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702
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aaronmk
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Installation:
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8458
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aaronmk
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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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Uninstall: make uninstall
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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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554
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aaronmk
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3674
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aaronmk
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Maintenance:
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9399
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aaronmk
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on a live machine, you should put the following in your .profile:
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umask ug=rwx,o= # prevent files from becoming web-accessible
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9400
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aaronmk
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unset TMOUT # TMOUT causes screen to exit even with background processes
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8459
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aaronmk
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to synchronize vegbiendev, jupiter, and your local machine:
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9886
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aaronmk
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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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8460
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aaronmk
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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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8459
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aaronmk
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when changes are made on vegbiendev:
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on vegbiendev, upload:
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8723
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aaronmk
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env overwrite=1 src=. dest='aaronmk@jupiter:~/bien' put --no-group --exclude=.svn --exclude=install.log.sql --exclude='*.backup' --exclude='/backups/analytical_aggregate.*.csv' --exclude='inputs/GBIF/**.data.sql' --exclude='bin/dotlockfile'
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8459
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aaronmk
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then rerun with env l=1 ...
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8723
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aaronmk
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env overwrite=1 del= src=. dest='aaronmk@jupiter:~/bien' put --no-group --exclude=.svn --exclude=install.log.sql --exclude='inputs/GBIF/**.data.sql'
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8459
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aaronmk
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then rerun with env l=1 ...
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on your machine, download:
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8945
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aaronmk
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env overwrite=1 swap=1 src=. dest='aaronmk@jupiter:~/bien' put --exclude=.svn inputs/VegBIEN/TWiki
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then rerun with env l=1 ...
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8723
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aaronmk
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env overwrite=1 del= swap=1 src=. dest='aaronmk@jupiter:~/bien' put --exclude=.svn --exclude=install.log.sql --exclude='*.backup' --exclude='/backups/analytical_aggregate.*.csv' --exclude='inputs/GBIF/**.data.sql' --exclude='bin/dotlockfile'
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8459
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aaronmk
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then rerun with env l=1 ...
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8462
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aaronmk
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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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8718
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aaronmk
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env overwrite=1 swap=1 src=~/Library/ dest='aaronmk@jupiter:~/Library/' put --exclude="/Saved Application State"
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8462
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aaronmk
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then rerun with env l=1 ...
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upload:
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8719
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aaronmk
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do step when changes are made on vegbiendev > on your machine, download
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8724
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aaronmk
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env overwrite=1 src=~ dest='aaronmk@jupiter:~' put --exclude="/Library/Saved Application State" --exclude="/.Trash" --exclude="/bin" --exclude="/bin/pg_ctl" --exclude="/bin/unzip" --exclude="/Documents/BIEN/large_files" --exclude="/Documents/BIEN/svn/backups/*.backup" --exclude="/Documents/BIEN/svn/backups/analytical_aggregate.*.csv" --exclude="/Dropbox/home"
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8462
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aaronmk
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then rerun with env l=1 ...
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8719
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aaronmk
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env overwrite=1 src=~ dest=~/Dropbox/home put --exclude="/Library/Saved Application State" --exclude="/.Trash" --exclude="/.dropbox" --exclude="/Documents/BIEN" --exclude="/Dropbox" --exclude="/software" --exclude="/VirtualBox VMs/**.sav" --exclude="/VirtualBox VMs/**.vdi" --exclude="/VirtualBox VMs/**.vmdk"
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8717
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aaronmk
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then rerun with env l=1 ...
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8720
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aaronmk
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to backup files not in Time Machine:
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env inplace=1 src=/ dest=/Volumes/Time\ Machine\ Backups/ put Users/aaronmk/VirtualBox\ VMs/
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then rerun with env l=1 ...
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stop the PostgreSQL server
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sudo env src=/ dest=/Volumes/Time\ Machine\ Backups/ put Library/PostgreSQL/9.1/data/
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then rerun with env l=1 ...
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start the PostgreSQL server
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8458
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aaronmk
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VegCore data dictionary:
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Regularly, or whenever the VegCore data dictionary page
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(https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore)
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is changed, regenerate mappings/VegCore.csv:
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make mappings/VegCore.htm-remake; make mappings/
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svn di mappings/VegCore.tables.redmine
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If there are changes, update the data dictionary's Tables section
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When moving terms, check that no terms were lost: svn di
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svn ci -m "mappings/VegCore.htm: Regenerated from wiki"
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Important: Whenever you install a system update that affects PostgreSQL or
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any of its dependencies, such as libc, you should restart the PostgreSQL
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server. Otherwise, you may get strange errors like "the database system
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is in recovery mode" which go away upon reimport, or you may not be able
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to access the database as the postgres superuser. This applies to both
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Linux and Mac OS X.
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3674
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aaronmk
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7287
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aaronmk
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Single datasource import:
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8458
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aaronmk
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(Re)import and scrub: make inputs/<datasrc>/reimport_scrub by_col=1
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(Re)import only: make inputs/<datasrc>/reimport by_col=1
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(Re)scrub: make inputs/<datasrc>/rescrub by_col=1
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Note that these commands also work if the datasource is not yet imported
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7287
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aaronmk
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Full database import:
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9499
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aaronmk
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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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9883
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aaronmk
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On jupiter: svn up --force
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8458
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aaronmk
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On local machine:
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./fix_perms
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9887
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aaronmk
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do steps under Maintenance > "to synchronize vegbiendev, jupiter, and
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your local machine" above
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9884
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aaronmk
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make inputs/upload test=1
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8458
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aaronmk
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make inputs/upload
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make test by_col=1
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See note under Testing below
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On vegbiendev:
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Ensure there are no local modifications: svn st
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svn up
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9884
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aaronmk
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make inputs/download test=1
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8458
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aaronmk
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make inputs/download
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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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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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To keep a previous import other than the public schema:
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export dump_opts='--exclude-schema=public --exclude-schema=<version>'
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Make sure there is at least 150GB of disk space on /: df -h
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The import schema is 100GB, and may use additional space for temp tables
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To free up space, remove backups that have been archived on jupiter:
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List backups/ to view older backups
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Check their MD5 sums using the steps under On jupiter below
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Remove these backups
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9899
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aaronmk
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Remove any leftover TNRS lockfile: rm inputs/.TNRS/tnrs/tnrs.make.lock
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Usually, the PID in it would not exist, but sometimes it now refers to
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a different, active process which blocks tnrs.make
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8458
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aaronmk
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screen
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Press ENTER
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9531
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aaronmk
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set -o ignoreeof #prevent Ctrl+D from exiting `screen` to keep attached jobs
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9532
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aaronmk
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unset TMOUT # TMOUT causes screen to exit even with background processes
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unset version
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8458
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aaronmk
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Start column-based import: . bin/import_all by_col=1
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To use row-based import: . bin/import_all
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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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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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Wait (overnight) for the import to finish
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To recover from a closed terminal window: screen -r
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When there are no more running jobs, exit the screen
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Get $version: echo $version
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Set $version in all vegbiendev terminals: export version=<version>
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Upload logs (run on vegbiendev): make inputs/upload
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On local machine: make inputs/download-logs
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In PostgreSQL:
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Check that the provider_count and source tables contain entries for all
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inputs
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9492
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aaronmk
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Check that TNRS ran successfully:
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tail -100 inputs/.TNRS/tnrs/logs/tnrs.make.log.sql
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If the log ends in an AssertionError
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"assert sql.table_col_names(db, table) == header":
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Figure out which TNRS CSV columns have changed
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On local machine:
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Make the changes in inputs/.TNRS/schema.sql
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rm inputs/.TNRS/tnrs/header.csv
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make inputs/.TNRS/reinstall schema_only=1
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make schemas/public/reinstall
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If there are errors "column ... does not exist", etc.:
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Make the necessary changes in schemas/vegbien.sql
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make schemas/public/reinstall
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make schemas/remake
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inputs/test_taxonomic_names/test_scrub
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aaronmk
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In inputs/test_taxonomic_names/_scrub/TNRS.sql, copy the
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"COPY tnrs ..." statement to inputs/.TNRS/data.sql
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9492
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aaronmk
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Commit
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On vegbiendev:
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If dropping a column, save the dependent views
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Make the same changes in the live TNRS.tnrs table on vegbiendev
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If dropping a column, recreate the dependent views
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Restart the TNRS client: make scrub by_col=1 &
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8458
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aaronmk
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tail inputs/{.,}*/*/logs/$version.log.sql
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In the output, search for "Command exited with non-zero status"
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For inputs that have this, fix the associated bug(s)
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If many inputs have errors, discard the current (partial) import:
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make schemas/$version/uninstall
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Otherwise, continue
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9498
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aaronmk
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Publish the new import:
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WARNING: Before proceeding, be sure you have done *every single*
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verification step listed above. Otherwise, a previous valid import
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could incorrectly be overwritten with a broken one.
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make schemas/$version/publish
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8458
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aaronmk
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unset version
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backups/fix_perms
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make backups/upload
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On jupiter:
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cd /data/dev/aaronmk/bien/backups
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For each newly-archived backup:
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make -s <backup>.md5/test
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Check that "OK" is printed next to the filename
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On nimoy:
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cd /home/bien/svn/
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svn up
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export version=<version>
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make backups/analytical_stem.$version.csv/download
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In the bien_web DB:
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Create the analytical_stem_<version> table using its schema
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in schemas/vegbien.my.sql
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make -s backups/analytical_stem.$version.csv.md5/test
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Check that "OK" is printed next to the filename
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env table=analytical_stem_$version bin/publish_analytical_db \
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backups/analytical_stem.$version.csv
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If desired, record the import times in inputs/import.stats.xls:
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Open inputs/import.stats.xls
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If the rightmost import is within 5 columns of column IV:
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Copy the current tab to <leftmost-date>~<rightmost-date>
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Remove the previous imports from the current tab because they are
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now in the copied tab instead
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Insert a copy of the leftmost "By column" column group before it
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export version=<version>
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bin/import_date inputs/{.,}*/*/logs/$version.log.sql
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Update the import date in the upper-right corner
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bin/import_times inputs/{.,}*/*/logs/$version.log.sql
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Paste the output over the # Rows/Time columns, making sure that the
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row counts match up with the previous import's row counts
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If the row counts do not match up, insert or reorder rows as needed
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until they do. Get the datasource names from the log file footers:
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tail inputs/{.,}*/*/logs/$version.log.sql
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Commit: svn ci -m "inputs/import.stats.xls: Updated import times"
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9497
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aaronmk
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To run TNRS:
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8458
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aaronmk
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export version=<version>
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9497
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aaronmk
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make scrub by_col=1 &
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8458
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aaronmk
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To view progress:
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tail -100 inputs/.TNRS/tnrs/logs/tnrs.make.log.sql
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9497
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aaronmk
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To remake analytical DB:
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8458
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aaronmk
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export version=<version>
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9497
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aaronmk
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bin/make_analytical_db &
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8458
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aaronmk
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To view progress:
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tail -100 inputs/analytical_db/logs/make_analytical_db.log.sql
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To back up DB (staging tables and last import):
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export version=<version>
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If before renaming to public: export dump_opts=--exclude-schema=public
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make backups/vegbien.$version.backup/test &
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3381
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aaronmk
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3545
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aaronmk
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Backups:
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8458
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aaronmk
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Archived imports:
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Back up: make backups/<version>.backup &
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Note: To back up the last import, you must archive it first:
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make schemas/rotate
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Test: make -s backups/<version>.backup/test &
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Restore: make backups/<version>.backup/restore &
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Remove: make backups/<version>.backup/remove
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Download: make backups/download
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TNRS cache:
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Back up: make backups/TNRS.backup-remake &
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Restore:
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yes|make inputs/.TNRS/uninstall
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make backups/TNRS.backup/restore &
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yes|make schemas/public/reinstall
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Must come after TNRS restore to recreate tnrs_input_name view
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Full DB:
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Back up: make backups/vegbien.<version>.backup &
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Test: make -s backups/vegbien.<version>.backup/test &
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Restore: make backups/vegbien.<version>.backup/restore &
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Download: make backups/download
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232 |
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Import logs:
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233 |
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Download: make inputs/download-logs
|
234 |
554
|
aaronmk
|
|
235 |
1773
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aaronmk
|
Datasource setup:
|
236 |
8469
|
aaronmk
|
umask ug=rwx,o= # prevent files from becoming web-accessible
|
237 |
8458
|
aaronmk
|
Add a new datasource: make inputs/<datasrc>/add
|
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<datasrc> may not contain spaces, and should be abbreviated.
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If the datasource is a herbarium, <datasrc> should be the herbarium code
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as defined by the Index Herbariorum <http://sweetgum.nybg.org/ih/>
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241 |
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For MySQL inputs (exports and live DB connections):
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For .sql exports:
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Place the original .sql file in _src/ (*not* in _MySQL/)
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Follow the steps starting with Install the staging tables below.
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This is for an initial sync to get the file onto vegbiendev.
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On vegbiendev:
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247 |
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Create a database for the MySQL export in phpMyAdmin
|
248 |
9494
|
aaronmk
|
Give the bien user all database-specific privileges *except*
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249 |
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UPDATE, DELETE, ALTER, DROP. This prevents bugs in the
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250 |
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import scripts from accidentally deleting data.
|
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8458
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aaronmk
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bin/mysql_bien database <inputs/<datasrc>/_src/export.sql &
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mkdir inputs/<datasrc>/_MySQL/
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253 |
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cp -p lib/MySQL.{data,schema}.sql.make inputs/<datasrc>/_MySQL/
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Edit _MySQL/*.make for the DB connection
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For a .sql export, use server=vegbiendev and --user=bien
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256 |
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Skip the Add input data for each table section
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For MS Access databases:
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Place the .mdb or .accdb file in _src/
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259 |
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Download and install Access To PostgreSQL from
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http://www.bullzip.com/download.php
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Use Access To PostgreSQL to export the database:
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Export just the tables/indexes to inputs/<datasrc>/<file>.schema.sql
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263 |
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Export just the data to inputs/<datasrc>/<file>.data.sql
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264 |
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In <file>.schema.sql, make the following changes:
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265 |
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Replace text "BOOLEAN" with "/*BOOLEAN*/INTEGER"
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266 |
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Replace text "DOUBLE PRECISION NULL" with "DOUBLE PRECISION"
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267 |
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Skip the Add input data for each table section
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268 |
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Add input data for each table present in the datasource:
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269 |
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For .sql exports, you must use the name of the table in the DB export
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270 |
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For CSV files, you can use any name. It's recommended to use a table
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name from <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV#Suggested-table-names>
|
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|
|
Note that if this table will be joined together with another table, its
|
273 |
|
|
name must end in ".src"
|
274 |
|
|
make inputs/<datasrc>/<table>/add
|
275 |
|
|
Important: DO NOT just create an empty directory named <table>!
|
276 |
|
|
This command also creates necessary subdirs, such as logs/.
|
277 |
|
|
If the table is in a .sql export: make inputs/<datasrc>/<table>/install
|
278 |
|
|
Otherwise, place the CSV(s) for the table in
|
279 |
|
|
inputs/<datasrc>/<table>/ OR place a query joining other tables
|
280 |
|
|
together in inputs/<datasrc>/<table>/create.sql
|
281 |
|
|
Important: When exporting relational databases to CSVs, you MUST ensure
|
282 |
|
|
that embedded quotes are escaped by doubling them, *not* by
|
283 |
|
|
preceding them with a "\" as is the default in phpMyAdmin
|
284 |
|
|
If there are multiple part files for a table, and the header is repeated
|
285 |
|
|
in each part, make sure each header is EXACTLY the same.
|
286 |
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(If the headers are not the same, the CSV concatenation script
|
287 |
|
|
assumes the part files don't have individual headers and treats the
|
288 |
|
|
subsequent headers as data rows.)
|
289 |
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|
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|
Add <table> to inputs/<datasrc>/import_order.txt before other tables
|
290 |
|
|
that depend on it
|
291 |
|
|
Install the staging tables:
|
292 |
|
|
make inputs/<datasrc>/reinstall quiet=1 &
|
293 |
|
|
For a MySQL .sql export:
|
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|
|
At prompt "[you]@vegbiendev's password:", enter your password
|
295 |
|
|
At prompt "Enter password:", enter the value in config/bien_password
|
296 |
|
|
To view progress: tail -f inputs/<datasrc>/<table>/logs/install.log.sql
|
297 |
|
|
View the logs: tail -n +1 inputs/<datasrc>/*/logs/install.log.sql
|
298 |
|
|
tail provides a header line with the filename
|
299 |
|
|
+1 starts at the first line, to show the whole file
|
300 |
|
|
For every file with an error 'column "..." specified more than once':
|
301 |
|
|
Add a header override file "+header.<ext>" in <table>/:
|
302 |
|
|
Note: The leading "+" should sort it before the flat files.
|
303 |
|
|
"_" unfortunately sorts *after* capital letters in ASCII.
|
304 |
|
|
Create a text file containing the header line of the flat files
|
305 |
|
|
Add an ! at the beginning of the line
|
306 |
|
|
This signals cat_csv that this is a header override.
|
307 |
|
|
For empty names, use their 0-based column # (by convention)
|
308 |
|
|
For duplicate names, add a distinguishing suffix
|
309 |
|
|
For long names that collided, rename them to <= 63 chars long
|
310 |
|
|
Do NOT make readability changes in this step; that is what the
|
311 |
|
|
map spreadsheets (below) are for.
|
312 |
|
|
Save
|
313 |
|
|
If you made any changes, re-run the install command above
|
314 |
|
|
Auto-create the map spreadsheets: make inputs/<datasrc>/
|
315 |
|
|
Map each table's columns:
|
316 |
|
|
In each <table>/ subdir, for each "via map" map.csv:
|
317 |
|
|
Open the map in a spreadsheet editor
|
318 |
|
|
Open the "core map" /mappings/Veg+-VegBIEN.csv
|
319 |
|
|
In each row of the via map, set the right column to a value from the
|
320 |
|
|
left column of the core map
|
321 |
|
|
Save
|
322 |
|
|
Regenerate the derived maps: make inputs/<datasrc>/
|
323 |
|
|
Accept the test cases:
|
324 |
|
|
make inputs/<datasrc>/test
|
325 |
|
|
When prompted to "Accept new test output", enter y and press ENTER
|
326 |
|
|
If you instead get errors, do one of the following for each one:
|
327 |
|
|
- If the error was due to a bug, fix it
|
328 |
|
|
- Add a SQL function that filters or transforms the invalid data
|
329 |
|
|
- Make an empty mapping for the columns that produced the error.
|
330 |
|
|
Put something in the Comments column of the map spreadsheet to
|
331 |
|
|
prevent the automatic mapper from auto-removing the mapping.
|
332 |
|
|
When accepting tests, it's helpful to use WinMerge
|
333 |
|
|
(see WinMerge setup below for configuration)
|
334 |
|
|
make inputs/<datasrc>/test by_col=1
|
335 |
|
|
If you get errors this time, this always indicates a bug, usually in
|
336 |
|
|
the VegBIEN unique constraints or column-based import itself
|
337 |
|
|
Add newly-created files: make inputs/<datasrc>/add
|
338 |
|
|
Commit: svn ci -m "Added inputs/<datasrc>/" inputs/<datasrc>/
|
339 |
|
|
Update vegbiendev:
|
340 |
|
|
On jupiter: svn up
|
341 |
|
|
On local machine:
|
342 |
|
|
./fix_perms
|
343 |
9950
|
aaronmk
|
make inputs/upload test=1
|
344 |
8458
|
aaronmk
|
make inputs/upload
|
345 |
|
|
On vegbiendev:
|
346 |
|
|
svn up
|
347 |
9950
|
aaronmk
|
make inputs/download test=1
|
348 |
8458
|
aaronmk
|
make inputs/download
|
349 |
|
|
Follow the steps under Install the staging tables above
|
350 |
1773
|
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|
|
351 |
6484
|
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|
Datasource refreshing:
|
352 |
8458
|
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|
VegBank:
|
353 |
|
|
make inputs/VegBank/vegbank.sql-remake
|
354 |
|
|
make inputs/VegBank/reinstall quiet=1 &
|
355 |
6484
|
aaronmk
|
|
356 |
702
|
aaronmk
|
Schema changes:
|
357 |
8458
|
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|
When changing the analytical views, run sync_analytical_..._to_view()
|
358 |
|
|
to update the corresponding table
|
359 |
|
|
Remember to update the following files with any renamings:
|
360 |
|
|
schemas/filter_ERD.csv
|
361 |
|
|
mappings/VegCore-VegBIEN.csv
|
362 |
|
|
mappings/verify.*.sql
|
363 |
|
|
Regenerate schema from installed DB: make schemas/remake
|
364 |
|
|
Reinstall DB from schema: make schemas/public/reinstall schemas/reinstall
|
365 |
|
|
WARNING: This will delete the current public schema of your VegBIEN DB!
|
366 |
8837
|
aaronmk
|
Reinstall staging tables:
|
367 |
|
|
On local machine:
|
368 |
8840
|
aaronmk
|
sudo -E -u postgres psql <<<'ALTER DATABASE vegbien RENAME TO vegbien_prev'
|
369 |
8845
|
aaronmk
|
make db
|
370 |
8837
|
aaronmk
|
. bin/reinstall_all
|
371 |
|
|
Fix any bugs and retry until no errors
|
372 |
8846
|
aaronmk
|
make schemas/public/install
|
373 |
|
|
This must be run *after* the datasources are installed, because
|
374 |
|
|
views in public depend on some of the datasources
|
375 |
8842
|
aaronmk
|
sudo -E -u postgres psql <<<'DROP DATABASE vegbien_prev'
|
376 |
8841
|
aaronmk
|
On vegbiendev: repeat the above steps
|
377 |
8837
|
aaronmk
|
WARNING: Do not run this until reinstall_all runs successfully on
|
378 |
|
|
the local machine, or the live DB may be unrestorable!
|
379 |
8458
|
aaronmk
|
Sync ERD with vegbien.sql schema:
|
380 |
|
|
Run make schemas/vegbien.my.sql
|
381 |
|
|
Open schemas/vegbien.ERD.mwb in MySQLWorkbench
|
382 |
|
|
Go to File > Export > Synchronize With SQL CREATE Script...
|
383 |
|
|
For Input File, select schemas/vegbien.my.sql
|
384 |
|
|
Click Continue
|
385 |
|
|
In the changes list, select each table with an arrow next to it
|
386 |
|
|
Click Update Model
|
387 |
|
|
Click Continue
|
388 |
|
|
Note: The generated SQL script will be empty because we are syncing in
|
389 |
|
|
the opposite direction
|
390 |
|
|
Click Execute
|
391 |
|
|
Reposition any lines that have been reset
|
392 |
|
|
Add any new tables by dragging them from the Catalog in the left sidebar
|
393 |
|
|
to the diagram
|
394 |
|
|
Remove any deleted tables by right-clicking the table's diagram element,
|
395 |
|
|
selecting Delete '<table name>', and clicking Delete
|
396 |
|
|
Save
|
397 |
|
|
If desired, update the graphical ERD exports (see below)
|
398 |
|
|
Update graphical ERD exports:
|
399 |
|
|
Go to File > Export > Export as PNG...
|
400 |
|
|
Select schemas/vegbien.ERD.png and click Save
|
401 |
|
|
Go to File > Export > Export as SVG...
|
402 |
|
|
Select schemas/vegbien.ERD.svg and click Save
|
403 |
|
|
Go to File > Export > Export as Single Page PDF...
|
404 |
|
|
Select schemas/vegbien.ERD.1_pg.pdf and click Save
|
405 |
|
|
Go to File > Print...
|
406 |
|
|
In the lower left corner, click PDF > Save as PDF...
|
407 |
|
|
Set the Title and Author to ""
|
408 |
|
|
Select schemas/vegbien.ERD.pdf and click Save
|
409 |
|
|
Commit: svn ci -m "schemas/vegbien.ERD.mwb: Regenerated exports"
|
410 |
|
|
Refactoring tips:
|
411 |
|
|
To rename a table:
|
412 |
|
|
In vegbien.sql, do the following:
|
413 |
|
|
Replace regexp (?<=_|\b)<old>(?=_|\b) with <new>
|
414 |
|
|
This is necessary because the table name is *everywhere*
|
415 |
|
|
Search for <new>
|
416 |
|
|
Manually change back any replacements inside comments
|
417 |
|
|
To rename a column:
|
418 |
|
|
Rename the column: ALTER TABLE <table> RENAME <old> TO <new>;
|
419 |
|
|
Recreate any foreign key for the column, removing CONSTRAINT <name>
|
420 |
|
|
This resets the foreign key name using the new column name
|
421 |
|
|
Creating a poster of the ERD:
|
422 |
|
|
Determine the poster size:
|
423 |
|
|
Measure the line height (from the bottom of one line to the bottom
|
424 |
|
|
of another): 16.3cm/24 lines = 0.679cm
|
425 |
|
|
Measure the height of the ERD: 35.4cm*2 = 70.8cm
|
426 |
|
|
Zoom in as far as possible
|
427 |
|
|
Measure the height of a capital letter: 3.5mm
|
428 |
|
|
Measure the line height: 8.5mm
|
429 |
|
|
Calculate the text's fraction of the line height: 3.5mm/8.5mm = 0.41
|
430 |
|
|
Calculate the text height: 0.679cm*0.41 = 0.28cm
|
431 |
|
|
Calculate the text height's fraction of the ERD height:
|
432 |
|
|
0.28cm/70.8cm = 0.0040
|
433 |
|
|
Measure the text height on the *VegBank* ERD poster: 5.5mm = 0.55cm
|
434 |
|
|
Calculate the VegBIEN poster height to make the text the same size:
|
435 |
|
|
0.55cm/0.0040 = 137.5cm H; *1in/2.54cm = 54.1in H
|
436 |
|
|
The ERD aspect ratio is 11 in W x (2*8.5in H) = 11x17 portrait
|
437 |
|
|
Calculate the VegBIEN poster width: 54.1in H*11W/17H = 35.0in W
|
438 |
|
|
The minimum VegBIEN poster size is 35x54in portrait
|
439 |
|
|
Determine the cost:
|
440 |
|
|
The FedEx Kinkos near NCEAS (1030 State St, Santa Barbara, CA 93101)
|
441 |
|
|
charges the following for posters:
|
442 |
|
|
base: $7.25/sq ft
|
443 |
|
|
lamination: $3/sq ft
|
444 |
|
|
mounting on a board: $8/sq ft
|
445 |
203
|
aaronmk
|
|
446 |
1459
|
aaronmk
|
Testing:
|
447 |
8458
|
aaronmk
|
On a development machine, you should put the following in your .profile:
|
448 |
8469
|
aaronmk
|
umask ug=rwx,o= # prevent files from becoming web-accessible
|
449 |
8458
|
aaronmk
|
export log= n=2
|
450 |
|
|
Mapping process: make test
|
451 |
|
|
Including column-based import: make test by_col=1
|
452 |
|
|
If the row-based and column-based imports produce different inserted
|
453 |
|
|
row counts, this usually means that a table is underconstrained
|
454 |
|
|
(the unique indexes don't cover all possible rows).
|
455 |
|
|
This can occur if you didn't use COALESCE(field, null_value) around
|
456 |
|
|
a nullable field in a unique index. See sql_gen.null_sentinels for
|
457 |
|
|
the appropriate null value to use.
|
458 |
|
|
Map spreadsheet generation: make remake
|
459 |
|
|
Missing mappings: make missing_mappings
|
460 |
|
|
Everything (for most complete coverage): make test-all
|
461 |
702
|
aaronmk
|
|
462 |
7183
|
aaronmk
|
Debugging:
|
463 |
8458
|
aaronmk
|
"Binary chop" debugging:
|
464 |
|
|
(This is primarily useful for regressions that occurred in a previous
|
465 |
|
|
revision, which was committed without running all the tests)
|
466 |
|
|
svn up -r <rev>; make inputs/.TNRS/reinstall; make schemas/public/reinstall; make <failed-test>.xml
|
467 |
8470
|
aaronmk
|
.htaccess:
|
468 |
|
|
mod_rewrite:
|
469 |
8471
|
aaronmk
|
IMPORTANT: whenever you change the DirectorySlash setting for a
|
470 |
|
|
directory, you *must* clear your browser's cache to ensure that
|
471 |
|
|
a cached redirect is not used. this is because RewriteRule
|
472 |
|
|
redirects are (by default) temporary, but DirectorySlash
|
473 |
|
|
redirects are permanent.
|
474 |
8470
|
aaronmk
|
for Firefox:
|
475 |
|
|
press Cmd+Shift+Delete
|
476 |
|
|
check only Cache
|
477 |
|
|
press Enter or click Clear Now
|
478 |
7183
|
aaronmk
|
|
479 |
3783
|
aaronmk
|
WinMerge setup:
|
480 |
8458
|
aaronmk
|
Install WinMerge from <http://winmerge.org/>
|
481 |
|
|
Open WinMerge
|
482 |
|
|
Go to Edit > Options and click Compare in the left sidebar
|
483 |
|
|
Enable "Moved block detection", as described at
|
484 |
|
|
<http://manual.winmerge.org/Configuration.html#d0e5892>.
|
485 |
|
|
Set Whitespace to Ignore change, as described at
|
486 |
|
|
<http://manual.winmerge.org/Configuration.html#d0e5758>.
|
487 |
3783
|
aaronmk
|
|
488 |
3133
|
aaronmk
|
Documentation:
|
489 |
8458
|
aaronmk
|
To generate a Redmine-formatted list of steps for column-based import:
|
490 |
|
|
make schemas/public/reinstall
|
491 |
|
|
make inputs/ACAD/Specimen/logs/steps.by_col.log.sql
|
492 |
|
|
To import and scrub just the test taxonomic names:
|
493 |
|
|
inputs/test_taxonomic_names/test_scrub
|
494 |
3133
|
aaronmk
|
|
495 |
702
|
aaronmk
|
General:
|
496 |
8458
|
aaronmk
|
To see a program's description, read its top-of-file comment
|
497 |
|
|
To see a program's usage, run it without arguments
|
498 |
|
|
To remake a directory: make <dir>/remake
|
499 |
|
|
To remake a file: make <file>-remake
|