Activity
From 11/28/2011 to 12/27/2011
12/23/2011
- 04:03 PM Revision 296: Commit after inserting each row
- 03:59 PM Revision 295: Commit after inserting each row
- 03:54 PM Revision 294: Use traceback.print_exc() to print Exceptions for each row instead of exiting
- 03:26 PM Revision 293: env_password: Allow user to change saved password
- 03:14 PM Revision 292: env_password: Don't print instructions for storing password for the session if called *to* store password for the session
- 03:00 PM Revision 291: env_password: Print absolute path to env_password in case invoking script changed the working directory
- 02:57 PM Revision 290: env_password: Print instructions for storing password for the session
- 02:32 PM Revision 289: Updated SALVIAS plots mappings and corresponding VegX-VegBank mappings to parse date_start and date_finish
- 02:11 PM Revision 288: xml_func.py: Print XML of XML functions with SyntaxExceptions
- 02:08 PM Revision 287: xml_func.py: Added support for parsing dates
- 01:56 PM Revision 286: ex.py: repl_msg(): take replacements as keyword args
- 01:44 PM Revision 285: fix_permissions: Also change user to bien
- 01:31 PM Revision 284: Makefile: Added python-dateutil dependency
- 12:57 PM Revision 283: input.Makefile: Renamed from_db-<map_file> target to import-<type> so it can be more easily run as a command-line target rather than just a prerequisite
- 12:40 PM Revision 282: Added inputs/SALVIAS organisms map
12/22/2011
- 08:30 PM Revision 281: map: Print xml_func.SyntaxExceptions without stack traces by using SystemExit
- 08:22 PM Revision 280: xml_func.py: Add function name to SyntaxException message
- 08:22 PM Revision 279: ex.py: Added repl_msg() to format a message with the % operator
- 07:48 PM Revision 278: xml_func.py: Return string->number conversion errors as xml_func.SyntaxExceptions
- 07:29 PM Revision 277: psql_vegbien: Fixed comment to vegbien instead of vegbank
- 07:11 PM Revision 276: psql_vegbien: Use new location of bien_password
- 07:05 PM Revision 275: Makefile: Fixed paths to mappings dir for new scripts dir location
- 07:02 PM Revision 274: Renamed util to bin
- 06:59 PM Revision 273: Moved inputs_Makefile to inputs/input.Makefile
- 06:55 PM Revision 272: Moved bien_password to new config dir
- 06:52 PM Revision 271: Moved sample inputs to test dir
- 06:42 PM Revision 270: Added symlink from scripts to new scripts destination
- 06:40 PM Revision 269: Removed now-empty scripts dir
- 06:39 PM Revision 268: Moved everything in scripts to root. inputs_Makefile: Don't run "all" when installing.
- 06:24 PM Revision 267: Renamed bien_map to map
- 06:22 PM Revision 266: Moved map to util
- 06:14 PM Revision 265: fix_permissions: Don't chmod symlinks
- 06:00 PM Revision 264: inputs_Makefile: Auto-generate map to VegBIEN and import data into vegbien from input DB
- 05:59 PM Revision 263: inputs/SALVIAS: maps to VegX and VegBIEN
- 05:58 PM Revision 262: bien_map: Runs map with BIEN defaults
- 05:56 PM Revision 261: join_sort: Sorts a join on the output col
- 03:20 PM Revision 260: inputs_Makefile: Require dbEngine var instead of defaulting to MySQL
- 02:22 PM Revision 259: Moved inputs into svn
- 01:46 PM Revision 258: Moved pre-BIEN 3 files into _archive folder
- 01:46 PM Revision 257: test/map: Use db.sh syntax in *.sh tests
- 01:45 PM Revision 256: inputs_Makefile: Generate db.sh with DB access info
- 12:59 PM Revision 255: inputs_Makefile: Changed GRANT ALL to GRANT SELECT. Added REVOKE ALL. Added $(db).sql as prerequisite of install in case it needs to be auto-generated.
- 12:30 PM Revision 254: scripts/Makefile: Added action for postgres-Darwin target
- 12:11 PM Revision 253: scripts/Makefile: Added postgresql to postgres-Linux apt-get packages
12/21/2011
- 08:23 PM Revision 252: test/map: Changed to work on both nimoy and vegbiendev by selecting the appropriate MySQL user and password
- 08:22 PM Revision 251: env_password: Added optional message arg
- 07:47 PM Revision 250: Added uninstallation of inputs to Makefiles
- 07:15 PM Revision 249: scripts/Makefile: Create bien user w/o prompting for password. Fixed syntax error.
- 07:06 PM Revision 248: scripts/Makefile: Fixed syntax error
- 07:03 PM Revision 247: Inputs now include inputs_Makefile to get mysql command, etc.
- 06:30 PM Revision 246: scripts/Makefile: Use bien MySQL user for installing inputs
- 06:26 PM Revision 245: scripts/Makefile: Use root MySQL user for creating bien user
- 05:53 PM Revision 244: scripts/Makefile: Don't use root as MySQL admin user. Removed no-longer-needed sub-makes for setting DB login vars.
- 05:10 PM Revision 243: Changed vegbien_dest and users of it to use separate bien_password file
- 04:55 PM Revision 242: fix_permissions: Extend all user permissions to group
- 04:26 PM Revision 241: scripts/Makefile: Added inputs
- 03:24 PM Revision 240: mappings/Makefile: Cleaned up
- 03:02 PM Revision 239: fix_permissions: Don't add group write perms to read-only files
- 01:54 PM Revision 238: scripts/Makefile: Made read command syntax compatible with /bin/sh
- 01:37 PM Revision 237: scripts/Makefile: Ignore errors about missing packages
- 01:30 PM Revision 236: scripts/Makefile: Fixed escape character for /bin/sh
- 01:25 PM Revision 235: scripts/Makefile: Added dependency installation. Makefiles: Use _not_file instead of FORCE for clarity. Use $(os) var
12/20/2011
- 07:52 PM Revision 234: fix_permissions: Configured output verbosity
- 07:44 PM Revision 233: Added fix_permissions to set correct permissions on shared bien files
- 07:31 PM Revision 232: Removed VegBank scripts which are no longer needed
- 07:30 PM Revision 231: Removed VegBank scripts which are no longer needed
- 06:55 PM Revision 230: Renamed vegbien_dest.sh to vegbien_dest to reflect that it is also includable by Makefiles
- 06:52 PM Revision 229: DB user creation: Clarified instructions
- 06:51 PM Revision 228: scripts/Makefile includes vegbien_dest.sh directly
- 06:28 PM Revision 227: Moved db user creation to scripts/Makefile. Removed now-unneeded admin scripts.
- 06:12 PM Revision 226: Removed VegBank scripts which are no longer needed
- 06:11 PM Revision 225: scripts/Makefile: Added empty_db target which uses vegbien_empty.sql
- 05:55 PM Revision 224: mappings/Makefile: Fixed bug where var containing prerequisistes needed to be defined before used. Added support for different sed flags to use extended regular expressions.
- 05:42 PM Revision 223: Added auto-generated vegbien_empty.sql to empty the vegbien db
- 04:55 PM Revision 222: Test output to VegBIEN instead of VegBank
- 04:54 PM Revision 221: VegX-VegBIEN.organisms.csv: sort output of repl
- 04:46 PM Revision 220: review: Added nullglob
- 04:44 PM Revision 219: review: Don't process replacements spreadsheets
- 04:44 PM Revision 218: Moved schema replacements from VegBank-VegBIEN.csv to VegBank-VegBIEN.schema.csv
- 04:32 PM Revision 217: VegBank-VegBIEN.csv: Support PostgreSQL before 8.4
- 04:29 PM Revision 216: repl: Added support for blank lines. Only add whole word regexp code to inputs w/o *any* regexp metachars.
- 04:13 PM Revision 215: Create vegbien db from mappings/schemas/vegbien.sql
- 04:12 PM Revision 214: VegBank-VegBIEN.csv: Added replacements for SQL create script conversion
- 03:56 PM Revision 213: Generate vegbien db create SQL from vegbank.sql using repl
- 03:55 PM Revision 212: Generate vegbien db create SQL from vegbank.sql using repl
- 03:54 PM Revision 211: repl: Fixed bug in reading arguments
- 03:38 PM Revision 210: repl: Don't add whole-word regexp for inputs that already have regexp metachars
- 03:26 PM Revision 209: Removed mappings/VegBank-VegBIEN.organisms.csv because now using replacements spreadsheet
- 03:24 PM Revision 208: mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet
- 03:23 PM Revision 207: mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet
- 03:23 PM Revision 206: mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet
- 02:57 PM Revision 205: Added repl to perform replacements on a spreadsheet or file
- 01:38 PM Revision 204: scripts/Makefile: removed extra test-% target
- 01:38 PM Revision 203: README.TXT: Updated
- 01:36 PM Revision 202: scripts/Makefile: install/uninstall targets
- 01:36 PM Revision 201: bien_user_create: Print instructions in sequence with password prompts
12/19/2011
- 06:16 PM Revision 200: mappings to VegBIEN: Accounted for remaining ALTER TABLE statements
- 05:48 PM Revision 199: Renamed format*_for_review to review and added for_review to make clean
- 05:41 PM Revision 198: mappings: Added mappings to VegBIEN
- 05:25 PM Revision 197: mappings/Makefile: Simplified
- 05:22 PM Revision 196: mappings/Makefile: Simplified
- 04:59 PM Revision 195: README.TXT: Updated
- 04:47 PM Revision 194: Added vegbien DB admin scripts
12/16/2011
- 03:54 PM Revision 193: join_all_vegbank: Sort output by both columns
- 03:48 PM Revision 192: mappings/VegX-VegBank.organisms.csv: Sorted by both columns
- 03:48 PM Revision 191: mappings/Makefile: Sort VegBank-VegBIEN.organisms.csv by both columns
- 03:47 PM Revision 190: extract_plot_map: Removed because functionality now in Makefile
- 03:46 PM Revision 189: sort: Can sort on multiple columns
- 03:17 PM Revision 188: Added basic VegX-VegBIEN mapping
- 02:02 PM Revision 187: Added union and join_passthru
- 02:02 PM Revision 186: env_password: Print Usage message to stderr
- 01:29 PM Revision 185: test/map: Create output dir if it doesn't exist
- 01:24 PM Revision 184: Converted scripts back to bash that required bash-specific features
- 01:23 PM Revision 183: Converted scripts back to bash that required bash-specific features
- 01:13 PM Revision 182: Fixed test/map to work with sh
- 01:05 PM Revision 181: Replaced /bin/bash with /bin/sh
12/15/2011
- 04:16 PM Revision 180: join: Added usage item for repeated joins
- 04:13 PM Revision 179: join: Changed order of args and redirects to be more intuitive
- 04:09 PM Revision 178: Renamed ch_map_root to ch_root
- 04:08 PM Revision 177: Renamed join_maps to join
- 12:20 PM Revision 176: Merged test Makefile into main scripts Makefile
- 12:05 PM Revision 175: test/map: Turn off test mode (don't run diff) when env var n (for # rows) is set
- 11:39 AM Revision 174: Added SALVIAS DB mapping for plots data
- 11:37 AM Revision 173: VegX-VegBank mapping: Fixed VegBank XPath for commName.commName field
- 11:35 AM Revision 172: db_xml.py: Use pointer target's name as pointer type where possible. Emphasize that pointer type determined from the pointer name itself is a guess based on common database conventions.
- 11:31 AM Revision 171: xpath.py: Changed backward (child-to-parent) pointer ID abbr expansion to happen in get() when source node's tag name is known. This deals with XPath elements that are '.' being used as a pointer source.
12/14/2011
- 05:31 PM Revision 170: xpath.py: Moved abbr expansion code to separate function
- 04:41 PM Revision 169: test/map: Process all tables for a given DB (.sh) input
- 03:26 PM Revision 168: Removed /'s from DB input mappings
- 01:46 PM Revision 167: map: Use row's index instead of pkey as ID in XML output
- 01:45 PM Revision 166: test/map: Compare via-VegX output to direct output
- 01:13 PM Revision 165: xpath.py: Changed order that main and other branches are processed in so it is consistent with the order the branches are specified in the XPath
- 12:03 PM Revision 164: map: Handle metadata in order with regular mappings
- 11:33 AM Revision 163: Accepted VegBank test output for new CSV mapping order
- 11:26 AM Revision 162: map: Changed CSV input to process mappings in the order they are in the spreadsheet, rather than the order of the CSV columns
12/13/2011
- 05:18 PM Revision 161: map: Added support for XML input
- 05:17 PM Revision 160: Accepted new test output for sorted SALVIAS_db-VegBank mapping
- 05:07 PM Revision 159: mappings to VegBank: Sorted by output column to help VegX-VegBank conversion put elements in the same order as source-VegBank
- 04:57 PM Revision 158: join_all_vegbank: Updated to sort output maps
- 04:57 PM Revision 157: Added script to sort a spreadsheet
- 03:51 PM Revision 156: xpath.py: Allowed empty names in XPaths
- 03:48 PM Revision 155: xpath.py: Added automatic conversion of strings to paths where needed.
- 03:00 PM Revision 154: xpath.py: Added caching of parsed XPaths. Added automatic conversion of strings to paths where needed.
- 02:59 PM Revision 153: Added __str__() method to XML nodes
- 02:58 PM Revision 152: Fixed VegX-VegBank mapping syntax error
- 02:17 PM Revision 151: Added faded beginning of string in Parser syntax errors
- 02:01 PM Revision 150: Updated mappings Makefile
- 02:00 PM Revision 149: Added Makefiles for scripts and test
- 01:54 PM Revision 148: Added mappings Makefile
- 12:28 PM Revision 147: Added human-readable SALVIAS_db mappings
- 12:28 PM Revision 146: db_xml.get(): Pass limit through to SQL query
- 11:48 AM Revision 145: Regenerated human-readable mappings
12/12/2011
- 05:39 PM Revision 144: Fixed documentation for xml_funcs
- 05:38 PM Revision 143: Refactored xml_dom.set_value() to avoid needing a doc parameter for the XML document
- 05:35 PM Revision 142: xpath.py: Refactored xml_func.py to avoid needing a doc parameter for the XML document
- 05:30 PM Revision 141: xpath.py: Refactored to avoid needing a doc parameter for the XML document
- 04:41 PM Revision 140: Fixed DB input to ignore NULL values
- 04:27 PM Revision 139: xml_dom.py: Changed all uses of name_of(node) to node.tagName
- 04:23 PM Revision 138: Made XML node names case-sensitive
- 04:20 PM Revision 137: mappings to VegBank: Fixed incorrect mappings found after disabling heuristic search for missing fields
- 03:49 PM Revision 136: test/map: Ignore diff exit status
- 03:34 PM Revision 135: map: Implemented DB input support for querying a single table
12/09/2011
- 05:36 PM Revision 134: Added SALVIAS_db test accepted output
- 05:35 PM Revision 133: map: Continued to add DB input support
- 04:54 PM Revision 132: test/map: Echo command used to import db config
- 04:02 PM Revision 131: Added support for multiple database engines. Changed SALVIAS_db input to use user-entered password.
- 01:58 PM Revision 130: map: Allow db config vars to be optional. SALVIAS_db test: Changed to use salvias_plots and XPath mapping syntax.
- 01:32 PM Revision 129: Renamed SALVIAS_db test input to use organisms table
- 01:29 PM Revision 128: Re-committed accepted_outputs
- 01:23 PM Revision 127: Renamed test/map output to remove CSV/DB indicator because that is now specified in the datasource name
- 01:18 PM Revision 126: map: Started adding database get by XPath functionality
12/08/2011
- 06:48 PM Revision 125: format_for_review: Fixed bug where Comments column would be reformatted in addition to mappings columns
- 05:35 PM Revision 124: Regenerated human-readable mappings
- 05:15 PM Revision 123: Added human-readable versions of mappings and scripts to generate them
- 05:14 PM Revision 122: VegX-VegBank mapping: Removed a duplicated mapping
- 05:13 PM Revision 121: NYBG-VegX mapping: Added conference call feedback
- 01:48 PM Revision 120: Added Comments column with Brad's and Aaron's comments to mapping spreadsheets
12/07/2011
- 05:01 PM Revision 119: Added stub for SALVIAS database test
- 05:00 PM Revision 118: test/map: Added support for database input
- 04:14 PM Revision 117: Preparing map to input from DB
- 03:32 PM Revision 116: Started preparing map to input from DB
- 01:27 PM Revision 115: xml_func.py: Added optimization to first check if function name starts with _ before looking it up in the table
- 12:24 PM Revision 114: Added _alt functions for mappings to VegBank authorPlotCode
- 12:17 PM Revision 113: xml_func.py: Added _alt function to choose between alternative values and used it for the collector plantName mapping
- 11:54 AM Revision 112: VegX-VegBank mapping: Added mapping from taxonName/Simple (NYBG ScientificName) to collector plantName so that collector plantName will always have a value
- 11:27 AM Revision 111: xml_func.py: Added support for decimal years (with day as the fraction)
- 11:16 AM Revision 110: test/map: Added echoing of commands run
12/06/2011
- 04:19 PM Revision 109: Added psql_vegbank to easily access vegbank db from the command line
- 04:07 PM Revision 108: Ignore OpenOffice lock files in mappings
- 04:05 PM Revision 107: Added SALVIAS data CSVs and accepted test output
- 03:52 PM Revision 106: test/map: Expanded to include all input CSVs in test/input
- 03:31 PM Revision 105: Removed unneeded joins dir
- 03:30 PM Revision 104: Moved VegBank mapping joins to main mappings dir so they would have similar paths for the upcoming all-sources tester
- 03:11 PM Revision 103: Moved test scripts and files from util to test
- 02:50 PM Revision 102: xml_func.py: Added _namepart function for extracting parts of names
- 02:11 PM Revision 101: Finished NYBG mapping to VegBank\!
- 02:04 PM Revision 100: test_map: Added debug option to print VegBank XML instead of importing it into the database
- 01:34 PM Revision 99: xpath.py: Created is_positive() function
- 01:28 PM Revision 98: Further refinements to mappings to support database constraints
- 01:27 PM Revision 97: xpath.py: Added support for negative attribute assertions with !
- 10:54 AM Revision 96: Changed mappings to use keys vs. attrs
- 10:53 AM Revision 95: xpath.py: Fixed creation of attrs so it happens even when node already exists
- 09:59 AM Revision 94: xpath.py: Added concept of keys vs attrs in XPath elem
12/05/2011
- 05:25 PM Revision 93: Started filling in required values for VegBank fields in mappings. Will need to refactor to move these to metadata for the datasources.
- 05:24 PM Revision 92: Now allow empty rows. Added support for select statement limit.
- 04:17 PM Revision 91: Added support for quoted values in XPaths
- 04:02 PM Revision 90: Fixed name XML function. Fixed accept_test_output.
- 03:59 PM Revision 89: Added support for name XML function. Added error handling for empty rows.
- 03:28 PM Revision 88: Made it easier to accept test output
- 03:18 PM Revision 87: Added NYBG stemCount metadata
- 03:11 PM Revision 86: Added xml_func.py to process mappings whose output needs postprocessing
- 01:53 PM Revision 85: Changed VegBank mappings to use XML functions (not implemented yet) to calculate averages and ranges
- 01:25 PM Revision 84: Added support for mapping datasource metadata
- 12:53 PM Revision 83: Changed for loops to use enumerate() where the index is also needed
- 12:50 PM Revision 82: Moved XPath prep code (setting ID, value) to xpath.py
12/02/2011
- 05:27 PM Revision 81: xpath.py: Added deepcopy() before setting value of other branches to traverse
- 05:12 PM Revision 80: NYSpecimenDataAmericas.test.xml: Updated for new NYBG-VegX.organisms.csv
- 05:11 PM Revision 79: NYBG-VegX.organisms.csv: Changed voucher (primary key) column to be UniqueNYInternalRecordNumber because CatalogNumber contained an empty value
- 05:10 PM Revision 78: xpath.py: Added basic support for split paths
- 04:30 PM Revision 77: Merged xml_xpath.py into xpath.py in preparation for changing the XPath parse tree to be the XML DOM tree itself
- 03:58 PM Revision 76: Refactored xpath.parse() to use a nested function instead of a class extending Parser
- 03:04 PM Revision 75: map: Fixed mislocated import for Parser.SyntaxException
- 02:21 PM Revision 74: Removed SALVIAS voucher_string mapping per conference call discussion
- 02:16 PM Revision 73: map: Fixed bugs to enable mapping straight from CSV to a database. Still need a way to set plot.authorPlotCode for specimens data.
- 12:05 PM Revision 72: Fixed ch_map_root to support subpaths which follow the root by -> rather than /. Changed spreadsheet syntax to have : between label and root.
12/01/2011
- 01:55 PM Revision 71: Updated extract_plot_map to use new name for VegX-VegBank mapping and re-ran it and join_all_vegbank
- 01:51 PM Revision 70: Finished VegX-VegBank mapping and created VegBank joins of mappings to VegX
- 11:53 AM Revision 69: Finished ch_map_root (renamed from submap)
11/30/2011
- 05:36 PM Revision 68: Added submap and extract_plot_map to extract plot subpaths from VegX-VegBank.csv
- 04:56 PM Revision 67: Moved env usage string creation to opts.py. Changed db config var names to use in/out instead of from/to.
- 04:24 PM Revision 66: Keep *.test.xml out of version control
- 04:22 PM Revision 65: Moved options-processing code to opts.py: Added opts.py
- 04:21 PM Revision 64: Moved options-processing code to opts.py
- 04:04 PM Revision 63: test_map: Compares generated XML to correct version
- 03:55 PM Revision 62: Fixed xml_xpath.get() last_only optimization to handle attrs correctly. Turned off stack traces for errors intended for the user to see.
- 02:32 PM Revision 61: Changed mappings to place prefix common to all XPaths in the column header
- 01:31 PM Revision 60: simplify_xpath: Made it case-insensitive
- 01:25 PM Revision 59: map: Added support for custom fkeys to parent in db XML trees. Removed extraneous csv reader/writer config because Excel format is default. Improved documentation.
11/29/2011
- 05:36 PM Revision 58: map: Added stub for database input
- 05:33 PM Revision 57: map: Added more stubs for XML-XML mapping
- 05:15 PM Revision 56: Started adding XML-XML mapping support to map
- 04:43 PM Revision 55: Split off xpath.py XML functionality into xml_xpath.py
- 04:28 PM Revision 54: map: Using SystemExit for usage errors to avoid stack trace
- 04:22 PM Revision 53: Merged data2xml and xml2db into map
- 03:03 PM Revision 52: Removed trailing whitespace from VegX-VegBank.csv map
- 02:59 PM Revision 51: Created join_maps to join two 2-column map spreadsheets
- 02:11 PM Revision 50: Renamed mappings to be compatible with Redmine allowed characters in attachment filenames
- 01:59 PM Revision 49: Added refactored mappings and changed data2xml to use the new 2-column format
- 01:25 PM Revision 48: Refactored db_xml.py's db insertion function to avoid extra nested functions
- 01:06 PM Revision 47: Added README.TXT
- 01:02 PM Revision 46: Renamed modules to remove _util
- 12:47 PM Revision 45: Added svn:ignore for *.pyc
- 12:42 PM Revision 44: Renamed xml2db_ and data2xml_ to remove _
- 12:42 PM Revision 43: Moved scripts to main directory and associated files to util
- 12:31 PM Revision 42: Moved Python modules to shared lib folder
11/28/2011
- 05:32 PM Revision 41: xml2db: Started refactoring xml2db() to support getting as well as inserting data
- 05:29 PM Revision 40: xml2db: Started refactoring xml2db() to support getting as well as inserting data
- 05:05 PM Revision 39: xml2db: Changed to return ID (pkey) of inserted record and use this returned value as parent_id instead of getting the parent_id from the parent XML node
- 03:16 PM Revision 38: data2xml: Added syntax for split paths, which map to multiple leaves
- 01:52 PM Revision 37: xml2db: Improved empty_db to use TRUNCATE instead of DROP DATABASE. Added xml2vegbank to automatically set db env vars.
- 01:51 PM Revision 36: data2xml: Improved syntax for XPath lookahead assertions. Changed XML printing to print multiple text nodes on separate lines.
- 12:15 PM Revision 35: Moved vegbank_example_ver1.0.2.xml to xml2db, where it should have been
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