavish
    snacktavish committed Apr 12, 2020
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Commits on Apr 13, 2020

  1. lots of interactive steps too

    @snacktavish
    snacktavish committed Apr 13, 2020
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  2. big web2py jump

    @snacktavish
    snacktavish committed Apr 13, 2020
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  3. Fix number of expected args

    @jimallman
    jimallman committed Apr 13, 2020
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  4. TMP change to user

    @snacktavish
    snacktavish committed Apr 13, 2020
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  5. web2py updates

    @snacktavish
    snacktavish committed Apr 13, 2020
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  6. or exit everywhere

    @mtholder
    mtholder committed Apr 13, 2020
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  7. noweb2py in apache config

    @snacktavish
    snacktavish committed Apr 13, 2020
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  8. no web2py common, change echo to log

    @snacktavish
    snacktavish committed Apr 13, 2020
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  9. some controller updates

    @mtholder
    mtholder committed Apr 13, 2020
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Commits on Apr 14, 2020

  1. No push

    @snacktavish
    snacktavish committed Apr 14, 2020
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  2. Merge branch 'phylesystemapi' of github.com:OpenTreeOfLife/germinator… 

    … into phylesystemapi
    @snacktavish
    snacktavish committed Apr 14, 2020
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  3. forwarding hack for machine running otcetera

    @snacktavish
    snacktavish committed Apr 14, 2020
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Commits on Apr 15, 2020

  1. Merge branch 'phylesystemapi' into otcetera-conf

    @snacktavish
    snacktavish committed Apr 15, 2020
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  2. unify changes

    @snacktavish
    snacktavish committed Apr 15, 2020
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  3. no java

    @snacktavish
    snacktavish committed Apr 15, 2020
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  4. current on ot54

    @snacktavish
    snacktavish committed Apr 15, 2020
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Commits on Apr 16, 2020

  1. new certs, web2pyversion

    @snacktavish
    snacktavish committed Apr 16, 2020
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  2. devtree

    @snacktavish
    snacktavish committed Apr 16, 2020
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  3. hardcoded user change to opentree

    @snacktavish
    snacktavish committed Apr 16, 2020
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  4. fix caching

    @snacktavish
    snacktavish committed Apr 16, 2020
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  5. Add a minimal parametric router w/ default app

    @jimallman
    jimallman committed Apr 16, 2020
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  6. Merge branch 'easter-fix' of github.com:OpenTreeOfLife/germinator int… 

    …o easter-fix
    @jimallman
    jimallman committed Apr 16, 2020
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  7. Add minimal router for phylesystem-api

    @jimallman
    jimallman committed Apr 16, 2020
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  8. Adding diagnostic pwd for web2py install scripts.

    @jimallman
    jimallman committed Apr 16, 2020
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  9. Fix pwd output in install scripts

    @jimallman
    jimallman committed Apr 16, 2020
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  10. Don't extract the synth tree each time.

    @bredelings
    bredelings committed Apr 16, 2020
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Commits on Apr 23, 2020

  1. update apache conf

    @snacktavish
    snacktavish committed Apr 23, 2020
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  2. don't rewrite confs

    @snacktavish
    snacktavish committed Apr 23, 2020
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  3. no caching for now

    @snacktavish
    snacktavish committed Apr 23, 2020
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  4. Merge branch 'easter-fix' of github.com:OpenTreeOfLife/germinator int… 

    …o easter-fix
    @snacktavish
    snacktavish committed Apr 23, 2020
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  5. fix restart apache typo

    @snacktavish
    snacktavish committed Apr 23, 2020
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Commits on May 6, 2020

  1. Add switches for web2py and apache config 

    This lets us apply these changes only where and when needed.
    @jimallman
    jimallman committed May 6, 2020
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  2. Revert "don't rewrite confs" 

    This reverts commit 990ffa7.
    @jimallman
    jimallman committed May 6, 2020
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  3. Replace hard-coded ot51 with PHYLAPI_BASE_URL

    @jimallman
    jimallman committed May 6, 2020
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Commits on May 7, 2020

  1. Back up existing config files at start of push

    @jimallman
    jimallman committed May 7, 2020
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  2. Add do-nothing builtin for valid bash script

    @jimallman
    jimallman committed May 7, 2020
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  3. Fix bash errors in restart-apache.sh

    @jimallman
    jimallman committed May 7, 2020
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  4. Replace shortcut '~' with /home/admin

    @jimallman
    jimallman committed May 7, 2020
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  5. Restore test of local path to private key files

    @jimallman
    jimallman committed May 7, 2020
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  6. Merge branch 'master' into easter-fix

    @jimallman
    jimallman committed May 7, 2020
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Commits on May 8, 2020

  1. Restore wget commands to files.opentreeoflife.org

    @jimallman
    jimallman committed May 8, 2020
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  2. Removing unused apache config (shared forwards)

    @jimallman
    jimallman committed May 8, 2020
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  3. Revert "No push" 

    This reverts commit a74348e.
    @jimallman
    jimallman committed May 8, 2020
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  4. Restore URLs for cached content (fingers crossed!)

    @jimallman
    jimallman committed May 8, 2020
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  5. Merge pull request #154 from OpenTreeOfLife/easter-fix 

    merging easter-fix into migrate-oauth-to-github-app for full testing on dev* servers
    @jimallman
    jimallman committed May 8, 2020
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Commits on May 9, 2020

  1. Fix bad error message

    @jimallman
    jimallman committed May 9, 2020
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Commits on May 10, 2020

  1. Move web2py patches into germinator repo

    @jimallman
    jimallman committed May 10, 2020
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  2. Commit vanilla version from web2py 2.19.1

    @jimallman
    jimallman committed May 10, 2020
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  3. Revive old hot fix to always add CORS headers 

    This prevents errors when (e.g.) sending a CORS preflight 'OPTONS'
request to fetch cached API responses. Test: If this patch is not
applied, no tree will appear in our synth-tree viewer webapp.
    @jimallman
    jimallman committed May 10, 2020
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  4. Update source path of web2py patch(es)

    @jimallman
    jimallman committed May 10, 2020
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  5. Patch existing web2py as well as new installations

    @jimallman
    jimallman committed May 10, 2020
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Commits on May 12, 2020

  1. Add confirmation message for web2py patches

    @jimallman
    jimallman committed May 12, 2020
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  2. Add unchanged source file from web2py v2.19.1

    @jimallman
    jimallman committed May 12, 2020
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  3. Revive old hot fix to handle OAuth when proxied 

    This prevents errors when authorizing to a GitHub app (or OAuth app)
on proxied web2py servers, as is common in our setup.

Test: If this patch is not applied, we'll be unable to successfully
login to the synth-tree viewer or curation app. (This error usually
manifests as a mismatched-uri, even when the requested and registered
URLs are identical.)
    @jimallman
    jimallman committed May 12, 2020
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  4. Correct commit-history URL (still in original repo)

    @jimallman
    jimallman committed May 12, 2020
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  5. Revive another web2py patch

    @jimallman
    jimallman committed May 12, 2020
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  6. Remove third legacy patch (FIXED in recent web2py) 

    Happily newer versions of web2py correctly handle non-ASCII names when
importing a python module.
    @jimallman
    jimallman committed May 12, 2020
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  7. Customize phylesystem-api config for read-only

    @jimallman
    jimallman committed May 12, 2020
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Commits on May 18, 2020

  1. pip install redis as well

    @snacktavish
    snacktavish committed May 18, 2020
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Commits on May 19, 2020

  1. Merge branch 'master' into migrate-oauth-to-github-app

    @jimallman
    jimallman committed May 19, 2020
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