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Installation:
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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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Maintenance:
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to synchronize vegbiendev, jupiter, and your local machine:
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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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when changes are made on vegbiendev:
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on vegbiendev, upload:
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env overwrite=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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then rerun with env l=1 ...
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env overwrite=1 del= src=. dest='aaronmk@jupiter:~/bien' put --exclude=.svn --exclude=install.log.sql --exclude='inputs/GBIF/**.data.sql'
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then rerun with env l=1 ...
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on your machine, download:
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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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then rerun with env 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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env overwrite=1 swap=1 src=~/Library/ dest='aaronmk@jupiter:~/Library/' put --exclude="/Saved Application State/**"
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then rerun with env l=1 ...
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upload:
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env overwrite=1 src=~/Library/ dest='aaronmk@jupiter:~/Library/' put --exclude="/Saved Application State/**"
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then rerun with env l=1 ...
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to backup the Ubuntu VM:
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env src=/Users/aaronmk/VirtualBox\ VMs/Ubuntu dest=/Volumes/Macintosh\ HD\ backup/Ubuntu put --exclude=/Ubuntu.prev.vdi
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then rerun with env l=1 ...
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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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Single datasource import:
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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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Full database import:
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On jupiter: svn up
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On local machine:
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./fix_perms
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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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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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unset version
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screen
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Press ENTER
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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 $version in all vegbiendev terminals: export version=<version>
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Upload logs (run on vegbiendev): make inputs/upload
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On local machine: make inputs/download-logs
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In PostgreSQL:
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Check that the provider_count and source tables contain entries for all
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inputs
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tail inputs/{.,}*/*/logs/$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/$version/uninstall
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Otherwise, continue
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make schemas/$version/publish
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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/$version.log.sql
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Commit: svn ci -m "inputs/import.stats.xls: Updated import times"
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To run TNRS: make scrub by_col=1 &
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export version=<version>
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To view progress:
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tail -100 inputs/.TNRS/tnrs/logs/tnrs.make.log.sql
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To remake analytical DB: bin/make_analytical_db &
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export version=<version>
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To view progress:
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tail -100 inputs/analytical_db/logs/make_analytical_db.log.sql
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To back up DB (staging tables and last import):
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export version=<version>
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If before renaming to public: export dump_opts=--exclude-schema=public
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make backups/vegbien.$version.backup/test &
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Backups:
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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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Import logs:
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Download: make inputs/download-logs
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Datasource setup:
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umask ug=rwx,o= # prevent files from becoming web-accessible
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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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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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Create a database for the MySQL export in phpMyAdmin
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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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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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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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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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Export just the data to inputs/<datasrc>/<file>.data.sql
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In <file>.schema.sql, make the following changes:
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Replace text "BOOLEAN" with "/*BOOLEAN*/INTEGER"
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Replace text "DOUBLE PRECISION NULL" with "DOUBLE PRECISION"
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Skip the Add input data for each table section
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Add input data for each table present in the datasource:
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For .sql exports, you must use the name of the table in the DB export
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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
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name must end in ".src"
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make inputs/<datasrc>/<table>/add
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Important: DO NOT just create an empty directory named <table>!
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This command also creates necessary subdirs, such as logs/.
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If the table is in a .sql export: make inputs/<datasrc>/<table>/install
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Otherwise, place the CSV(s) for the table in
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inputs/<datasrc>/<table>/ OR place a query joining other tables
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together in inputs/<datasrc>/<table>/create.sql
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Important: When exporting relational databases to CSVs, you MUST ensure
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that embedded quotes are escaped by doubling them, *not* by
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preceding them with a "\" as is the default in phpMyAdmin
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If there are multiple part files for a table, and the header is repeated
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in each part, make sure each header is EXACTLY the same.
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(If the headers are not the same, the CSV concatenation script
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assumes the part files don't have individual headers and treats the
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subsequent headers as data rows.)
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Add <table> to inputs/<datasrc>/import_order.txt before other tables
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that depend on it
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Install the staging tables:
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make inputs/<datasrc>/reinstall quiet=1 &
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For a MySQL .sql export:
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At prompt "[you]@vegbiendev's password:", enter your password
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At prompt "Enter password:", enter the value in config/bien_password
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To view progress: tail -f inputs/<datasrc>/<table>/logs/install.log.sql
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View the logs: tail -n +1 inputs/<datasrc>/*/logs/install.log.sql
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tail provides a header line with the filename
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+1 starts at the first line, to show the whole file
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For every file with an error 'column "..." specified more than once':
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Add a header override file "+header.<ext>" in <table>/:
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Note: The leading "+" should sort it before the flat files.
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"_" unfortunately sorts *after* capital letters in ASCII.
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Create a text file containing the header line of the flat files
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Add an ! at the beginning of the line
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This signals cat_csv that this is a header override.
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For empty names, use their 0-based column # (by convention)
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For duplicate names, add a distinguishing suffix
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For long names that collided, rename them to <= 63 chars long
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Do NOT make readability changes in this step; that is what the
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map spreadsheets (below) are for.
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Save
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If you made any changes, re-run the install command above
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Auto-create the map spreadsheets: make inputs/<datasrc>/
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Map each table's columns:
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In each <table>/ subdir, for each "via map" map.csv:
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Open the map in a spreadsheet editor
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Open the "core map" /mappings/Veg+-VegBIEN.csv
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In each row of the via map, set the right column to a value from the
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left column of the core map
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Save
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Regenerate the derived maps: make inputs/<datasrc>/
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Accept the test cases:
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make inputs/<datasrc>/test
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When prompted to "Accept new test output", enter y and press ENTER
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If you instead get errors, do one of the following for each one:
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- If the error was due to a bug, fix it
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- Add a SQL function that filters or transforms the invalid data
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- Make an empty mapping for the columns that produced the error.
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Put something in the Comments column of the map spreadsheet to
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prevent the automatic mapper from auto-removing the mapping.
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When accepting tests, it's helpful to use WinMerge
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(see WinMerge setup below for configuration)
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make inputs/<datasrc>/test by_col=1
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If you get errors this time, this always indicates a bug, usually in
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the VegBIEN unique constraints or column-based import itself
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Add newly-created files: make inputs/<datasrc>/add
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Commit: svn ci -m "Added inputs/<datasrc>/" inputs/<datasrc>/
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Update vegbiendev:
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On jupiter: svn up
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On local machine:
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./fix_perms
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make inputs/upload
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On vegbiendev:
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svn up
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make inputs/download
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Follow the steps under Install the staging tables above
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Datasource refreshing:
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VegBank:
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make inputs/VegBank/vegbank.sql-remake
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make inputs/VegBank/reinstall quiet=1 &
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Schema changes:
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When changing the analytical views, run sync_analytical_..._to_view()
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to update the corresponding table
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Remember to update the following files with any renamings:
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schemas/filter_ERD.csv
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mappings/VegCore-VegBIEN.csv
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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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Reinstall staging tables: . bin/reinstall_all
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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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Go to File > Export > Synchronize With SQL CREATE Script...
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For Input File, select schemas/vegbien.my.sql
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Click Continue
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In the changes list, select each table with an arrow next to it
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Click Update Model
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Click Continue
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Note: The generated SQL script will be empty because we are syncing in
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the opposite direction
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Click Execute
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Reposition any lines that have been reset
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Add any new tables by dragging them from the Catalog in the left sidebar
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to the diagram
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Remove any deleted tables by right-clicking the table's diagram element,
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selecting Delete '<table name>', and clicking Delete
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Save
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If desired, update the graphical ERD exports (see below)
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Update graphical ERD exports:
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Go to File > Export > Export as PNG...
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Select schemas/vegbien.ERD.png and click Save
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Go to File > Export > Export as SVG...
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Select schemas/vegbien.ERD.svg and click Save
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Go to File > Export > Export as Single Page PDF...
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Select schemas/vegbien.ERD.1_pg.pdf and click Save
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Go to File > Print...
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In the lower left corner, click PDF > Save as PDF...
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Set the Title and Author to ""
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Select schemas/vegbien.ERD.pdf and click Save
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Commit: svn ci -m "schemas/vegbien.ERD.mwb: Regenerated exports"
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Refactoring tips:
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To rename a table:
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In vegbien.sql, do the following:
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Replace regexp (?<=_|\b)<old>(?=_|\b) with <new>
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This is necessary because the table name is *everywhere*
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Search for <new>
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Manually change back any replacements inside comments
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To rename a column:
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Rename the column: ALTER TABLE <table> RENAME <old> TO <new>;
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Recreate any foreign key for the column, removing CONSTRAINT <name>
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This resets the foreign key name using the new column name
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Creating a poster of the ERD:
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Determine the poster size:
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Measure the line height (from the bottom of one line to the bottom
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of another): 16.3cm/24 lines = 0.679cm
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Measure the height of the ERD: 35.4cm*2 = 70.8cm
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Zoom in as far as possible
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Measure the height of a capital letter: 3.5mm
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357
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Measure the line height: 8.5mm
|
358
|
Calculate the text's fraction of the line height: 3.5mm/8.5mm = 0.41
|
359
|
Calculate the text height: 0.679cm*0.41 = 0.28cm
|
360
|
Calculate the text height's fraction of the ERD height:
|
361
|
0.28cm/70.8cm = 0.0040
|
362
|
Measure the text height on the *VegBank* ERD poster: 5.5mm = 0.55cm
|
363
|
Calculate the VegBIEN poster height to make the text the same size:
|
364
|
0.55cm/0.0040 = 137.5cm H; *1in/2.54cm = 54.1in H
|
365
|
The ERD aspect ratio is 11 in W x (2*8.5in H) = 11x17 portrait
|
366
|
Calculate the VegBIEN poster width: 54.1in H*11W/17H = 35.0in W
|
367
|
The minimum VegBIEN poster size is 35x54in portrait
|
368
|
Determine the cost:
|
369
|
The FedEx Kinkos near NCEAS (1030 State St, Santa Barbara, CA 93101)
|
370
|
charges the following for posters:
|
371
|
base: $7.25/sq ft
|
372
|
lamination: $3/sq ft
|
373
|
mounting on a board: $8/sq ft
|
374
|
|
375
|
Testing:
|
376
|
On a development machine, you should put the following in your .profile:
|
377
|
umask ug=rwx,o= # prevent files from becoming web-accessible
|
378
|
export log= n=2
|
379
|
Mapping process: make test
|
380
|
Including column-based import: make test by_col=1
|
381
|
If the row-based and column-based imports produce different inserted
|
382
|
row counts, this usually means that a table is underconstrained
|
383
|
(the unique indexes don't cover all possible rows).
|
384
|
This can occur if you didn't use COALESCE(field, null_value) around
|
385
|
a nullable field in a unique index. See sql_gen.null_sentinels for
|
386
|
the appropriate null value to use.
|
387
|
Map spreadsheet generation: make remake
|
388
|
Missing mappings: make missing_mappings
|
389
|
Everything (for most complete coverage): make test-all
|
390
|
|
391
|
Debugging:
|
392
|
"Binary chop" debugging:
|
393
|
(This is primarily useful for regressions that occurred in a previous
|
394
|
revision, which was committed without running all the tests)
|
395
|
svn up -r <rev>; make inputs/.TNRS/reinstall; make schemas/public/reinstall; make <failed-test>.xml
|
396
|
.htaccess:
|
397
|
mod_rewrite:
|
398
|
IMPORTANT: whenever you change the DirectorySlash setting for a
|
399
|
directory, you *must* clear your browser's cache to ensure that
|
400
|
a cached redirect is not used. this is because RewriteRule
|
401
|
redirects are (by default) temporary, but DirectorySlash
|
402
|
redirects are permanent.
|
403
|
for Firefox:
|
404
|
press Cmd+Shift+Delete
|
405
|
check only Cache
|
406
|
press Enter or click Clear Now
|
407
|
|
408
|
WinMerge setup:
|
409
|
Install WinMerge from <http://winmerge.org/>
|
410
|
Open WinMerge
|
411
|
Go to Edit > Options and click Compare in the left sidebar
|
412
|
Enable "Moved block detection", as described at
|
413
|
<http://manual.winmerge.org/Configuration.html#d0e5892>.
|
414
|
Set Whitespace to Ignore change, as described at
|
415
|
<http://manual.winmerge.org/Configuration.html#d0e5758>.
|
416
|
|
417
|
Documentation:
|
418
|
To generate a Redmine-formatted list of steps for column-based import:
|
419
|
make schemas/public/reinstall
|
420
|
make inputs/ACAD/Specimen/logs/steps.by_col.log.sql
|
421
|
To import and scrub just the test taxonomic names:
|
422
|
inputs/test_taxonomic_names/test_scrub
|
423
|
|
424
|
General:
|
425
|
To see a program's description, read its top-of-file comment
|
426
|
To see a program's usage, run it without arguments
|
427
|
To remake a directory: make <dir>/remake
|
428
|
To remake a file: make <file>-remake
|