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aaronmk
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Installation:
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6886
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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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6887
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aaronmk
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cd bien/
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702
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aaronmk
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Install: make install
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3370
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aaronmk
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WARNING: This will delete the current public schema of your VegBIEN DB!
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702
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aaronmk
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Uninstall: make uninstall
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3370
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aaronmk
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WARNING: This will delete your entire VegBIEN DB!
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3374
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aaronmk
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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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6846
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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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6856
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aaronmk
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make mappings/VegCore.htm-remake; make mappings/
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6987
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aaronmk
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svn ci -m "mappings/VegCore.csv: Regenerated from wiki"
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3674
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aaronmk
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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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6820
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aaronmk
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is in recovery mode" which go away upon reimport, or you may not be able
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aaronmk
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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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aaronmk
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Single datasource import:
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(Re)import and scrub: make inputs/<datasrc>/reimport_scrub
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(Re)import only: make inputs/<datasrc>/reimport
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(Re)scrub: make inputs/<datasrc>/rescrub
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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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4487
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aaronmk
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On local machine:
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7114
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aaronmk
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make inputs/upload
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4487
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aaronmk
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make test by_col=1
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5016
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aaronmk
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See note under Testing below
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4487
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aaronmk
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On vegbiendev:
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7032
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aaronmk
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Ensure there are no local modifications: svn st
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4482
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aaronmk
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svn up
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7114
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aaronmk
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For each newly-uploaded datasource above: make inputs/<datasrc>/reinstall
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6952
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aaronmk
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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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6962
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aaronmk
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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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7205
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aaronmk
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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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7224
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aaronmk
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Make sure there is at least 150GB of disk space on /: df -h
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7300
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aaronmk
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The import schema is 100GB, and may use additional space for temp tables
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6804
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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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6995
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unset version
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5206
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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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4481
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aaronmk
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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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6797
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Note that import_all will take several hours to import the NCBI backbone
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and TNRS names before returning control to the shell.
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4481
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aaronmk
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Wait (overnight) for the import to finish
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6796
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aaronmk
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On local machine: make inputs/download-logs
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7318
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aaronmk
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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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Check that unscrubbed_taxondetermination_view returns no rows
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7319
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Check that there are taxondeterminations whose source_id is
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source_by_shortname('TNRS')
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6964
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tail inputs/{.,}*/*/logs/$version.log.sql
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6799
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In the output, search for "Command exited with non-zero status"
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For inputs that have this, fix the associated bug(s)
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If many inputs have errors, discard the current (partial) import:
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6953
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aaronmk
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make schemas/$version/uninstall
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6103
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aaronmk
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Otherwise, continue
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6959
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make schemas/$version/publish
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7299
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unset version
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6848
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aaronmk
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sudo backups/fix_perms
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6666
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aaronmk
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make backups/upload
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6719
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aaronmk
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On jupiter:
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6888
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aaronmk
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cd /data/dev/aaronmk/bien/backups
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6719
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aaronmk
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For each newly-archived backup:
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7326
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aaronmk
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make -s <backup>.md5/test
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6719
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aaronmk
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Check that "OK" is printed next to the filename
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6494
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aaronmk
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On nimoy:
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cd /home/bien/svn/
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svn up
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6993
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aaronmk
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export version=<version>
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6948
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aaronmk
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make backups/analytical_aggregate.$version.csv/download
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7326
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aaronmk
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make -s backups/analytical_aggregate.$version.csv.md5/test
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6723
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aaronmk
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Check that "OK" is printed next to the filename
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6494
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aaronmk
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In the bien_web DB:
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6994
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aaronmk
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Create the analytical_aggregate_<version> table using its schema
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6652
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aaronmk
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in schemas/vegbien.my.sql
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6948
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aaronmk
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env table=analytical_aggregate_$version bin/publish_analytical_db \
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backups/analytical_aggregate.$version.csv
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4677
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aaronmk
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If desired, record the import times in inputs/import.stats.xls:
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Open inputs/import.stats.xls
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7027
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aaronmk
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Insert a copy of the leftmost "By column" column group before it
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7344
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aaronmk
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export version=<version>
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6996
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aaronmk
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bin/import_date inputs/{.,}*/*/logs/$version.log.sql
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4677
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aaronmk
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Update the import date in the upper-right corner
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6996
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aaronmk
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bin/import_times inputs/{.,}*/*/logs/$version.log.sql
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4677
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aaronmk
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Paste the output over the # Rows/Time columns, making sure that the
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row counts match up with the previous import's row counts
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If the row counts do not match up, insert or reorder rows as needed
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until they do
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4777
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aaronmk
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Commit: svn ci -m "inputs/import.stats.xls: Updated import times"
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7325
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aaronmk
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To scrub unscrubbed taxondeterminations: make scrub by_col=1 &
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To view progress:
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tail -f inputs/.TNRS/public.unscrubbed_taxondetermination_view/logs/$version.log.sql
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6956
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aaronmk
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To remake analytical DB: bin/make_analytical_db &
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6212
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aaronmk
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To view progress:
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tail -f inputs/analytical_db/logs/make_analytical_db.log.sql
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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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3408
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aaronmk
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Archived imports:
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6942
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aaronmk
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Back up: make backups/<version>.backup &
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6516
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aaronmk
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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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7326
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aaronmk
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Test: make -s backups/<version>.backup/test &
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6942
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aaronmk
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Restore: make backups/<version>.backup/restore &
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Remove: make backups/<version>.backup/remove
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3701
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aaronmk
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Download: make backups/download
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5801
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aaronmk
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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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3408
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aaronmk
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Full DB:
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6942
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aaronmk
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Back up: make backups/vegbien.<version>.backup &
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7326
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aaronmk
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Test: make -s backups/vegbien.<version>.backup/test &
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6942
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aaronmk
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Restore: make backups/vegbien.<version>.backup/restore &
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3701
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aaronmk
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Download: make backups/download
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3698
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aaronmk
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Import logs:
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Download: make inputs/download-logs
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554
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aaronmk
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1773
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aaronmk
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Datasource setup:
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4219
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aaronmk
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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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6366
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aaronmk
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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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Create a database for the MySQL export in phpMyAdmin
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mysql -p 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 your local MySQL DB
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6372
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aaronmk
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Install the export according to Install the staging tables below
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152 |
4218
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aaronmk
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Add input data for each table present in the datasource:
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6365
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aaronmk
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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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4264
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aaronmk
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Note that if this table will be joined together with another table, its
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157 |
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name must end in ".src"
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4219
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aaronmk
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make inputs/<datasrc>/<table>/add
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4342
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aaronmk
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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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6373
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aaronmk
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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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6370
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aaronmk
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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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4212
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aaronmk
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Important: When exporting relational databases to CSVs, you MUST ensure
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166 |
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that embedded quotes are escaped by doubling them, *not* by
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167 |
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preceding them with a "\" as is the default in phpMyAdmin
|
168 |
3612
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aaronmk
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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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4255
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aaronmk
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Add <table> to inputs/<datasrc>/import_order.txt before other tables
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4220
|
aaronmk
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that depend on it
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3611
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aaronmk
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Install the staging tables:
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176 |
4219
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aaronmk
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make inputs/<datasrc>/reinstall quiet=1 &
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177 |
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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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3611
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aaronmk
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tail provides a header line with the filename
|
180 |
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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':
|
182 |
4182
|
aaronmk
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Add a header override file "+header.<ext>" in <table>/:
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183 |
3611
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aaronmk
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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
|
191 |
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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
|
194 |
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If you made any changes, re-run the install command above
|
195 |
6015
|
aaronmk
|
Auto-create the map spreadsheets: make inputs/<datasrc>/
|
196 |
3576
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aaronmk
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Map each table's columns:
|
197 |
4125
|
aaronmk
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In each <table>/ subdir, for each "via map" map.csv:
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198 |
3576
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aaronmk
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Open the map in a spreadsheet editor
|
199 |
4125
|
aaronmk
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Open the "core map" /mappings/Veg+-VegBIEN.csv
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200 |
3576
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aaronmk
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In each row of the via map, set the right column to a value from the
|
201 |
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left column of the core map
|
202 |
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Save
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203 |
4219
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aaronmk
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Regenerate the derived maps: make inputs/<datasrc>/
|
204 |
3593
|
aaronmk
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Accept the test cases:
|
205 |
4219
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aaronmk
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make inputs/<datasrc>/test
|
206 |
3593
|
aaronmk
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When prompted to "Accept new test output", enter y and press ENTER
|
207 |
3690
|
aaronmk
|
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
|
209 |
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- Add a SQL function that filters or transforms the invalid data
|
210 |
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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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212 |
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prevent the automatic mapper from auto-removing the mapping.
|
213 |
3783
|
aaronmk
|
When accepting tests, it's helpful to use WinMerge
|
214 |
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(see WinMerge setup below for configuration)
|
215 |
4476
|
aaronmk
|
make inputs/<datasrc>/test by_col=1
|
216 |
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If you get errors this time, this always indicates a bug, usually in
|
217 |
6368
|
aaronmk
|
the VegBIEN unique constraints or column-based import itself
|
218 |
5881
|
aaronmk
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Add newly-created files: make inputs/<datasrc>/add
|
219 |
4219
|
aaronmk
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Commit: svn ci -m "Added inputs/<datasrc>/" inputs/<datasrc>/
|
220 |
3585
|
aaronmk
|
Update vegbiendev:
|
221 |
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On vegbiendev: svn up
|
222 |
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On local machine: make inputs/upload
|
223 |
4291
|
aaronmk
|
On vegbiendev:
|
224 |
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Follow the steps under Install the staging tables above
|
225 |
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make inputs/<datasrc>/test
|
226 |
1773
|
aaronmk
|
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227 |
6484
|
aaronmk
|
Datasource refreshing:
|
228 |
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VegBank:
|
229 |
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make inputs/VegBank/vegbank.sql-remake
|
230 |
|
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make inputs/VegBank/reinstall quiet=1 &
|
231 |
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|
232 |
702
|
aaronmk
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Schema changes:
|
233 |
7347
|
aaronmk
|
When changing the analytical views, run sync_analytical_..._to_view()
|
234 |
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to update the corresponding table
|
235 |
5227
|
aaronmk
|
Remember to update the following files with any renamings:
|
236 |
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schemas/filter_ERD.csv
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237 |
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mappings/VegCore-VegBIEN.csv
|
238 |
6058
|
aaronmk
|
mappings/verify.*.sql
|
239 |
702
|
aaronmk
|
Regenerate schema from installed DB: make schemas/remake
|
240 |
6951
|
aaronmk
|
Reinstall DB from schema: make schemas/public/reinstall schemas/reinstall
|
241 |
3370
|
aaronmk
|
WARNING: This will delete the current public schema of your VegBIEN DB!
|
242 |
3589
|
aaronmk
|
Reinstall staging tables: . bin/reinstall_all
|
243 |
702
|
aaronmk
|
Sync ERD with vegbien.sql schema:
|
244 |
|
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Run make schemas/vegbien.my.sql
|
245 |
|
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Open schemas/vegbien.ERD.mwb in MySQLWorkbench
|
246 |
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Go to File > Export > Synchronize With SQL CREATE Script...
|
247 |
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For Input File, select schemas/vegbien.my.sql
|
248 |
|
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Click Continue
|
249 |
6369
|
aaronmk
|
In the changes list, select each table with an arrow next to it
|
250 |
702
|
aaronmk
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Click Update Model
|
251 |
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Click Continue
|
252 |
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Note: The generated SQL script will be empty because we are syncing in
|
253 |
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the opposite direction
|
254 |
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Click Execute
|
255 |
|
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Reposition any lines that have been reset
|
256 |
|
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Add any new tables by dragging them from the Catalog in the left sidebar
|
257 |
|
|
to the diagram
|
258 |
|
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Remove any deleted tables by right-clicking the table's diagram element,
|
259 |
|
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selecting Delete '<table name>', and clicking Delete
|
260 |
|
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Save
|
261 |
1774
|
aaronmk
|
If desired, update the graphical ERD exports (see below)
|
262 |
|
|
Update graphical ERD exports:
|
263 |
702
|
aaronmk
|
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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Measure the line height: 8.5mm
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Calculate the text's fraction of the line height: 3.5mm/8.5mm = 0.41
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Calculate the text height: 0.679cm*0.41 = 0.28cm
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Calculate the text height's fraction of the ERD height:
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0.28cm/70.8cm = 0.0040
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Measure the text height on the *VegBank* ERD poster: 5.5mm = 0.55cm
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Calculate the VegBIEN poster height to make the text the same size:
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0.55cm/0.0040 = 137.5cm H; *1in/2.54cm = 54.1in H
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The ERD aspect ratio is 11 in W x (2*8.5in H) = 11x17 portrait
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Calculate the VegBIEN poster width: 54.1in H*11W/17H = 35.0in W
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The minimum VegBIEN poster size is 35x54in portrait
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Determine the cost:
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The FedEx Kinkos near NCEAS (1030 State St, Santa Barbara, CA 93101)
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charges the following for posters:
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base: $7.25/sq ft
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lamination: $3/sq ft
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mounting on a board: $8/sq ft
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Testing:
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On a development machine, you should put the following in your .profile:
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export log= n=2
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Mapping process: make test
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Including column-based import: make test by_col=1
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If the row-based and column-based imports produce different inserted
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row counts, this usually means that a table is underconstrained
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(the unique indexes don't cover all possible rows).
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This can occur if you didn't use COALESCE(field, null_value) around
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a nullable field in a unique index. See sql_gen.null_sentinels for
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the appropriate null value to use.
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Map spreadsheet generation: make remake
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Missing mappings: make missing_mappings
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Everything (for most complete coverage): make test-all
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Debugging:
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"Binary chop" debugging:
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(This is primarily useful for regressions that occurred in a previous
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revision, which was committed without running all the tests)
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svn up -r <rev>; make inputs/.TNRS/reinstall; make schemas/public/reinstall; make <failed-test>.xml
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WinMerge setup:
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Install WinMerge from <http://winmerge.org/>
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Open WinMerge
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Go to Edit > Options and click Compare in the left sidebar
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Enable "Moved block detection", as described at
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<http://manual.winmerge.org/Configuration.html#d0e5892>.
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Set Whitespace to Ignore change, as described at
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<http://manual.winmerge.org/Configuration.html#d0e5758>.
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Documentation:
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To generate a Redmine-formatted list of steps for column-based import:
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make schemas/public/reinstall
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make inputs/ACAD/Specimen/logs/steps.by_col.log.sql
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To import and scrub just the test taxonomic names:
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inputs/test_taxonomic_names/test_scrub
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|
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General:
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To see a program's description, read its top-of-file comment
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To see a program's usage, run it without arguments
|
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To remake a directory: make <dir>/remake
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To remake a file: make <file>-remake
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