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702
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aaronmk
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Installation:
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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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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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702
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aaronmk
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Data import:
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1550
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aaronmk
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Import data into VegBIEN: . bin/import_all
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aaronmk
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Using column-based import: . bin/with_all 'import by_col=1'
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Stop all running imports: . bin/stop_imports
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aaronmk
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Archive the last import: make schemas/rotate
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3381
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aaronmk
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Remove the last import: make schemas/public/reinstall
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WARNING: This will delete the current public schema of your VegBIEN DB!
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aaronmk
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Re-import data: make schemas/rotate; . bin/import_all
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Note: This will archive the last import.
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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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3547
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aaronmk
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After a new import:
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make schemas/rotate
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Rename the rotated schema using the date in the first datasource's log
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file name
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aaronmk
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Delete previous imports so they won't bloat the full DB backup:
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make backups/public.<date>.backup/remove
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3547
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aaronmk
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make backups/<schema>.backup/test & make backups/vegbien.backup/all &
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aaronmk
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Archived imports:
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Back up: make backups/public.<date>.backup &
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3546
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aaronmk
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Note: To back up the last import, you must archive it first (above)
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aaronmk
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Test: make backups/public.<date>.backup/test &
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aaronmk
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Restore: make backups/public.<date>.backup/restore &
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Remove: make backups/public.<date>.backup/remove
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Full DB:
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3546
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aaronmk
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Back up, test, and rotate: make backups/vegbien.backup/all &
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3439
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aaronmk
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Back up and rotate: make backups/vegbien.backup/rotate &
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Test: make backups/vegbien.<date>.backup/test &
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Restore: make backups/vegbien.<date>.backup/restore &
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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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3586
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aaronmk
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Add a new datasource: make inputs/<name>/add
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<name> may not contain spaces, and should be abbreviated.
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If the datasource is a herbarium, <name> should be the herbarium code as
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defined by the Index Herbariorum <http://sweetgum.nybg.org/ih/>
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3557
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aaronmk
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Populate the src/ subdir with input data:
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3586
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aaronmk
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Obtain/create CSVs for the table(s) present in the datasource:
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aaronmk
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specimens, plots, organisms, stems
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Rename each CSV so it ends in ".<table>.<ext>" (see tables above)
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3593
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aaronmk
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Auto-create the map spreadsheets:
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make inputs/<name>/; make inputs/<name>/
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Note: Must be run twice to properly bootstrap all maps.
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svn add inputs/<name>/maps/{*.csv,.*.last_cleanup}
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Install the staging tables: make inputs/<name>/install quiet=1 &
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To view the log: tail -f inputs/<name>/import/install-<table>.log.sql
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aaronmk
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Map each table's columns:
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In the maps/ subdir, for each "via map" of the form "<via>.<table>.csv":
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Open the map in a spreadsheet editor
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In /mappings, open the corresponding "core map" of the form
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"<via>-VegBIEN.<table>.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/<name>/
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aaronmk
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Accept the test cases:
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make inputs/<name>/test/
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When prompted to "Accept new test output", enter y and press ENTER
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svn add inputs/<name>/test/*.ref
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Commit: svn ci -m "Added inputs/<name>/" inputs/<name>/
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aaronmk
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Update vegbiendev:
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On vegbiendev: svn up
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On local machine: make inputs/upload
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On vegbiendev: Follow the steps under Install the staging tables above
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1773
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aaronmk
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702
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aaronmk
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Schema changes:
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Regenerate schema from installed DB: make schemas/remake
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1967
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aaronmk
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Reinstall DB from schema: make schemas/reinstall
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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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3441
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aaronmk
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Reinstall errors tables: make inputs/install errors_table_only=1
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aaronmk
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Reinstall staging tables: . bin/reinstall_all
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702
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aaronmk
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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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Click in the changes list and press Ctrl+A or Apple+A to select all
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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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aaronmk
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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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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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aaronmk
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Select schemas/vegbien.ERD.pdf and click Save
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Go to File > Print...
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For Pages, choose From 1 To 1
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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.core.pdf and click Save
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203
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aaronmk
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1459
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aaronmk
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Testing:
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Mapping process: make test
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Map spreadsheet generation: make remake
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1744
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aaronmk
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Missing mappings: make missing_mappings
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1459
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aaronmk
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Everything (for most complete coverage): make test-all
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702
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aaronmk
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aaronmk
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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 inputs/QMOR/import/steps.by_col.sql
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702
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aaronmk
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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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aaronmk
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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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