Activity
From 11/12/2011 to 12/11/2011
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
11/23/2011
- 05:22 PM Revision 34: data2xml: Small correction to NYBG mapping
- 04:58 PM Revision 33: data2xml: Created simplify_xpath script to remove duplication from XPath expressions
- 04:15 PM Revision 32: data2xml: Added support for * abbrs for backward (child-to-parent) pointers
- 02:52 PM Revision 31: In data2xml, fixed determination of which nesting level to put IDs on
- 02:45 PM Revision 30: Simplified expansion of * abbrs
- 02:23 PM Revision 29: Removed no longer necessary strip() from node value getter
- 02:22 PM Revision 28: Added patch for xml.dom.minidom.Element.writexml to avoid adding extra whitespace around text nodes
- 12:45 PM Revision 27: Added pointer field name abbreviations to data2xml and NYBG mappings
11/22/2011
- 04:35 PM Revision 26: In data2xml, fixed pointer handling to deal with pointer targets that are themselves pointers
- 04:01 PM Revision 25: In data2xml, added shortcut for lookahead assertion using ! symbol
- 02:32 PM Revision 24: In data2xml, fixed backward (child-to-parent) pointer handling to get and set attribute values properly
- 01:52 PM Revision 23: In data2xml, fixed xpath.get() to do last_only optimization properly for pointer targets
- 01:32 PM Revision 22: In data2xml, added support for XPath pointers
11/21/2011
- 05:48 PM Revision 21: Merged data2xml XPath functionality into xpath.py. Merged data2xml xml_dom.py and xml2db xml_util.py into identical xml_util.py for each script.
- 04:50 PM Revision 20: Added empty_db script to reset the vegbank database after running xml2db/test in commit mode
- 02:01 PM Revision 19: Changed xml2db and vegbank db to be owned by new user vegbank
11/18/2011
- 05:38 PM Revision 18: Changed xml2db and data2xml to help standardize mapping to different XML formats
- 02:48 PM Revision 17: Added DROP DATABASE and CREATE DATABASE to vegbank.sql
- 12:52 PM Revision 16: Changed xml2db to use primarily node contents to determine whether a node is a field or a child table
11/17/2011
- 04:42 PM Revision 15: Changed xml2db to use the first column in a table as its primary key
- 04:08 PM Revision 14: Changed xml2db to avoid inserting duplicate rows
- 03:31 PM Revision 13: Initial version of xml2db. Doesn't yet handle all duplicate rows correctly.
- 11:29 AM Revision 12: Removed .pyc files
- 10:29 AM Revision 11: Added BIEN 3 scripts
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