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702
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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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6 |
702
|
aaronmk
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Uninstall: make uninstall
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7 |
3370
|
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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aaronmk
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VegCore data dictionary:
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12 |
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Regularly, or whenever the VegCore data dictionary page
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13 |
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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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7482
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aaronmk
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When moving terms, check that no terms were lost: svn di
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7513
|
aaronmk
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svn ci -m "mappings/VegCore.htm: 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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6821
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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
|
aaronmk
|
|
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7287
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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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35 |
5016
|
aaronmk
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See note under Testing below
|
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4487
|
aaronmk
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On vegbiendev:
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7032
|
aaronmk
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Ensure there are no local modifications: svn st
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4482
|
aaronmk
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svn up
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7564
|
aaronmk
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make inputs/download
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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
|
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
|
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
|
aaronmk
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Make sure there is at least 150GB of disk space on /: df -h
|
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7300
|
aaronmk
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The import schema is 100GB, and may use additional space for temp tables
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6804
|
aaronmk
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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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53 |
6995
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aaronmk
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unset version
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5206
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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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4481
|
aaronmk
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To stop all running imports: . bin/stop_imports
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5318
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aaronmk
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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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7410
|
aaronmk
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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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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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7598
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aaronmk
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(takes 90 s with LIMIT 1)
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7319
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aaronmk
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Check that there are taxondeterminations whose source_id is
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69 |
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source_by_shortname('TNRS')
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6964
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aaronmk
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tail inputs/{.,}*/*/logs/$version.log.sql
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6799
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aaronmk
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In the output, search for "Command exited with non-zero status"
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For inputs that have this, fix the associated bug(s)
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If many inputs have errors, discard the current (partial) import:
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6953
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aaronmk
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make schemas/$version/uninstall
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6103
|
aaronmk
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Otherwise, continue
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6959
|
aaronmk
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make schemas/$version/publish
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7299
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aaronmk
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unset version
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6848
|
aaronmk
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sudo backups/fix_perms
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79 |
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
|
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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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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7640
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aaronmk
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make -s backups/analytical_aggregate.$version.csv.md5/test
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Check that "OK" is printed next to the filename
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6948
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aaronmk
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env table=analytical_aggregate_$version bin/publish_analytical_db \
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backups/analytical_aggregate.$version.csv
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4677
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aaronmk
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If desired, record the import times in inputs/import.stats.xls:
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98 |
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Open inputs/import.stats.xls
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7027
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aaronmk
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Insert a copy of the leftmost "By column" column group before it
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7344
|
aaronmk
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export version=<version>
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6996
|
aaronmk
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bin/import_date inputs/{.,}*/*/logs/$version.log.sql
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102 |
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/$version.log.sql
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104 |
4677
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aaronmk
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Paste the output over the # Rows/Time columns, making sure that the
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row counts match up with the previous import's row counts
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106 |
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If the row counts do not match up, insert or reorder rows as needed
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107 |
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until they do
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108 |
4777
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aaronmk
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Commit: svn ci -m "inputs/import.stats.xls: Updated import times"
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109 |
7325
|
aaronmk
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To scrub unscrubbed taxondeterminations: make scrub by_col=1 &
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110 |
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To view progress:
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tail -f inputs/.TNRS/public.unscrubbed_taxondetermination_view/logs/$version.log.sql
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112 |
6956
|
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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114 |
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tail -f inputs/analytical_db/logs/make_analytical_db.log.sql
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115 |
3381
|
aaronmk
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|
116 |
3545
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aaronmk
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Backups:
|
117 |
3408
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aaronmk
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Archived imports:
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118 |
6942
|
aaronmk
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Back up: make backups/<version>.backup &
|
119 |
6516
|
aaronmk
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Note: To back up the last import, you must archive it first:
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120 |
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make schemas/rotate
|
121 |
7326
|
aaronmk
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Test: make -s backups/<version>.backup/test &
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122 |
6942
|
aaronmk
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Restore: make backups/<version>.backup/restore &
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123 |
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Remove: make backups/<version>.backup/remove
|
124 |
3701
|
aaronmk
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Download: make backups/download
|
125 |
5801
|
aaronmk
|
TNRS cache:
|
126 |
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Back up: make backups/TNRS.backup-remake &
|
127 |
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Restore:
|
128 |
|
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yes|make inputs/.TNRS/uninstall
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129 |
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make backups/TNRS.backup/restore &
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130 |
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yes|make schemas/public/reinstall
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131 |
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Must come after TNRS restore to recreate tnrs_input_name view
|
132 |
3408
|
aaronmk
|
Full DB:
|
133 |
6942
|
aaronmk
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Back up: make backups/vegbien.<version>.backup &
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134 |
7326
|
aaronmk
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Test: make -s backups/vegbien.<version>.backup/test &
|
135 |
6942
|
aaronmk
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Restore: make backups/vegbien.<version>.backup/restore &
|
136 |
3701
|
aaronmk
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Download: make backups/download
|
137 |
3698
|
aaronmk
|
Import logs:
|
138 |
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Download: make inputs/download-logs
|
139 |
554
|
aaronmk
|
|
140 |
1773
|
aaronmk
|
Datasource setup:
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141 |
4219
|
aaronmk
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Add a new datasource: make inputs/<datasrc>/add
|
142 |
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<datasrc> may not contain spaces, and should be abbreviated.
|
143 |
|
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If the datasource is a herbarium, <datasrc> should be the herbarium code
|
144 |
|
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as defined by the Index Herbariorum <http://sweetgum.nybg.org/ih/>
|
145 |
6366
|
aaronmk
|
For MySQL inputs (exports and live DB connections):
|
146 |
|
|
For .sql exports:
|
147 |
|
|
Place the original .sql file in _src/ (*not* in _MySQL/)
|
148 |
|
|
Create a database for the MySQL export in phpMyAdmin
|
149 |
7578
|
aaronmk
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bin/mysql_bien database <inputs/<datasrc>/_src/export.sql
|
150 |
6366
|
aaronmk
|
mkdir inputs/<datasrc>/_MySQL/
|
151 |
|
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cp -p lib/MySQL.{data,schema}.sql.make inputs/<datasrc>/_MySQL/
|
152 |
|
|
Edit _MySQL/*.make for the DB connection
|
153 |
|
|
For a .sql export, use your local MySQL DB
|
154 |
7529
|
aaronmk
|
Skip the Add input data for each table section
|
155 |
7530
|
aaronmk
|
For MS Access databases:
|
156 |
|
|
Place the .mdb or .accdb file in _src/
|
157 |
|
|
Download and install Access To PostgreSQL from
|
158 |
|
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http://www.bullzip.com/download.php
|
159 |
|
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Use Access To PostgreSQL to export the database:
|
160 |
|
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Export just the tables/indexes to inputs/<datasrc>/<file>.schema.sql
|
161 |
|
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Export just the data to inputs/<datasrc>/<file>.data.sql
|
162 |
|
|
In <file>.schema.sql, make the following changes:
|
163 |
|
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Replace text "BOOLEAN" with "/*BOOLEAN*/INTEGER"
|
164 |
|
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Replace text "DOUBLE PRECISION NULL" with "DOUBLE PRECISION"
|
165 |
|
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Skip the Add input data for each table section
|
166 |
4218
|
aaronmk
|
Add input data for each table present in the datasource:
|
167 |
6365
|
aaronmk
|
For .sql exports, you must use the name of the table in the DB export
|
168 |
|
|
For CSV files, you can use any name. It's recommended to use a table
|
169 |
|
|
name from <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV#Suggested-table-names>
|
170 |
4264
|
aaronmk
|
Note that if this table will be joined together with another table, its
|
171 |
|
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name must end in ".src"
|
172 |
4219
|
aaronmk
|
make inputs/<datasrc>/<table>/add
|
173 |
4342
|
aaronmk
|
Important: DO NOT just create an empty directory named <table>!
|
174 |
|
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This command also creates necessary subdirs, such as logs/.
|
175 |
6373
|
aaronmk
|
If the table is in a .sql export: make inputs/<datasrc>/<table>/install
|
176 |
|
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Otherwise, place the CSV(s) for the table in
|
177 |
6370
|
aaronmk
|
inputs/<datasrc>/<table>/ OR place a query joining other tables
|
178 |
|
|
together in inputs/<datasrc>/<table>/create.sql
|
179 |
4212
|
aaronmk
|
Important: When exporting relational databases to CSVs, you MUST ensure
|
180 |
|
|
that embedded quotes are escaped by doubling them, *not* by
|
181 |
|
|
preceding them with a "\" as is the default in phpMyAdmin
|
182 |
3612
|
aaronmk
|
If there are multiple part files for a table, and the header is repeated
|
183 |
|
|
in each part, make sure each header is EXACTLY the same.
|
184 |
|
|
(If the headers are not the same, the CSV concatenation script
|
185 |
|
|
assumes the part files don't have individual headers and treats the
|
186 |
|
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subsequent headers as data rows.)
|
187 |
4255
|
aaronmk
|
Add <table> to inputs/<datasrc>/import_order.txt before other tables
|
188 |
4220
|
aaronmk
|
that depend on it
|
189 |
3611
|
aaronmk
|
Install the staging tables:
|
190 |
4219
|
aaronmk
|
make inputs/<datasrc>/reinstall quiet=1 &
|
191 |
|
|
To view progress: tail -f inputs/<datasrc>/<table>/logs/install.log.sql
|
192 |
|
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View the logs: tail -n +1 inputs/<datasrc>/*/logs/install.log.sql
|
193 |
3611
|
aaronmk
|
tail provides a header line with the filename
|
194 |
|
|
+1 starts at the first line, to show the whole file
|
195 |
|
|
For every file with an error 'column "..." specified more than once':
|
196 |
4182
|
aaronmk
|
Add a header override file "+header.<ext>" in <table>/:
|
197 |
3611
|
aaronmk
|
Note: The leading "+" should sort it before the flat files.
|
198 |
|
|
"_" unfortunately sorts *after* capital letters in ASCII.
|
199 |
|
|
Create a text file containing the header line of the flat files
|
200 |
|
|
Add an ! at the beginning of the line
|
201 |
|
|
This signals cat_csv that this is a header override.
|
202 |
|
|
For empty names, use their 0-based column # (by convention)
|
203 |
|
|
For duplicate names, add a distinguishing suffix
|
204 |
|
|
For long names that collided, rename them to <= 63 chars long
|
205 |
|
|
Do NOT make readability changes in this step; that is what the
|
206 |
|
|
map spreadsheets (below) are for.
|
207 |
|
|
Save
|
208 |
|
|
If you made any changes, re-run the install command above
|
209 |
6015
|
aaronmk
|
Auto-create the map spreadsheets: make inputs/<datasrc>/
|
210 |
3576
|
aaronmk
|
Map each table's columns:
|
211 |
4125
|
aaronmk
|
In each <table>/ subdir, for each "via map" map.csv:
|
212 |
3576
|
aaronmk
|
Open the map in a spreadsheet editor
|
213 |
4125
|
aaronmk
|
Open the "core map" /mappings/Veg+-VegBIEN.csv
|
214 |
3576
|
aaronmk
|
In each row of the via map, set the right column to a value from the
|
215 |
|
|
left column of the core map
|
216 |
|
|
Save
|
217 |
4219
|
aaronmk
|
Regenerate the derived maps: make inputs/<datasrc>/
|
218 |
3593
|
aaronmk
|
Accept the test cases:
|
219 |
4219
|
aaronmk
|
make inputs/<datasrc>/test
|
220 |
3593
|
aaronmk
|
When prompted to "Accept new test output", enter y and press ENTER
|
221 |
3690
|
aaronmk
|
If you instead get errors, do one of the following for each one:
|
222 |
|
|
- If the error was due to a bug, fix it
|
223 |
|
|
- Add a SQL function that filters or transforms the invalid data
|
224 |
|
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- Make an empty mapping for the columns that produced the error.
|
225 |
|
|
Put something in the Comments column of the map spreadsheet to
|
226 |
|
|
prevent the automatic mapper from auto-removing the mapping.
|
227 |
3783
|
aaronmk
|
When accepting tests, it's helpful to use WinMerge
|
228 |
|
|
(see WinMerge setup below for configuration)
|
229 |
4476
|
aaronmk
|
make inputs/<datasrc>/test by_col=1
|
230 |
|
|
If you get errors this time, this always indicates a bug, usually in
|
231 |
6368
|
aaronmk
|
the VegBIEN unique constraints or column-based import itself
|
232 |
5881
|
aaronmk
|
Add newly-created files: make inputs/<datasrc>/add
|
233 |
4219
|
aaronmk
|
Commit: svn ci -m "Added inputs/<datasrc>/" inputs/<datasrc>/
|
234 |
3585
|
aaronmk
|
Update vegbiendev:
|
235 |
|
|
On vegbiendev: svn up
|
236 |
|
|
On local machine: make inputs/upload
|
237 |
4291
|
aaronmk
|
On vegbiendev:
|
238 |
|
|
Follow the steps under Install the staging tables above
|
239 |
|
|
make inputs/<datasrc>/test
|
240 |
1773
|
aaronmk
|
|
241 |
6484
|
aaronmk
|
Datasource refreshing:
|
242 |
|
|
VegBank:
|
243 |
|
|
make inputs/VegBank/vegbank.sql-remake
|
244 |
|
|
make inputs/VegBank/reinstall quiet=1 &
|
245 |
|
|
|
246 |
702
|
aaronmk
|
Schema changes:
|
247 |
7347
|
aaronmk
|
When changing the analytical views, run sync_analytical_..._to_view()
|
248 |
|
|
to update the corresponding table
|
249 |
5227
|
aaronmk
|
Remember to update the following files with any renamings:
|
250 |
|
|
schemas/filter_ERD.csv
|
251 |
|
|
mappings/VegCore-VegBIEN.csv
|
252 |
6058
|
aaronmk
|
mappings/verify.*.sql
|
253 |
702
|
aaronmk
|
Regenerate schema from installed DB: make schemas/remake
|
254 |
6951
|
aaronmk
|
Reinstall DB from schema: make schemas/public/reinstall schemas/reinstall
|
255 |
3370
|
aaronmk
|
WARNING: This will delete the current public schema of your VegBIEN DB!
|
256 |
3589
|
aaronmk
|
Reinstall staging tables: . bin/reinstall_all
|
257 |
702
|
aaronmk
|
Sync ERD with vegbien.sql schema:
|
258 |
|
|
Run make schemas/vegbien.my.sql
|
259 |
|
|
Open schemas/vegbien.ERD.mwb in MySQLWorkbench
|
260 |
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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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aaronmk
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In the changes list, select each table with an arrow next to it
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702
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aaronmk
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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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1774
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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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702
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aaronmk
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Go to File > Export > Export as PNG...
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1774
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aaronmk
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Select schemas/vegbien.ERD.png and click Save
|
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702
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aaronmk
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Go to File > Export > Export as SVG...
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1774
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aaronmk
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Select schemas/vegbien.ERD.svg and click Save
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702
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aaronmk
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Go to File > Export > Export as Single Page PDF...
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4087
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aaronmk
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Select schemas/vegbien.ERD.1_pg.pdf and click Save
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1774
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aaronmk
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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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|
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Set the Title and Author to ""
|
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4087
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aaronmk
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Select schemas/vegbien.ERD.pdf and click Save
|
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7003
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aaronmk
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Commit: svn ci -m "schemas/vegbien.ERD.mwb: Regenerated exports"
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5226
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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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|
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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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|
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Recreate any foreign key for the column, removing CONSTRAINT <name>
|
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|
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This resets the foreign key name using the new column name
|
299 |
6320
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aaronmk
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Creating a poster of the ERD:
|
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6326
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aaronmk
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Determine the poster size:
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6320
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aaronmk
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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
|
303 |
|
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Measure the height of the ERD: 35.4cm*2 = 70.8cm
|
304 |
|
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Zoom in as far as possible
|
305 |
|
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Measure the height of a capital letter: 3.5mm
|
306 |
|
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Measure the line height: 8.5mm
|
307 |
|
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Calculate the text's fraction of the line height: 3.5mm/8.5mm = 0.41
|
308 |
|
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Calculate the text height: 0.679cm*0.41 = 0.28cm
|
309 |
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Calculate the text height's fraction of the ERD height:
|
310 |
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0.28cm/70.8cm = 0.0040
|
311 |
|
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Measure the text height on the *VegBank* ERD poster: 5.5mm = 0.55cm
|
312 |
|
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Calculate the VegBIEN poster height to make the text the same size:
|
313 |
|
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0.55cm/0.0040 = 137.5cm H; *1in/2.54cm = 54.1in H
|
314 |
|
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The ERD aspect ratio is 11 in W x (2*8.5in H) = 11x17 portrait
|
315 |
|
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Calculate the VegBIEN poster width: 54.1in H*11W/17H = 35.0in W
|
316 |
|
|
The minimum VegBIEN poster size is 35x54in portrait
|
317 |
6327
|
aaronmk
|
Determine the cost:
|
318 |
|
|
The FedEx Kinkos near NCEAS (1030 State St, Santa Barbara, CA 93101)
|
319 |
|
|
charges the following for posters:
|
320 |
|
|
base: $7.25/sq ft
|
321 |
|
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lamination: $3/sq ft
|
322 |
|
|
mounting on a board: $8/sq ft
|
323 |
203
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aaronmk
|
|
324 |
1459
|
aaronmk
|
Testing:
|
325 |
7090
|
aaronmk
|
On a development machine, you should put the following in your .profile:
|
326 |
7122
|
aaronmk
|
export log= n=2
|
327 |
1459
|
aaronmk
|
Mapping process: make test
|
328 |
4292
|
aaronmk
|
Including column-based import: make test by_col=1
|
329 |
4985
|
aaronmk
|
If the row-based and column-based imports produce different inserted
|
330 |
|
|
row counts, this usually means that a table is underconstrained
|
331 |
|
|
(the unique indexes don't cover all possible rows).
|
332 |
|
|
This can occur if you didn't use COALESCE(field, null_value) around
|
333 |
|
|
a nullable field in a unique index. See sql_gen.null_sentinels for
|
334 |
|
|
the appropriate null value to use.
|
335 |
1459
|
aaronmk
|
Map spreadsheet generation: make remake
|
336 |
1744
|
aaronmk
|
Missing mappings: make missing_mappings
|
337 |
1459
|
aaronmk
|
Everything (for most complete coverage): make test-all
|
338 |
702
|
aaronmk
|
|
339 |
7183
|
aaronmk
|
Debugging:
|
340 |
|
|
"Binary chop" debugging:
|
341 |
|
|
(This is primarily useful for regressions that occurred in a previous
|
342 |
|
|
revision, which was committed without running all the tests)
|
343 |
|
|
svn up -r <rev>; make inputs/.TNRS/reinstall; make schemas/public/reinstall; make <failed-test>.xml
|
344 |
|
|
|
345 |
3783
|
aaronmk
|
WinMerge setup:
|
346 |
|
|
Install WinMerge from <http://winmerge.org/>
|
347 |
3785
|
aaronmk
|
Open WinMerge
|
348 |
|
|
Go to Edit > Options and click Compare in the left sidebar
|
349 |
3783
|
aaronmk
|
Enable "Moved block detection", as described at
|
350 |
|
|
<http://manual.winmerge.org/Configuration.html#d0e5892>.
|
351 |
3784
|
aaronmk
|
Set Whitespace to Ignore change, as described at
|
352 |
|
|
<http://manual.winmerge.org/Configuration.html#d0e5758>.
|
353 |
3783
|
aaronmk
|
|
354 |
3133
|
aaronmk
|
Documentation:
|
355 |
|
|
To generate a Redmine-formatted list of steps for column-based import:
|
356 |
7178
|
aaronmk
|
make schemas/public/reinstall
|
357 |
6291
|
aaronmk
|
make inputs/ACAD/Specimen/logs/steps.by_col.log.sql
|
358 |
5210
|
aaronmk
|
To import and scrub just the test taxonomic names:
|
359 |
5415
|
aaronmk
|
inputs/test_taxonomic_names/test_scrub
|
360 |
3133
|
aaronmk
|
|
361 |
702
|
aaronmk
|
General:
|
362 |
|
|
To see a program's description, read its top-of-file comment
|
363 |
|
|
To see a program's usage, run it without arguments
|
364 |
3389
|
aaronmk
|
To remake a directory: make <dir>/remake
|
365 |
|
|
To remake a file: make <file>-remake
|