Revision 12226
Added by Aaron Marcuse-Kubitza almost 11 years ago
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Check out svn: svn co https://code.nceas.ucsb.edu/code/projects/bien |
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cd bien/ |
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Install: make install |
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WARNING: This will delete the current public schema of your VegBIEN DB!
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**WARNING**: This will delete the public schema of your VegBIEN DB!
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Uninstall: make uninstall |
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WARNING: This will delete your entire VegBIEN DB!
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**WARNING**: This will delete your entire VegBIEN DB!
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This includes all archived imports and staging tables. |
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Connecting to vegbiendev: |
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Remake analytical DB: see Full database import > To remake analytical DB |
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Full database import: |
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WARNING: You must perform *every single* step listed below, to avoid
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**WARNING**: You must perform *every single* step listed below, to avoid
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breaking column-based import |
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**WARNING**: always start with a clean shell, as described above under |
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"Notes on running programs" |
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make inputs/download live=1 |
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For each newly-uploaded datasource above: make inputs/<datasrc>/reinstall |
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Update the auxiliary schemas: make schemas/reinstall |
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WARNING: requires sudo access!
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**WARNING**: requires sudo access!
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The public schema will be installed separately by the import process |
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Delete imports before the last so they won't bloat the full DB backup: |
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make backups/vegbien.<version>.backup/remove |
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Start column-based import: . bin/import_all |
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To use row-based import: . bin/import_all by_col= |
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To stop all running imports: . bin/stop_imports |
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WARNING: Do NOT run import_all in the background, or the jobs it creates
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won't be owned by your shell. |
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**WARNING**: Do NOT run import_all in the background, or the jobs it
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creates won't be owned by your shell.
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Note that import_all will take up to an hour to import the NCBI backbone |
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and other metadata before returning control to the shell. |
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To view progress: |
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make schemas/$version/uninstall |
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Otherwise, continue |
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Publish the new import: |
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WARNING: Before proceeding, be sure you have done *every single*
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**WARNING**: Before proceeding, be sure you have done *every single*
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verification step listed above. Otherwise, a previous valid import |
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could incorrectly be overwritten with a broken one. |
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make schemas/$version/publish # runtime: 1 min ("real 1m10.451s")
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if http://vegbiendev.nceas.ucsb.edu/phppgadmin/ goes down: |
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on vegbiendev: make postgres-Linux |
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to synchronize vegbiendev, jupiter, and your local machine: |
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WARNING: pay careful attention to all files that will be deleted or
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**WARNING**: pay careful attention to all files that will be deleted or
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overwritten! |
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install put if needed: |
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download https://uutils.googlecode.com/svn/trunk/bin/put to ~/bin/ and `chmod +x` it |
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then rerun with l=1 ... |
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to synchronize a Mac's settings with my testing machine's: |
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download: |
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WARNING: this will overwrite all your user's settings!
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**WARNING**: this will overwrite all your user's settings!
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on your machine: |
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overwrite=1 swap=1 sync_local_dir=~/Library/ sync_remote_subdir=Library/ bin/sync_upload --exclude="/Saved Application State" |
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then rerun with l=1 ... |
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mappings/verify.*.sql |
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Regenerate schema from installed DB: make schemas/remake |
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Reinstall DB from schema: make schemas/public/reinstall schemas/reinstall |
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WARNING: This will delete the current public schema of your VegBIEN DB!
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**WARNING**: This will delete the public schema of your VegBIEN DB!
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Reinstall staging tables: |
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On local machine: |
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sudo -E -u postgres psql <<<'ALTER DATABASE vegbien RENAME TO vegbien_prev' |
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views in public depend on some of the datasources |
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sudo -E -u postgres psql <<<'DROP DATABASE vegbien_prev' |
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On vegbiendev: repeat the above steps |
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WARNING: Do not run this until reinstall_all runs successfully on
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the local machine, or the live DB may be unrestorable! |
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**WARNING**: Do not run this until reinstall_all runs successfully
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on the local machine, or the live DB may be unrestorable!
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Sync ERD with vegbien.sql schema: |
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Run make schemas/vegbien.my.sql |
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Open schemas/vegbien.ERD.mwb in MySQLWorkbench |
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svn up -r <rev>; make inputs/.TNRS/reinstall; make schemas/public/reinstall; make <failed-test>.xml |
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.htaccess: |
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mod_rewrite: |
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IMPORTANT: whenever you change the DirectorySlash setting for a
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**IMPORTANT**: whenever you change the DirectorySlash setting for a
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directory, you *must* clear your browser's cache to ensure that |
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a cached redirect is not used. this is because RewriteRule |
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redirects are (by default) temporary, but DirectorySlash |
Also available in: Unified diff
/README.TXT: put ... around all uppercased text, for consistency