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Installation:
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Install: make install
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WARNING: This will delete the current public schema of your VegBIEN DB!
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Uninstall: make uninstall
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WARNING: This will delete your entire VegBIEN DB!
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This includes all archived imports and staging tables.
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Maintenance:
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Important: Whenever you install a system update that affects PostgreSQL or
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any of its dependencies, such as libc, you should restart the PostgreSQL
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server. Otherwise, you may get strange errors like "the database system
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is in recovery mode" which go away upon reimport.
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Data import:
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Import data into VegBIEN: . bin/import_all
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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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Archive the last import: make schemas/rotate
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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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Re-import data: make schemas/rotate; . bin/import_all
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Note: This will archive the last import.
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Backups:
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After a new import:
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On vegbiendev:
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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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tail inputs/*/*/logs/<date>-*.log.sql
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Check that every input's log ends in "Encountered 0 error(s)"
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If many do not, fix the bug and discard the current (partial) import
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Otherwise, continue
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Delete previous imports so they won't bloat the full DB backup:
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make backups/public.<datetime>.backup/remove
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make backups/<schema>.backup/test & make backups/vegbien.backup/all &
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On local machine:
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make inputs/download-logs
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make backups/download &
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If desired, record the import times in inputs/import.stats.xls
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Archived imports:
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Back up: make backups/public.<date>.backup &
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Note: To back up the last import, you must archive it first (above)
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Test: make backups/public.<date>.backup/test &
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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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Download: make backups/download
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Full DB:
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Back up, test, and rotate: make backups/vegbien.backup/all &
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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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Download: make backups/download
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Import logs:
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Download: make inputs/download-logs
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Datasource setup:
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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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Add input data for each table present in the datasource:
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Choose a table name from <https://projects.nceas.ucsb.edu/nceas/projects
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/bien/wiki/VegCSV#Suggested-table-names>, or use a custom name
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Note that if this table will be joined together with another table, its
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name must end in ".src"
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make inputs/<datasrc>/<table>/add
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Important: DO NOT just create an empty directory named <table>!
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This command also creates necessary subdirs, such as logs/.
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Place the CSV for the table in inputs/<datasrc>/<table>/
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OR place a query joining other tables together in
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inputs/<datasrc>/<table>/create.sql and svn add this file
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Important: When exporting relational databases to CSVs, you MUST ensure
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that embedded quotes are escaped by doubling them, *not* by
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preceding them with a "\" as is the default in phpMyAdmin
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If there are multiple part files for a table, and the header is repeated
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in each part, make sure each header is EXACTLY the same.
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(If the headers are not the same, the CSV concatenation script
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assumes the part files don't have individual headers and treats the
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subsequent headers as data rows.)
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Add <table> to inputs/<datasrc>/import_order.txt before other tables
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that depend on it
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Auto-create the map spreadsheets:
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make inputs/<datasrc>/; make inputs/<datasrc>/
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Note: Must be run twice to properly bootstrap all maps.
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svn add inputs/<datasrc>/*/{,.}{header,src,map*,VegBIEN}.csv{,.*}
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Install the staging tables:
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make inputs/<datasrc>/reinstall quiet=1 &
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To view progress: tail -f inputs/<datasrc>/<table>/logs/install.log.sql
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View the logs: tail -n +1 inputs/<datasrc>/*/logs/install.log.sql
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tail provides a header line with the filename
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+1 starts at the first line, to show the whole file
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For every file with an error 'column "..." specified more than once':
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Add a header override file "+header.<ext>" in <table>/:
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Note: The leading "+" should sort it before the flat files.
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"_" unfortunately sorts *after* capital letters in ASCII.
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Create a text file containing the header line of the flat files
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Add an ! at the beginning of the line
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This signals cat_csv that this is a header override.
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For empty names, use their 0-based column # (by convention)
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For duplicate names, add a distinguishing suffix
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For long names that collided, rename them to <= 63 chars long
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Do NOT make readability changes in this step; that is what the
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map spreadsheets (below) are for.
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Save
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svn add inputs/<datasrc>/<table>/<header_override>
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If you made any changes, re-run the install command above
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Map each table's columns:
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In each <table>/ subdir, for each "via map" map.csv:
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Open the map in a spreadsheet editor
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Open the "core map" /mappings/Veg+-VegBIEN.csv
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In each row of the via map, set the right column to a value from the
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left column of the core map
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Save
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Regenerate the derived maps: make inputs/<datasrc>/
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Accept the test cases:
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make inputs/<datasrc>/test
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When prompted to "Accept new test output", enter y and press ENTER
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If you instead get errors, do one of the following for each one:
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- If the error was due to a bug, fix it
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- Add a SQL function that filters or transforms the invalid data
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- Make an empty mapping for the columns that produced the error.
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Put something in the Comments column of the map spreadsheet to
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prevent the automatic mapper from auto-removing the mapping.
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When accepting tests, it's helpful to use WinMerge
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(see WinMerge setup below for configuration)
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svn add inputs/<datasrc>/*/test.xml.ref
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Commit: svn ci -m "Added inputs/<datasrc>/" inputs/<datasrc>/
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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:
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Follow the steps under Install the staging tables above
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make inputs/<datasrc>/test
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Schema changes:
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Regenerate schema from installed DB: make schemas/remake
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Reinstall DB from schema: make schemas/reinstall
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WARNING: This will delete the current public schema of your VegBIEN DB!
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Reinstall errors tables: make inputs/install errors_table_only=1
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Reinstall staging tables: . bin/reinstall_all
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Sync ERD with vegbien.sql schema:
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Run make schemas/vegbien.my.sql
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Open schemas/vegbien.ERD.mwb in MySQLWorkbench
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Go to File > Export > Synchronize With SQL CREATE Script...
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For Input File, select schemas/vegbien.my.sql
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Click Continue
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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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If desired, update the graphical ERD exports (see below)
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Update graphical ERD exports:
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Go to File > Export > Export as PNG...
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Select schemas/vegbien.ERD.png and click Save
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Go to File > Export > Export as SVG...
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Select schemas/vegbien.ERD.svg and click Save
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Go to File > Export > Export as Single Page PDF...
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Select schemas/vegbien.ERD.1_pg.pdf and click Save
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Go to File > Print...
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In the lower left corner, click PDF > Save as PDF...
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Set the Title and Author to ""
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Select schemas/vegbien.ERD.pdf and click Save
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Testing:
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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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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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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 inputs/QMOR/specimens/logs/steps.by_col.log.sql
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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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