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This is a place for technical notes describing how some problems were solved, which may help others who would implement deployments in the future.

  1. Problem Solved!! Lombok Installation on Linux ( AMP-140) :
    1. cp -r the official installation of eclipse from /snap/eclipse/40 to my own ~/snap/eclipse/40

    2. find out which eclipse is pointed to, turns out to be /snap/bin/eclipse, which is a soft link pointing to the /snap/eclipse/40/eclipse. Modify that soft link to point to my own snap eclipse ~/snap/eclipse/40/eclipse

    3. run lombok jar, and tell it to look for eclipse installation under mt own snap dir  ~/snap/eclipse/40/

    4. the installation succeeded, I can see ini file updated, lombok jar copied to my eclipse dir.

    5. I can now launch my eclipse from cmd line (I can't figure out how to add it to ubuntu app bar. it seems that one can only add system installed one).

    6. run project update which triggers rebuild, and all compilation errors cleared away. 

  2. Dropbox file paths use the pattern /{unit name}/{collection name}.  Because unit and collection names can contain special characters, anything outside of A-Z, 0-9, ".", "-", and "-" will be encoded using the pattern %(char hex).
    1. For example, for the unit AMP Pilot Unit and collection Music Library, the path will be /AMP%20Pilot%20Unit/Music%20Library
  3. To test AMPPD backend only (for ex, with Postman) when auth is turned on, one needs to first get a token then add it to the request header, as follows (below ex uses local env, replace localhost with test server URL otherwise):
    1. GET http://localhost:8200/account/authenticate, copy the response, which is the token needed below
    2. In your request, add Header with key "Authorization" and value "Bearer <token>" (<token> is the value from above step)
  4. Staging environment: update
    1. Before merging master into staging, check if any of the following need to be updated before (and sometimes after) the deploy:
      1. amppd application properties
      2. galaxy config files
      3. DB changes that can't be picked by spring boot
    2. When merging on all 3 repositories, do in the order of galaxy, amppd, and ampp-ui. This is due to the dependencies among the 3 applications.
    3. Monitor Bamboo logs to make sure the depended application is successfully deployed before merging the next one. For ex, if amppd and galaxy are both merged within a short period, amppd might fail to deploy if Galaxy hasn't started at the time Bamboo tries to start amppd.
  5. If symlink for primaryfiles or workflow outputs aren't working (getting 403 permission denied error)
    1. Check symlink and the linked file permission, all parent dirs and file should be www readable
    2. If that's not the cause, it could be selinux issue, as app_amp in the galaxy directory run "restorecon -vr ." to fix the issue.
  6. Upgrading Galaxy Error: /usr/local/include/Block.h:16:3: error: Never include this file directly. Use <lzma.h> instead.
    # error Never include this file directly. Use <lzma.h> instead.
    1. sudo mv /usr/local/include /usr/local/include_old

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