Activity
From 12/26/2011 to 01/24/2012
01/24/2012
- 06:32 PM Task #339 (New): have "schema showdown"
- Discuss different meanings everyone has for various ecological terms, especially:
* taxonoccurrence
* specimen - 06:10 PM Revision 639: VegX-VegBIEN mapping: Map additional taxondetermination.determinationdate input formats straight through
- 06:08 PM Revision 638: test/input/SALVIAS_db.sh: Updated DB name
- 05:57 PM Revision 637: Regenerated vegbien.ERD exports
- 05:55 PM Revision 636: input.Makefile: Added documentation for why import errors for one input do not abort the import process for all inputs
- 05:53 PM Revision 635: input.Makefile: Determine DB name from input directory name, rather than DB file name
- 05:20 PM Revision 634: input.Makefile: Added documentation for accepting a test output
- 05:07 PM Revision 633: mappings/Makefile: Don't delete DwC-VegBIEN.specimens.csv in clean
- 05:05 PM Revision 632: VegBIEN: Renamed taxondetermination.*determination to is*
- 04:16 PM Revision 631: inputs/SALVIAS/test: Ignore test outputs
- 04:12 PM Revision 630: input.Makefile: Added test that generates VegBIEN.2-step.xml by mapping via a VegX.xml
- 03:39 PM Revision 629: input.Makefile: Added test that generates VegX.xml
- 03:29 PM Revision 628: input.Makefile: Added test that generates VegBIEN.xml
- 02:50 PM Revision 627: input.Makefile: Factored test/import.out out of DB section
- 02:43 PM Revision 626: input.Makefile: Renamed test/import.ref to import.out.ref. Changed syntax for accepting a test output to work with all types of test outputs.
- 02:32 PM Revision 625: Makefiles: Recurse into outermost subdir rather than bypassing it and going directly to innermost subdir
- 02:08 PM Revision 624: input.Makefile: Deal with inputs without a DB file, tests, verifications, etc.
- 02:07 PM Revision 623: inputs/Makefile: Don't use subdir makefiles because they are no longer needed
- 01:28 PM Revision 622: input.Makefile: Detect DB engine automatically from SQL file available in src subdir
- 01:00 PM Revision 621: input.Makefile: Factored as much as possible out of section for each DB engine
- 12:58 PM Revision 620: input.Makefile: Moved tests into test subdir
- 12:51 PM Revision 619: input.Makefile: Moved tests into test subdir
- 12:46 PM Revision 618: Added initial DwC-VegBIEN mappings spreadsheet with DwC terms
- 12:36 PM Revision 617: inputs/SALVIAS/verify: Updated to use new names for renamed tables
- 12:34 PM Revision 616: inputs/SALVIAS/verify: Updated to use new names for renamed tables
- 12:18 PM Revision 615: vegbien.sql: Removed no longer needed specimen.collector_id
- 12:16 PM Revision 614: VegX-VegBIEN mapping: Map collector name to new verbatimcollectorname field
- 12:11 PM Revision 613: vegbien.sql: Removed specimen.collectornumber_dwc and replaced it with verbatimcollectorname to reflect that the collectornumber_dwc is actually an ID of the specimen, and the collector's name is what we want to store
01/23/2012
- 05:33 PM Revision 612: mappings/Makefile: Run simplify_xpath on VegX-VegBIEN.organisms.csv
- 05:33 PM Revision 611: simplify_xpath: Be case sensitive to handle VegX correctly
- 05:18 PM Revision 610: VegX-VegBIEN mapping: Avoid using a dummy taxondetermination with role=collector
- 04:50 PM Revision 609: VegX-VegBIEN mapping: Map stem count to new stemcount field
- 04:48 PM Revision 608: VegX-VegBIEN mapping: Take advantage of aggregateoccurrence.count being optional
- 04:46 PM Revision 607: vegbien.sql: Made aggregateoccurrence.count to handle individuals data (for which count should be dynamically determined from # individual plants inside the aggregateoccurrence)
- 04:43 PM Revision 606: NYBG-VegBIEN mapping: Don't map dummy values to locationcode, etc. (e.g. in specimens data) because these tables are no longer required
- 04:42 PM Revision 605: vegbien.sql: Made several pointers to parent elements optional to deal with specimens data that might not have a location, etc.
- 04:29 PM Revision 604: vegbien.sql: Added taxondetermination UNIQUE constraint
- 04:18 PM Revision 603: VegX-VegBIEN mapping: Took advantage of location.confidentialitystatus being optional
- 04:16 PM Revision 602: VegX-VegBIEN mapping: Took advantage of userdefined.userdefinedtype being optional
- 04:13 PM Revision 601: vegbien.sql: Gave userdefined.userdefinedtype a default value
- 04:10 PM Revision 600: VegX-VegBIEN mappings: Took advantage of plantconcept.reference_id becoming optional
- 04:07 PM Revision 599: vegbien.sql: Made plantconcept.reference_id optional. Merge plantconcepts with no reference_id when eliminating duplicates.
- 04:05 PM Revision 598: PostgreSQL-MySQL.csv: Deal with all non-NOT NULL timestamp fields
- 04:00 PM Revision 597: vegbien.sql: Removed confusing plantconcept.plantname field since we are using plantname.plantname instead
- 03:54 PM Revision 596: VegBIEN: Renamed aux_role to role
- 03:47 PM Revision 595: VegX-VegBIEN mappings: Took advantage of several fields becoming optional
- 03:43 PM Revision 594: VegX-VegBIEN mappings: Took advantage of several fields becoming optional
- 03:36 PM Revision 593: Regenerated vegbien.ERD exports
- 03:36 PM Revision 592: vegbien.sql: taxonbinmethod points to stratumtype instead of stratum because stratumtype is a method table, but stratum is a measurements table. stratum does not point directly to stratummethod because it points to it via stratumtype.
- 03:04 PM Revision 591: vegbien.sql: Made taxondetermination.determinationdate optional because some determinations might not have a date
- 02:47 PM Revision 590: Regenerated vegbien.ERD exports
- 02:46 PM Revision 589: vegbien.sql: Added specimen.authorspecimencode
- 02:36 PM Revision 588: Adjusted vegbien.ERD.mwb
- 02:34 PM Revision 587: Regenerated vegbien.ERD exports
- 02:33 PM Revision 586: VegBIEN: Renamed sourceaccessionnumber to sourceaccessioncode to show that they are the data source's analog of accessioncode. Added sourceaccessioncode to all applicable tables because this is the database pkey, which is distinct from any author*code applied by the collector.
- 01:56 PM Revision 585: vegbien.sql: Changed taxonbinmethod_keys to UNIQUE INDEX to take advantage of COALESCE() for dealing with NULL values
- 01:43 PM Revision 584: vegbien.sql: Renamed taxonbin to taxonbinmethod to reflect that it does not contain actual organisms (those go in aggregateoccurrence), but rather defined a *method* of aggregating organisms
- 01:39 PM Revision 583: vegbien.sql: Removed taxonbin.count because that belongs in aggregateoccurrence and taxonbin is more similar to a sampling method. Added taxonbin UNIQUE constraint.
- 01:24 PM Revision 582: vegbien.sql: Do location duplicate elimination independently on code or lat/long, allowing duplicate entries with NULLs to exist when a location is incompletely specified
- 01:15 PM Revision 581: vegbien.sql: Require location to have either an authorlocationcode or a lat/long. Distinguish between regular and subplots in UNIQUE constraint.
- 01:10 PM Revision 580: vegbien.sql: Renamed location.latitude and longitude to publiclatitude, publiclongitude to reflect that they are not the actual lat/long. Switched to requiring reallatitude/reallongitude.
- 01:02 PM Revision 579: Added inputs/TurboVeg
- 12:58 PM Revision 578: vegbien.ERD.mwb: Deal with MySQL assuming that a timestamp field is NOT NULL
- 12:57 PM Revision 577: PostgreSQL-MySQL.csv: Deal with MySQL assuming that a timestamp field is NOT NULL
- 12:53 PM Revision 576: vegbien.sql: Made specimen.taxonoccurrence_id required
- 12:47 PM Revision 575: vegbien.sql: Made several fields optional, adding defaults where needed
- 12:47 PM Revision 574: PostgreSQL-MySQL.csv: Deal with PostgreSQL-style :: casts
- 12:14 PM Revision 573: NYBG mappings: Add mapping for CollectorNumber to specimen.collectornumber_dwc
- 12:08 PM Revision 572: vegbien.sql: Added specimen.collectornumber_dwc
- 12:03 PM Revision 571: VegBIEN: Renamed sourceid to author*code
- 12:01 PM Revision 570: VegBIEN: Renamed sourceid to author*code
- 11:44 AM Revision 569: mappings: Map ScientificNameAuthor to plantconcept with rank author
- 10:53 AM Revision 568: vegbien.sql: Removed sizeclass.*precision fields
- 10:50 AM Revision 567: vegbien.sql: Added count field to taxonBin
- 10:47 AM Revision 566: VegBIEN: Renamed place to locationplace
- 10:40 AM Revision 565: vegbien.sql.make: Exclude 'CREATE OR REPLACE PROCEDURAL LANGUAGE plpgsql' to avoid restore errors
- 10:20 AM Revision 564: repl: When matching words, treat _ as word boundary and ignore case.
01/20/2012
- 05:09 PM Revision 563: VegBIEN: Renamed individualplant.height to overallheight
- 03:02 PM Task #337 (Closed): VegBIEN table renames
- E-mail from Brad on 2012-1-20:
Hi Mike,
You and Aaron have convinced me. Bob & I were advocating a return to th... - 02:34 PM Revision 562: Regenerated vegbien.ERD exports
- 02:32 PM Revision 561: PostgreSQL-MySQL.csv: Convert double quotes to backticks (`)
- 02:10 PM Revision 560: Regenerated vegbien.ERD exports
- 02:09 PM Revision 559: vegbien.for_ERD.sql: Fixed syntax error in stratum table
- 02:00 PM Revision 558: Regenerated vegbien.ERD exports
- 01:39 PM Revision 557: vegbien.sql: Renamed sizeclass.*accuracy to *precision to reflect intended purpose
- 01:33 PM Revision 556: vegbien.sql: Added stem.diameteraccuracy
- 01:22 PM Revision 555: vegbien.sql: Removed taxonoccurrence.currentdetermination_id and originaldetermination_id because it's not possible to create a two-way pointer when the child-to-parent pointer is required (chicken-and-egg problem)
- 01:05 PM Revision 554: README.TXT: Added make empty_db
- 12:52 PM Revision 553: vegbien.sql: Added taxonoccurrence.currentdetermination_id and originaldetermination_id
- 12:41 PM Revision 552: vegbien.ERD.mwb: Added stratum and place tables
- 12:29 PM Task #338 (Resolved): put together samples of SALVIAS data that aggregates individuals and stems in different ways
- * individual count
* stem count
* individuals
* stems
01/19/2012
- 06:06 PM Task #337: VegBIEN table renames
- "observation" can be confusing, because it's not obvious what it's an observation of (a plot, an organism, a stem?). ...
- 06:02 PM Task #337 (Closed): VegBIEN table renames
- E-mail from Brad:
Conceptual definitions of tables:
observation: permanent attributes of a unit or area of obse... - 05:32 PM Task #336 (Resolved): create VegBIEN ERD
- Now live on [[VegBIEN schema]]!
- 04:56 PM Task #336: create VegBIEN ERD
- I discovered that MySQL Workbench can synchronize its model with an existing CREATE script. So, it looks like we can ...
- 04:54 PM Task #336 (Resolved): create VegBIEN ERD
- 05:28 PM Revision 551: Added vegbien.ERD.png
- 05:24 PM Revision 550: Added vegbien.ERD.svg
- 05:21 PM Revision 549: Added vegbien.ERD.pdf
- 05:19 PM Revision 548: Added vegbien ERD
- 05:19 PM Revision 547: Ignore *.bak in schemas
- 05:07 PM Revision 546: VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant
- 04:43 PM Revision 545: vegbien.sql: Made voucher fields NOT NULL
- 04:41 PM Revision 544: vegbien.sql: Added voucher table
- 04:26 PM Revision 543: VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant
- 04:22 PM Revision 542: VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant
- 04:12 PM Revision 541: Create schemas/vegbien.for_wiki.sql from schemas/vegbien.for_ERD.sql
- 04:11 PM Revision 540: Added lib/ERD-wiki.csv to convert ERD SQL to human-readable wiki format
- 04:10 PM Revision 539: schemas/vegbien.for_ERD.sql: Removed VegBank-internal fields from taxonoccurrence
- 03:51 PM Revision 538: Removed no longer needed schemas/vegbien.my.sql
- 03:51 PM Revision 537: PostgreSQL-MySQL.csv: Use \g<0> instead of \0 in replacements because \0 not supported. Replace fulltext with fulltext__ (note fulltext_ doesn't work).
- 01:34 PM Revision 536: Added schemas/vegbien.for_ERD.sql and generated MySQL
- 01:34 PM Revision 535: Regenerated schemas/vegbien.for_ERD.sql
- 01:33 PM Revision 534: PostgreSQL-MySQL.csv: Deal with serial NOT NULL fields
- 01:22 PM Revision 533: Generate MySQL DDL schemas/vegbien.my.sql from vegbien.sql
- 01:22 PM Revision 532: Added repl spreadsheet to map PostgreSQL DDL to MySQL
- 12:56 PM Revision 531: Ignore src subdirectories in inputs
- 12:46 PM Revision 530: VegBIEN: Use stem instead of individualplant to store diameter/dbh
- 11:35 AM Task #302 (Resolved): Make changes to VegBIEN schema
- Extensive changes have been made
- 11:33 AM Task #331 (Resolved): use VegX's individualOrganismObservation/relatedItem to model stems
- Stems are now modeled in VegX. (Note that _VegBIEN_ stems import not complete yet)
- 11:32 AM Task #319: Update statistics/lists of user-defined fields in use in VegX and VegBIEN
- I've done this for NYBG to VegX
- 11:31 AM Task #322 (Resolved): get access to raw CTFS data
- I have the data from Shash, including a SQL dump
- 11:30 AM Task #334 (Resolved): which DarwinCore attributes do we want to include in the specimen table?
- Desired fields have been added or moved from other tables
- 11:30 AM Task #314: Import CTFS data
- I have data from Shash and am working with her to make sure we can parse it
- 11:29 AM Task #318 (Resolved): decide whether to switch to VegX 1.5.2
- In fact, we will switch to 1.5.3, which is now available
01/18/2012
- 05:57 PM Revision 529: vegbien.sql: Removed no longer needed taxondetermination.plantname_id
- 05:53 PM Revision 528: VegBIEN: Made taxondetermination.plantconcept_id required and plantname_id optional
- 04:28 PM Revision 527: vegbien.sql: Added specimen.taxonoccurrence_id fkey
- 03:47 PM Revision 526: vegbien.sql: Removed no longer needed taxondetermination.individualplant_id, specimen_id fields
- 01:57 PM Revision 525: VegBIEN: Renamed plot to location to reflect that a location can also be used for specimens
- 01:29 PM Revision 524: vegbien.sql: Added individualplant.stemcount
- 12:38 PM Revision 523: vegbien.sql: Added accessioncode fields to existing, modified tables
- 12:21 PM Revision 522: vegbien.sql: Added accessioncode fields to new tables
01/17/2012
- 04:56 PM Revision 521: vegbien.sql: Removed no longer needed individualplant.taxonarea
- 04:40 PM Revision 520: VegBIEN: Moved taxondetermination.sourceaccessionnumber and museum_id to specimen
- 03:32 PM Revision 519: vegbien.sql: Split taxondetermination UNIQUE CONSTRAINT into one constraint for each main key (taxonoccurrence_id, specimen_id, individualplant_id) to deal with Postgres treating a row with NULL in any of those columns as distinct. Added CHECK constraint to require one of taxonoccurrence_id, specimen_id, individualplant_id to be NOT NULL.
- 02:47 PM Revision 518: VegBIEN: Renamed museumaccessionnumber to sourceaccessionnumber
- 02:42 PM Revision 517: VegBIEN: Renamed authorcode to sourceid
- 02:33 PM Revision 516: vegbien.sql: Updated sizeclass to use ranges for parameters and remove taxonarea
01/13/2012
- 05:25 PM Revision 515: input.Makefile: Fixed verify by making %.out: % rule use %.make instead
- 05:24 PM Revision 514: input.Makefile: Moved verifications into one set of verify.* files
- 05:18 PM Revision 513: input.Makefile: All tests are run in the same transaction, with output to test.out
- 05:04 PM Revision 512: bin/map: Added support for processing multiple map_paths at once in the same transaction
- 04:50 PM Revision 511: SALVIAS organisms mapping: Removed redundant PlotCode mapping because the association to plotevent is done with PlotID
- 04:49 PM Revision 510: bin/map: Started adding support for multiple map_paths, all run in the same db transaction
- 04:35 PM Revision 509: Filled in SALVIAS stems mappings. make test2's stems test fails because we don't wrap the import transaction around all the tests so that organisms are already in the database when stems are imported.
- 04:28 PM Revision 508: mappings/Makefile: Corrected stemobservation to stem
- 03:46 PM Revision 507: Use baseDistance/complexUserDefined/method to distinguish between different dbhs in VegX
- 03:41 PM Revision 506: VegX mappings: Use baseDistance/value instead of baseDistance so we can later use complexUserDefined to distinguish between different types of dbh
- 03:28 PM Task #335 (Rejected): Look into using Sybase Powerbuilder or IBM Enterprise Vision to map data
- The TACC (Texas Advanced Computing Center) people might have individual licenses they could let us use
- 03:07 PM Revision 505: VegX-VegBIEN.organisms.csv: Added initial stems mappings
- 03:06 PM Revision 504: mappings/Makefile: Updated VegX-VegBIEN.stems.csv input/output roots
- 03:05 PM Revision 503: ch_root: Deal with roots followed by something other than \b
- 02:41 PM Revision 502: input.Makefile: Remove *.out in new verify and test subdirs
- 02:38 PM Revision 501: Moved inputs files into subdirs for maps, verify, and test operations
- 02:00 PM Revision 500: vegbien.sql: Removed taxondetermination.collector_id because that's now in specimen
- 01:58 PM Revision 499: VegBIEN: Map to specimen.collector_id instead of taxondetermination
- 01:27 PM Revision 498: vegbien.sql: Added specimen.collector_id column
- 01:20 PM Revision 497: vegbien.sql: Changed taxondetermination.stem_id to individualplant_id
- 01:16 PM Revision 496: vegbien.sql: Removed taxondetermination columns that have been moved to specimen
- 01:14 PM Revision 495: VegBIEN: Merged specimen.collectionnumber and catalognumber_dwc fields. Removed NOT NULL constraints on several specimen columns because not all specimens have all identifiers. Mapped to new specimen fields.
- 12:59 PM Revision 494: VegX-VegBIEN mapping: Map collectiondate to specimen table
- 12:55 PM Revision 493: vegbien.sql: Added specimen.collectionnumber and collectiondate fields
- 12:50 PM Revision 492: Updated README.TXT to reflect new make targets
01/12/2012
- 04:40 PM Task #334 (Resolved): which DarwinCore attributes do we want to include in the specimen table?
- 04:37 PM Task #314: Import CTFS data
- e-mails on 2012-1-12:
Steve Dolins:
We used the identical aggregate data file used for BIEN I... I think the da... - 04:30 PM Task #333 (Resolved): add traits table to VegBIEN
- 04:25 PM Task #318: decide whether to switch to VegX 1.5.2
- Brad: Yes! Latest version please, 1.5.2. It's about to get a lot less stable in any case, as we make more changes.
- 04:10 PM Task #318 (Resolved): decide whether to switch to VegX 1.5.2
- We have been mapping to VegX 1.5.1 (the latest stable version) but a release candidate VegX 1.5.2 is also available. ...
- 04:24 PM Task #332 (Rejected): switch to VegX 1.5.3
- 04:22 PM Task #331 (Resolved): use VegX's individualOrganismObservation/relatedItem to model stems
- 04:22 PM Task #330 (Rejected): DwC extension to VegX
- 04:22 PM Task #329 (New): make website user-protected
- 04:21 PM Task #328 (New): get raw data rather than flat file exports from RAINFOR
- 04:21 PM Task #327 (Resolved): look into Clio
- 04:21 PM Task #326 (Rejected): generic MOU template to request data
- 04:21 PM Task #325 (Resolved): map CTFS data
- 04:21 PM Task #324 (Resolved): NYBG validations
- 04:20 PM Task #323 (Resolved): map NYBG data
- 04:20 PM Task #322 (Resolved): get access to raw CTFS data
- 04:20 PM Task #321 (Resolved): Convert user-defined VegBIEN fields to first-class fields
- 04:20 PM Task #320 (Rejected): Convert user-defined VegX fields to first-class fields
- 04:20 PM Task #319 (Resolved): Update statistics/lists of user-defined fields in use in VegX and VegBIEN
- 01:25 PM Task #302: Make changes to VegBIEN schema
- I have applied most of Bob's changes to the VegBIEN schema, as well as many of Mark's suggestions. I posted a summary...
- 01:18 PM Revision 491: vegbien.sql: Added sizeclass columns
- 01:01 PM Revision 490: VegBIEN: Removed stem* prefix from stem measurements because it's redundant and because these same field names were reused in non-stem tables
- 12:51 PM Revision 489: VegBIEN: Renamed stemobservation to stem
- 12:49 PM Revision 488: vegbien.sql: Added comments to renamed tables specifying VegBank equivalent
- 12:45 PM Revision 487: vegbien.sql: Added comments to new tables
- 12:25 PM Revision 486: vegbien.sql: Removed r# prefix from foreign key constraints
- 12:21 PM Revision 485: vegbien.sql: Added plot.namedplace_id for theplots which are identified by a namedplace rather than lat/long or name
- 12:18 PM Revision 484: vegbien.sql: Made plot.authorcode optional as not all plots have names
- 12:16 PM Task #317 (Rejected): Direct mapping from VegX to VegBIEN
- When complete, this will be a complete, generic mapping of all elements in VegX to all corresponding elements in VegB...
- 12:15 PM Revision 483: vegbien.sql: Added _dwc to specimen columns that are from DwC
- 12:12 PM Revision 482: vegbien.sql: Added UNIQUE constraint for specimen table. Made catalognumber required so that all specimens can be uniquely identified.
- 12:09 PM Revision 481: vegbien.sql: Made specimen.individualplant_id optional because specimens are not required to have a corresponding plot event (which all individualplants must have)
- 12:05 PM Revision 480: VegBIEN-VegBank.csv: Updated to reflect renames
- 12:02 PM Revision 479: vegbien.sql: Renamed specimen.code to collectioncode to match DwC term
- 11:58 AM Revision 478: vegbien.sql: Added sizeclass table
- 11:51 AM Revision 477: vegbien.sql: Renamed collection to specimen to reflect that it's for a single collection specimen
- 11:45 AM Revision 476: VegBIEN: Renamed collectiveobservation to aggregateoccurrence to reflect VegX usage of aggregate and the new taxonoccurrence table
01/11/2012
- 02:47 PM Revision 475: VegBIEN: Renamed stemobservation.stemcode to authorcode
- 02:43 PM Revision 474: vegbien.sql: Renamed individualplant.code to authorcode
- 02:41 PM Revision 473: sql.py: Reordered get() args to match put()
- 02:40 PM Revision 472: db_xml.py: Use new sql.put() which only eliminates duplicates based on database UNIQUE constraints
- 02:38 PM Revision 471: sql.py: Added new function put() and changed get() to use it
- 02:32 PM Revision 470: sql.py: Fixed raising of NullValueException to pass array of columns rather than single column
- 02:25 PM Revision 469: vegbien.sql: Added UNIQUE constraints to tables used in the mapping so that duplicates are eliminated by the database
- 02:23 PM Revision 468: sql.py: ExceptionWithColumn now stores multiple columns so that they can all be used in DuplicateKeyExceptions
- 02:22 PM Revision 467: util.py: Fixed dict_subset() to work correctly when a key does not exist
- 02:13 PM Revision 466: util.py: Added dict_subset()
- 02:07 PM Revision 465: sql.py: Use constraint_cols() to determine DuplicateKeyException column in try_insert()
- 01:50 PM Revision 464: sql.py: Added constraint_cols() to get columns of a constraint for use in determining the columns for a DuplicateKeyException
- 11:59 AM Revision 463: db_xml.py: Map empty fields to None instead of ignoring them, to ensure that an existing row with a value in that field is not used in the duplicate elimination
- 11:56 AM Revision 462: bin/map: Use db_xml.put()'s new on_error handler
- 11:53 AM Revision 461: db_xml.py: put(): Added on_error handler. Reordered arguments according to how often they are likely to be used.
- 11:31 AM Revision 460: bin/map: Print # input rows processed
- 11:08 AM Task #314: Import CTFS data
- e-mail from Brad Boyle on 2012-1-10:
Interesting observation. I must admit, I haven't inspected Shash's VegX yet, ...
01/10/2012
- 05:32 PM Revision 459: VegX-VegBIEN mapping: Merge different sources of plot elevation
- 05:32 PM Revision 458: vegbien.sql: Added individualplant.code field
- 05:10 PM Revision 457: xml_func.py: Expand XML funcs in XML func args
- 05:06 PM Revision 456: xml_dom.py: In NodeTextEntryIter, return non-text children as-is instead of ignoring them so that XML functions can use them
- 04:46 PM Revision 455: xml_dom.py: Improved readability by separating into sections
- 04:41 PM Revision 454: db_xml.py: Ignore only fields that are actually empty (rather than just not having element children), as a field containing anything other than a comment should be flagged as invalid input
- 04:41 PM Revision 453: xml_dom.py: Changed is_empty() to consider nodes with only comments to be empty
- 04:23 PM Revision 452: bin/map: Add input row to exceptions
- 04:22 PM Revision 451: db_xml.py: Ignore empty fields. Fixes bug where a field that's not text but has no Element children will be treated as a table, and an error is triggered because the corresponding table does not exist in the database.
- 04:19 PM Revision 450: xml_dom.py: Added has_elems() to check if node has Element children
- 03:56 PM Revision 449: bin/map: Use xml_func.process()'s new on_error error handler. Add row to database errors and xml_func.SyntaxExceptions.
- 03:54 PM Revision 448: xml_func.py: Changed formatting of comment that node with syntax errors is replaced with so that it starts on its own line
- 03:50 PM Revision 447: xml_func.py: Use on_error exception handler to allow caller to print exceptions instead of raising them
- 03:41 PM Revision 446: db_xml.py: Add node to any database exceptions generated in put()
- 03:09 PM Revision 445: exc.py: Added raise_() wrapper for raise statement
- 02:45 PM Revision 444: Ignore .~* (lock files generated by OpenOffice.org) in inputs
- 02:44 PM Revision 443: inputs/SALVIAS: Added stems map
- 02:43 PM Revision 442: bin/map: Handle empty rows for db output
- 02:34 PM Revision 441: mappings: Use stemParent instead of stemOrganism to identify stems so that it's clear that the stemParent is an individualOrganismObservation, not an individualOrganism
- 02:25 PM Revision 440: input.Makefile: Include VegX maps not in tablesSort
- 02:20 PM Task #314: Import CTFS data
- e-mail from Mark Schildhauer on 2012-1-10:
I think tt would be best (and certainly most scaleable) if the elements... - 01:20 PM Task #314: Import CTFS data
- Looking at Shash's VegX file, I noticed that she uses different VegX elements than we do for SALVIAS and NYBG data. F...
- 02:13 PM Revision 439: mappings/Makefile: Generate initial VegX-VegBIEN.stems.csv
- 01:36 PM Revision 438: mappings/Makefile: Cleaned up in preparation for adding rule to generate VegX-VegBIEN.stems.csv
- 12:51 PM Revision 437: bin/map: Continue with database insertion even if a row had XML func syntax errors, because these errors have been fixed by removing the offending function node
- 12:49 PM Revision 436: xml_func.py: Remove function nodes with syntax errors to prevent them from causing DatabaseErrors later
- 12:48 PM Revision 435: xml_dom.py: Added remove() function to remove a node
- 12:39 PM Revision 434: bin/map: Track Exceptions with ExTracker
- 12:38 PM Revision 433: exc.py: Added ExTracker to track printed (suppressed) Exceptions and exit with nonzero status if any were encountered
- 12:12 PM Revision 432: bin/map: Parse each output XPath at the beginning so XPath syntax errors are detected right away
- 12:03 PM Revision 431: vegbien.sql: Reran renames to capture cases where a name is in the middle of an identifier
- 11:47 AM Revision 430: vegbien.sql: Use character varying(255) instead of text or character varying in new tables and columns
- 11:35 AM Revision 429: input.Makefile: Print Postgres NULL as NULL instead of empty string to match MySQL output
- 11:26 AM Revision 428: VegX-VegBIEN mapping: Fixed syntax error in mapping
01/09/2012
- 05:30 PM Revision 427: vegbien.sql: Added trait table
- 05:22 PM Revision 426: vegbien.sql: Added columns to stemobservation
- 05:13 PM Revision 425: vegbien.sql: Renamed collectiveobservation.stratum_id to taxonbin_id
- 04:51 PM Revision 424: vegbien.sql: Added some DarwinCore attributes to collection table
- 04:44 PM Task #302: Make changes to VegBIEN schema
- Added new tables and moved/updated columns
- 04:44 PM Task #302: Make changes to VegBIEN schema
- I asked Bob a few questions about the new Collection table in the VegBIEN modifications:
* Is the Collection table m... - 04:21 PM Revision 423: Makefiles: Added remake target to run clean and all
- 04:04 PM Revision 422: vegbien.sql: Added taxondetermination.collection_id column
- 03:56 PM Revision 421: VegBIEN: Made taxondetermination.plantname_id required
- 02:59 PM Revision 420: vegbien.sql: Made taxondetermination.plantconcept_id optional
- 02:49 PM Revision 419: VegBIEN: Renamed author*code to authorcode
- 02:47 PM Revision 418: Makefiles: Added empty rules for targets without a rule so that these rules wouldn't trigger the recursive subdir invocation for the default target
- 02:33 PM Revision 417: VegX-VegBIEN mapping: Convereted all database names to lowercase to correspond to their case in the database
- 02:04 PM Revision 416: Makefiles: Added empty Makefile target so that Makefiles are not included in the targets recursively run on subdirs
- 02:01 PM Revision 415: input.Makefile: Dependencies in other directories are included as prerequisistes. Use tablesSort variable instead of sort order prefix to order tables.
- 01:35 PM Revision 414: Makefile: Added default target that recursed into subdirs with Makefiles. Used default target for all and clean.
- 01:34 PM Revision 413: Regenerated inputs/SALVIAS/map.VegBIEN.0.plots.csv
- 01:32 PM Revision 412: Removed scripts symlink because it was causing Makefile recursion issues
- 01:28 PM Revision 411: Makefile: Take advantage of new inputs/Makefile
- 01:24 PM Revision 410: Added inputs/Makefile to run input targets recursively on each input
- 01:08 PM Revision 409: Makefile: Run inputs-* targets for all and clean
- 01:00 PM Revision 408: input.Makefile: all doesn't run import. import runs verify.
- 12:41 PM Revision 407: vegbien.sql: Set all FOREIGN KEY constraints to ON UPDATE CASCADE ON DELETE CASCADE
- 12:35 PM Revision 406: SALVIAS mappings: use PlotID as authorObsCode to link plot observations and organisms correctly for organisms without a PlotCode
- 12:32 PM Revision 405: SALVIAS mappings: use PlotID as authorObsCode to link plot observations and organisms correctly for organisms without a PlotCode
- 11:49 AM Revision 404: input.Makefile: Fixed bug in verify's diff rule
- 11:40 AM Task #314: Import CTFS data
- I uploaded Shash's VegX file to vegbiendev at @/home/bien/svn/inputs/CTFS/src.VegX.xml@ .
- 11:34 AM Revision 403: Added CTFS input
01/06/2012
- 05:01 PM Revision 402: Makefile: Generate error when trying to run subMake on a directory with no Makefile
- 04:37 PM Revision 401: input.Makefile: Tests use bin/map's new new test mode
- 04:37 PM Revision 400: bin/map: Added test mode that empties the database before doing anything
- 04:37 PM Revision 399: sql.py: Added functions to truncate tables, list all tables, and empty a database
- 04:35 PM Revision 398: Accepted new SALVIAS test outputs
- 03:38 PM Revision 397: Makefile: Print Finished message after running test2 (inputs tests)
- 03:38 PM Revision 396: Accepted test outputs for SALVIAS
- 03:37 PM Revision 395: input.Makefile: Added ability to accept a test output to use as the new reference output
- 03:01 PM Revision 394: vegbien db: Renamed all occurrences of interpretation to determination
- 02:56 PM Revision 393: Makefile: Tell make that subMake rules run make recursively
- 02:51 PM Revision 392: vegbien.sql: Updated collection table for recent refactorings
- 02:42 PM Revision 391: Made more of Bob Peet's changes to the vegbien db and updated VegX-VegBIEN mapping
- 02:32 PM Revision 390: Makefile: Fixed pattern for recursive invocation of subdirectory make
- 12:54 PM Revision 389: Moved mappings/schemas to schemas
- 12:50 PM Revision 388: Makefile: Changed all to make schemas and mappings instead of running install
- 12:34 PM Revision 387: Moved mappings/schemas to schemas
- 12:25 PM Revision 386: Makefile: Added inputs import target
- 12:24 PM Revision 385: input.Makefile: Fixed syntax error with use of import_cmd variable
- 12:19 PM Revision 384: vegbien.sql: Added collection table
- 12:18 PM Revision 383: Makefiles: Changed _not_file to _always because _not_file is sometimes used to force a file to always be remade
01/05/2012
- 04:53 PM Task #311 (Resolved): Decouple VegBIEN from VegBank and map directly from VegX to VegBIEN
- Decoupled VegBIEN from VegBank and removed mappings to VegBank
- 03:07 PM Task #311 (Resolved): Decouple VegBIEN from VegBank and map directly from VegX to VegBIEN
- 04:48 PM Revision 382: Decoupled VegBIEN from VegBank and removed mappings to VegBank
- 04:30 PM Revision 381: Regenerate vegbien.sql by dumping the vegbien db
- 04:06 PM Revision 380: Regenerate vegbien.sql by dumping the vegbien db
- 04:05 PM Revision 379: psql_vegbien: Changed to use postgres_vegbien
- 04:03 PM Revision 378: Added postgres_vegbien to run PostgreSQL command on the vegbien db
- 03:26 PM Revision 377: SALVIAS verification: Added plot methods
- 03:09 PM Task #315 (New): Import TurboVeg data
- 03:09 PM Task #314 (Resolved): Import CTFS data
- * coordinate with Shash
* CTFS has a lot of stems data - 03:08 PM Task #313 (Resolved): Import full NYBG data
- 03:08 PM Task #312 (Resolved): Finish importing SALVIAS data
- # -Import stems data-
# -Fix data format issues-: _Not sure what these were, probably long fixed_
# -Map invalid da... - 01:19 PM Revision 376: SALVIAS verification: Added # plots
- 01:06 PM Revision 375: Makefile: Added targets to run input targets on all inputs
- 12:54 PM Revision 374: SALVIAS verification: Added projects list to examine why project counts differ
- 12:41 PM Revision 373: SALVIAS verification: Made statement-label SELECT statements use the same syntax for MySQL and PostgreSQL so they are easy to copy and paste between the input and output queries
- 11:26 AM Task #290: benchmark tests for database loading
- You can view the validation results by running the following on vegbiendev:
@make verify --directory=/home/bien/svn/... - 11:25 AM Task #305: Complete full-dataset validations for NYBG & SALVIAS
- You can view the validation results by running the following on vegbiendev:
@make verify --directory=/home/bien/svn/... - 11:25 AM Task #302: Make changes to VegBIEN schema
- The vegbien db now contains some of the modifications Bob Peet made to the VegBank schema for VegBIEN, so some table ...
- 11:24 AM Task #304: Complete full dataset imports to VegBIEN via VegX of NYBG and SALVIAS
- I loaded the SALVIAS data (plots and organisms) into VegBIEN on vegbiendev. To browse the data, follow the [[phpPgAdm...
01/04/2012
- 05:00 PM Task #305: Complete full-dataset validations for NYBG & SALVIAS
- Created mechanism to write verification queries and compare to desired output
- 04:57 PM Task #304: Complete full dataset imports to VegBIEN via VegX of NYBG and SALVIAS
- Core SALVIAS data (plots and organisms) are on vegbiendev in VegBIEN.
Takes overnight to reinsert organisms data whe... - 04:54 PM Revision 372: input.Makefile: Don't remove logs in clean
- 04:49 PM Task #303: Mapping from VegBIEN to original VegBank
- Search-and-replace operations that transform VegBank to VegBIEN can in many cases be reversed to transform VegBIEN to...
- 04:48 PM Task #302: Make changes to VegBIEN schema
- All functions that used to output to VegBank now output to VegBIEN db.
The VegBIEN schema is automatically generated... - 04:45 PM Task #296: Direct mapping from native salvias_plots MySQL database to VegBIEN
- We will also need to import the projects, stems, and lookup_MethodCode tables in order for all the verification queri...
- 04:43 PM Task #290: benchmark tests for database loading
- Created mechanism to write verification queries and compare to desired output
- 04:32 PM Revision 371: input.Makefile: Added support for multi-column verification queries. inputs/SALVIAS: Added a multi-column verification query.
- 03:47 PM Revision 370: input.Makefile: Remove all *.out in clean
- 02:59 PM Revision 369: inputs: Don't keep *.out under version control
- 02:35 PM Revision 368: input.Makefile: Added rules to verify inserted data and run tests
- 11:38 AM Revision 367: Regenerated inputs/SALVIAS/map.VegBIEN.1.organisms.csv
- 11:32 AM Revision 366: exc.py: Print ! before error messages so they can be found and counted more easily in log files
- 11:13 AM Revision 365: input.Makefile: Only output to log if importing all rows
- 10:46 AM Revision 364: Moved vegbien CREATE DATABASE command to Makefile and run vegbien.sql as bien user
- 10:27 AM Revision 363: Renamed vegbien tables according to Bob Peet's new VegBank-VegBIEN mapping
- 10:16 AM Revision 362: input.Makefile: Don't print commands that use set -x to be echoed
- 10:14 AM Revision 361: input.Makefile: Use system's time utility instead of shell's time command
- 10:09 AM Revision 360: sql.py: Include sql.DbException in DatabaseErrors list
01/03/2012
- 04:28 PM Revision 359: Generate VegX-VegBIEN.organisms.csv from VegBank-VegBIEN.map.csv, which is generated from VegBank-VegBIEN.map_only.csv
- 04:21 PM Revision 358: repl: Process whole file as one string so that regexps can match EOF for appending
- 04:21 PM Revision 357: mappings/Makefile: Clean *-VegBIEN.*.csv maps
- 04:08 PM Revision 356: Generate VegBank-VegBIEN.schema.csv from VegBank-VegBIEN.schema_only.csv and VegBank-VegBIEN.csv
- 04:06 PM Revision 355: Added cat_csv to concatenate two spreadsheets
- 03:34 PM Revision 354: Removed no longer needed inputs/SALVIAS/db.sh
- 03:24 PM Revision 353: Add sort order prefixes to inputs/SALVIAS maps
- 02:49 PM Revision 352: VegX-VegBank organisms mapping: Added collectionDate mapping
- 02:36 PM Revision 351: VegX-VegBank organisms mapping: Added collectionDate mapping
- 02:36 PM Revision 350: mappings/Makefile: Sort VegX-VegBank organisms mapping automatically when anything that depends on it is remade
- 02:34 PM Revision 349: Added in_place to run a stream command on a file
- 02:14 PM Revision 348: join_sort: Use /bin/sh instead of /bin/bash
- 01:44 PM Revision 347: NYBG-VegX mapping: Removed no longer needed global stem count value
- 01:42 PM Revision 346: Renamed test/accept_output to accept
- 01:40 PM Revision 345: VegX-VegBank.organisms.csv: Made stemCount default to 1
- 01:17 PM Revision 344: bin/map: Print DatabaseErrors without stack traces
- 01:13 PM Revision 343: exc.py: Added print_ex()
- 01:13 PM Revision 342: exc.py: Added print_ex()
- 01:13 PM Revision 341: util.py: Added type_name()
- 01:12 PM Revision 340: strings.py: Added ensure_newl()
- 11:42 AM Revision 339: input.Makefile: Save map output in log file
- 11:27 AM Revision 338: bin/map: Print usage message when run with no arguments
- 10:10 AM Revision 337: Makefile: Removed unnecessary commenting out of "allow from 127.0.0.0..." lines in /etc/phppgadmin/apache.conf
12/29/2011
- 05:35 PM Revision 336: Makefile: Use --loose-exit-status for ed to avoid failing on no match. In editPhppgadminApacheConf, use ,s/// instead of /.../\ns/// to match lines regardless of position.
- 05:17 PM Revision 335: Makefile: Use tee instead of ed in sudoAppend. Don't change apache port to 8080 if apache already running on 80.
- 04:54 PM Revision 334: Makefile: Added phppgadmin apache config
- 01:16 PM Revision 333: bin/map: Only treat DatabaseErrors as warnings, not all Exceptions
- 01:04 PM Revision 332: xml_func.py: Print newline before func XML because XML is now pretty-printed with indents
- 12:59 PM Revision 331: xml_dom.py: Node.__str__() uses toprettyxml() instead of toxml()
- 12:58 PM Revision 330: util.py: Changed rename_key() not to suppress KeyError, since some callers might want to assert that a key exists
- 12:44 PM Revision 329: Makefile: Added phpPgAdmin dependency
- 12:42 PM Revision 328: xml_func.py: _name func doesn't require all name parts to be set. _namePart func throws SyntaxException for invalid name parts.
12/28/2011
- 02:03 PM Revision 327: bin/map: Fixed syntax error where db variable had not been renamed to out_db
- 01:58 PM Revision 326: xml_func.py: Generate SyntaxExceptions on missing XML func args
- 01:46 PM Revision 325: VegX-VegBank mapping: Added default soilObs.soilHorizon value
- 01:33 PM Revision 324: xml_func.py: Changed _date func to try parsing date field, rather than year field, as a decimal. Changed SALVIAS mappings to use new _date func syntax. Fixes SALVIAS plots data syntax error for decimal years.
- 01:10 PM Revision 323: Removed no longer needed VegBank accepted test outputs
- 01:09 PM Revision 322: test/map: Abort tester on failed diff
- 01:09 PM Revision 321: Added accepted test output SALVIAS_db.organisms.VegBIEN.xml
- 01:04 PM Revision 320: SALVIAS organisms mapping: Use _alt to merge tag1 and tag2. Fixes failing diff due to duplicate stemCodes.
- 12:49 PM Revision 319: test/map: Added tests to insert VegBIEN XML into VegBIEN db
- 12:47 PM Revision 318: bin/map: Fixed non-map input to set out_label
- 12:12 PM Revision 317: bin/map: Fixed row processing when no map is used
- 12:06 PM Revision 316: bin/map: Refactored to process each row separately when out_is_db
- 12:04 PM Revision 315: xml_dom.py: Added Node pop() and clear() methods
- 11:15 AM Revision 314: bin/map: Moved process_rows() exception handling around entire row, rather than each value, so that a broken value will not be ignored only to cause errors when outputing the row
- 11:12 AM Revision 313: bin/map: Moved process_rows() exception handling around entire row, rather than each value, so that a broken value will not be ignored only to cause errors when outputing the row
- 11:05 AM Revision 312: db_xml.py: Removed no longer needed xml2db()
- 11:04 AM Revision 311: bin/map: out_is_db uses use_row instead of xml2db()
- 10:53 AM Revision 310: bin/map: Added commit and exception-handling code to out_is_db use_row()
- 10:42 AM Revision 309: bin/map: Merged get_xml() into process_xml(). Renamed process*() functions to distinguish them better.
- 10:33 AM Revision 308: bin/map: Create separate document for printing XML opening and closing
- 10:28 AM Revision 307: bin/map: Refactored to print document opening, contents, and closing in separate steps so they can be separated later
- 10:27 AM Revision 306: xml_dom.py: Added support for integer indents
- 10:19 AM Revision 305: xml_dom.py: Added NodeIter() and Node.__iter__()
- 10:05 AM Revision 304: Use new xml_dom.prettyxml_config instead of Node.writeprettyxml because it can be passed as keyword args to any writexml function
- 10:00 AM Revision 303: xml_dom.py: Removed no longer needed xml_dom.writexml()
- 10:00 AM Revision 302: bin/map: Use Node.writeprettyxml() instead of xml_dom.writexml()
- 09:57 AM Revision 301: xml_dom.py: Added minidom.Document write_opening() and write_closing() methods. Changed writexml(writer, node) to use new Node.writeprettyxml() method.
- 09:28 AM Revision 300: Renamed ex.py to exc.py
- 09:24 AM Revision 299: Import xml.dom.minidom as minidom
- 09:10 AM Revision 298: xml_dom.py: Refactored xml.dom.minidom.Element.writexml() to use new write_opening() and write_closing() methods. Use new functions is_elem() and is_text_node() to determine node type. Corrected definition of a text element to be an element that contains a single text node.
- 08:37 AM Revision 297: bin/map: Factored out input processing code
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