Activity
From 01/21/2013 to 02/19/2013
02/19/2013
- 11:16 PM Revision 7597: schemas/vegbien.sql: _taxon_family_require_std(): Also allow non-aceae families accepted by TNRS
- 09:38 PM Revision 7596: Added inputs/SALVIAS/_archive/salvias_plots.*.sql.zip.md5
- 09:35 PM Revision 7595: Added inputs/VegBank/_archive/vegbank_for_bien.tar.gz.url
- 09:29 PM Revision 7594: Added inputs/U/UtrechtHerbarium.csv.tar.gz.url
- 09:28 PM Revision 7593: Added inputs/TEAM/_archive/ci-team_extract.tar.gz.url
- 09:27 PM Revision 7592: Added inputs/SpeciesLink/_archive/specieslink*.txt.gz.url
- 09:22 PM Revision 7591: Added inputs/REMIB/_archive/remib_raw.csv.tar.gz.url
- 09:19 PM Revision 7590: Added inputs/NY/NYSpecimenDataAmericas.csv.tar.gz.url
- 09:17 PM Revision 7589: Added inputs/NCU/_archive/NCU-NCSC_2010-02-12.csv.tar.gz.url
- 09:14 PM Revision 7588: Added inputs/MO/mo_digirexport.tar.gz.url
- 09:13 PM Revision 7587: Added inputs/Madidi/_archive/2010-1-2/madidi_plots_original_12jan2010.zip.url
- 09:11 PM Revision 7586: Added inputs/GBIF/gbif_extract.tar.gz.url
- 09:10 PM Revision 7585: Added inputs/FIA/fia_extract.tar.gz.url
- 09:08 PM Revision 7584: Added inputs/CVS/_archive/CVS-allTaxonOccurrences_2010-01-12.txt.tar.gz.url
- 09:04 PM Revision 7583: Added inputs/ARIZ/ARIZ_DiGIR_21012010.csv.tar.gz.url
- 08:55 PM Revision 7582: Added inputs/UNCC/Specimen/UNCC.csv.url, UNCC.csv.md5
- 08:45 PM Revision 7581: Added inputs/XAL/_src/digir.xml.gz.md5
- 08:39 PM Revision 7580: Added inputs/UNCC/_src/ with UNCC.csv.zip.md5
- 08:23 PM Revision 7579: Added inputs/SpeciesLink/_src
02/16/2013
- 08:24 AM Revision 7578: README.TXT: Datasource setup: MySQL inputs: .sql exports: Use new mysql_bien to connect to the MySQL DB created for the datasource
- 08:22 AM Revision 7577: Added mysql_bien, which runs a MySQL command on the local MySQL server
- 08:06 AM Revision 7576: Added inputs/GBIF/_src/GBIFPortalDB-2012-12-11.dump.md5 (md5sum of the expanded file)
- 08:02 AM Revision 7575: root Makefile: MySQL: mysql-Linux: Also install phpMyAdmin
- 08:01 AM Revision 7574: root Makefile: MySQL: mysql-Linux: Split apt-get dependencies into separate commands, like for other apt-get commands, to avoid having one failed dependency prevent the following dependencies from being installed
- 07:57 AM Revision 7573: root Makefile: MySQL: *mysql_users: Also add bien_read user
- 07:49 AM Revision 7572: root Makefile: MySQL: Renamed *mysql_user to *mysql_users because there can be multiple users
- 06:51 AM Revision 7571: inputs/: Added .md5 files for all .zip, .gz
- 06:47 AM Revision 7570: Added inputs/HVAA/Specimen/Herbario_occur_1360871068.csv.url
- 06:39 AM Revision 7569: lib/common.Makefile: rsync: $(rsync*): Use --no-group because the file group is different depending on the machine
- 06:10 AM Revision 7568: input.Makefile: SVN: $(_svnFilesGlob): Also add .md5 files. This allows svn to track where unversioned files should be in the directory tree.
- 06:07 AM Revision 7567: input.Makefile: SVN: $(_svnFilesGlob): .url, .pdf, and README.TXT in the top-level dir: Fixed bug where had extra / after brace expr
- 06:00 AM Revision 7566: input.Makefile: SVN: $(_svnFilesGlob): Also add .url, .pdf, and README.TXT in the top-level dir
- 05:53 AM Revision 7565: input.Makefile: SVN: $(_svnFilesGlob): Add .url, .pdf, and README.TXT files in all subdirs, not just _src
- 05:25 AM Revision 7564: lib/common.Makefile: remote server: Use jupiter instead of vegbiendev, to ensure that all files get uploaded there rather than only to vegbiendev. This involves adding an extra database import step to download the uploaded files from jupiter onto vegbiendev.
- 02:50 AM Revision 7563: inputs/FIA/_src/Makefile: all: Extract zip files before running tables target, because it requires the created dirs
- 02:40 AM Revision 7562: schemas/vegbien.ERD.mwb: Fixed table sizes
- 01:17 AM Revision 7561: Removed no longer used fix_permissions. Use root fix_perms instead.
- 01:16 AM Revision 7560: Added root fix_perms
02/15/2013
- 11:58 PM Revision 7559: Moved Checksums from backups/Makefile to lib/common.Makefile so all dirs (including inputs/) can use md5sum testing
- 11:08 PM Revision 7558: lib/common.Makefile: $(remote): Made remote basepath configurable in $(remote_basepath)
- 11:04 PM Revision 7557: lib/common.Makefile: Renamed $(src_server) to $(remote_host) and $(src_user) to $(remote_user) for clarity
- 10:16 PM Revision 7556: inputs/GBIF/: Added refresh metadata
02/14/2013
- 11:49 AM Revision 7555: Added inputs/HVAA/
- 11:14 AM Revision 7554: Added inputs/ARIZ/_archive
- 11:13 AM Revision 7553: inputs/ARIZ/: Removed previous data now that it has been refreshed
- 11:08 AM Revision 7552: inputs/ARIZ/: Mapped refresh
- 11:04 AM Task #566 (New): automatically adjust staging tables for easier mapping
- * remove empty columns
* mark columns with data in every row as NOT NULL - 09:48 AM Revision 7551: Added inputs/ARIZ/import_order.txt
- 09:22 AM Revision 7550: Added inputs/NY/_archive/
- 09:20 AM Revision 7549: inputs/NY/: Removed tables from previous extract
- 08:59 AM Revision 7548: inputs/NY/: Mapped refresh
- 08:58 AM Revision 7547: inputs/*/*/VegBIEN.csv: Regenerated from mappings/VegCore-VegBIEN.csv
- 08:52 AM Revision 7546: Added inputs/NY/import_order.txt
- 07:20 AM Task #386 (Resolved): load Canadensys data
- 07:19 AM Task #470 (Resolved): source terms from old versions of DwC to the DwC history page
- 07:18 AM Task #472 (Rejected): replace accessioncodes with datasource_id+sourceaccessioncode
- Accessioncode fields have been removed instead. Globally unique ID fields (#561) will eventually serve the purpose th...
- 07:06 AM Task #565 (Resolved): partition the TaxonDetermination table by row into the different types of determinations
- * this makes it easy to horizontally join the different types of determinations for a row
** it avoids the need for ... - 06:37 AM Task #564 (New): make all VegBIEN column names globally unique
- * this enables creating a table to contain the results of a join, without needing to resolve column name collisions
... - 06:33 AM Task #563 (New): refactor VegBIEN to use VegCore terms
- * add key VegCore tables such as Occurrence and Record
* note that many VegCore tables have an inheritance relations... - 05:17 AM Task #562 (New): flatten the mappings
- * put the destination table at the beginning of the mapping, rather than nesting it within a hierarchy of tables it h...
- 04:47 AM Task #561 (New): make VegBIEN ID fields plain-text instead of numeric
- h3. Rationale
* this makes it possible to append data from multiple sources without having pkey collisions
h3. ... - 04:12 AM Task #560 (New): move VegCore data dictionary to a phpPgAdmin-accessible database
- * term details go in column comments, with Redmine formatting translated to HTML
* each synonym becomes a parameter ... - 02:51 AM Revision 7545: inputs/ARIZ/: Added SQL export for refresh
- 02:33 AM Revision 7544: my2pg.data: Translate indefinite (zero) months which have a definite day. This is unusual, but does appear in some data such as the ARIZ DB.
- 02:28 AM Revision 7543: my2pg.data: Translate indefinite dates (dates with 0 as the month or day)
- 02:23 AM Revision 7542: my2pg: Use my2pg.data to perform data-only replacements, instead of duplicating them in both my2pg and my2pg.data
- 02:01 AM Revision 7541: my2pg: named UNIQUE KEYs: Comment out the name because PostgreSQL requires it to be globally unique, but MySQL only requires it to be unique within the table
- 01:53 AM Revision 7540: my2pg: Translate UNIQUE KEYs instead of removing them
- 01:49 AM Revision 7539: my2pg*: Removed KEYs: Comment out the definition rather than removing it
- 01:45 AM Revision 7538: my2pg*: Remove FOREIGN KEYs because MySQL does not dump tables in dependency order, which prevents PostgreSQL from creating tables whose fkeys refer to a later table
- 01:33 AM Revision 7537: my2pg*: Replacing invalid table elements to remove them: Use a dummy CHECK constraint instead of a boolean field to avoid adding fields to the table. The elements can't always simply be removed because sed can't remove the trailing comma of the previous element, and removing the following comma doesn't work for the last element in the table.
- 12:11 AM Revision 7536: my2pg*: Replace '0000-00-00 00:00:00' with '-infinity'
- 12:04 AM Revision 7535: my2pg: Replace datetime with timestamp
02/13/2013
- 11:59 PM Revision 7534: my2pg: Remove COLLATE field attribute
- 11:56 PM Revision 7533: lib/MySQL.*.sql.make: Documented that $server user/host are for ssh, not the DB
- 11:55 PM Revision 7532: lib/MySQL.*.sql.make: Documented that $server can also contain a username (which will be used by ssh)
- 11:51 PM Revision 7531: my2pg_export: Use the --quick option to facilitate exporting large tables (it avoids retrieving all rows before outputting any of them)
- 11:00 PM Revision 7530: README.TXT: Datasource setup: Added instructions for MS Access databases
- 10:43 PM Revision 7529: README.TXT: Datasource setup: MySQL inputs: Added instruction to skip the Add input data for each table section
- 10:40 PM Revision 7528: inputs/NY/: Added SQL export for refresh
02/12/2013
- 01:08 PM Revision 7527: mappings/VegCore.htm: Regenerated from wiki. Brad's new DwC ID terms spreadsheet has now been added, and a number of the ID terms clarified, disambiguated, and recategorized. In particular, institutionCode has now been split into the custodialInstitutions and collectingInstitution, to differentiate between which institution has the specimen vs. stamped the specimen. This distinction is important because the catalogNumber, stamped on the specimen, is only unique within the collectingInstitution. Most datasources don't unambiguously specify which institution their institutionCode is referring to, so it has been assumed to be custodialInstitutions unless a data dictionary says otherwise (as is the case for UNCC). In addition, a MatchedTaxonDetermination table has been added with the *_matched fields from TNRS.
- 12:15 PM Revision 7526: inputs/CVS/observation_/map.csv: baseSaturation: Resolved ambiguous term
- 12:09 PM Revision 7525: mappings/Makefile: VegCore.vocab.csv: Ignore leading ? when sorting so that ambiguous terms sort alphabetically with other terms. This prevents terms from moving from their previous location when they become ambiguous.
- 12:07 PM Revision 7524: Added sort_ci to sort a spreadsheet, ignoring leading punctuation
- 12:05 PM Revision 7523: mappings/VegCore.vocab.csv: Changed line endings to \r\n in preparation for having a Python script run on it (which changes the line endings)
- 11:47 AM Revision 7522: mappings/Makefile: VegCore.vocab.csv: Added back ambiguous terms, so that the vocabulary contains all terms defined by VegCore, regardless of whether they are ambiguous or unambiguous terms
- 11:44 AM Revision 7521: mappings/Makefile: VegCore.vocab.csv: Added back synonyms, so that the vocabulary contains all terms defined by VegCore, regardless of whether they are synonyms or primary terms. This also prevents VegCore.vocab.csv from losing entries when terms are renamed, which made it difficult to verify that no terms were lost when refactoring.
- 05:50 AM Revision 7520: inputs/MO/Specimen/postprocess.sql: Remove frameshifted rows by detecting InstitutionCodes without any letters
- 04:59 AM Revision 7519: inputs/ARIZ/Specimen/map.csv: CollectorNumber/FieldNumber: Use /_first to map these identical fields to the same location
- 04:54 AM Revision 7518: inputs/ARIZ/Specimen/map.csv: Fixed bug where the column names for InstitutionCode and CollectionCode were reversed in the source data
- 04:14 AM Revision 7517: inputs/*/Specimen/map.csv for Canadensys sources: Remapped institutionID to UNUSED
02/09/2013
- 07:45 AM Revision 7516: mappings/VegCore.htm: Regenerated from wiki. The original*, accepted*, and verbatim* Taxon fields have now been moved to separate OriginalTaxonDetermination, AcceptedTaxonDetermination, and TaxonVerbatim tables.
- 06:52 AM Revision 7515: mappings/VegCore.htm: Regenerated from wiki
- 06:34 AM Revision 7514: mappings/VegCore.htm: Regenerated from wiki
- 04:08 AM Revision 7513: README.TXT: Maintenance: VegCore data dictionary: Replaced VegCore.*.csv with VegCore.htm because now that VegCore.*.csv are sorted alphabetically, they generally don't change when VegCore.htm changes
- 04:04 AM Revision 7512: mappings/VegCore.*.csv: Regenerated from wiki. A plain text label is now used for Replace with, which fixes a bug where the PRIVATE permalink pointed to its Replace with in realLatitude instead of its definition.
- 03:55 AM Revision 7511: redmine_synonyms: Support plain text labels other than Alternative, such as Replace with
- 03:13 AM Revision 7510: mappings/VegCore.*.csv: Regenerated from wiki. Alternatives now contain the "Alternative" label as plain text rather than as an image title, thus avoiding an HTML anchor conflict with the definition and allowing ambiguous terms to be placed before their alternatives as well as after.
- 03:11 AM Revision 7509: README.TXT: Maintenance: VegCore data dictionary: Updated VegCore.csv filename to VegCore.*.csv
- 02:57 AM Revision 7508: redmine_synonyms: Support alternatives which contain the "Alternative" label as plain text rather than as an image title. This is done to include the "Alternative" label in the HTML anchor and thus prevent the anchor from conflicting with the actual definition of the alternative (which would otherwise have the same anchor text). This allows ambiguous terms to be placed before their alternatives as well as after, because there won't be anchor conflicts that need to be resolved with careful ordering.
- 02:48 AM Revision 7507: mappings/VegCore.csv: Regenerated from wiki. Taxon terms with prefixes for other TaxonDeterminations now indicate the analogous term in an "analogous to" label next to the term
- 02:47 AM Revision 7506: mappings/VegCore.csv: Regenerated from wiki. Taxon terms with prefixes for other TaxonDeterminations now indicate the analogous term in an "analogous to" label next to the term
- 02:47 AM Revision 7505: mappings/VegCore.csv: Regenerated from wiki. Taxon terms with prefixes for other TaxonDeterminations now indicate the analogous term in an "analogous to" label next to the term
02/07/2013
- 01:57 PM Revision 7504: mappings/VegCore-VegBIEN.csv: datasourceRecordID: Fixed bug where also need to add datasourceRecordID next to occurrenceID for an institutionCode remap switch
- 01:57 PM Revision 7503: inputs/bien_web/observation/test.xml.ref: Regenerated
- 01:48 PM Revision 7502: inputs/import.stats.xls: Updated import times using the import_times bugfix for times longer than a day
- 01:45 PM Revision 7501: import_times: times(): Fixed bug where need to match whitespace in times, in order to match times with days
- 12:00 PM Revision 7500: inputs/*/Specimen/map.csv: Remapped ID to datasourceRecordID
- 11:55 AM Revision 7499: mappings/VegCore-VegBIEN.csv: Mapped datasourceRecordID
- 11:51 AM Revision 7498: inputs/import.stats.xls: Updated import times
- 08:38 AM Revision 7497: inputs/FIA/_src/_README.TXT: Documented that the refresh is missing some PLT_CN values present in the original version
- 08:33 AM Revision 7496: inputs/FIA/import_order.txt: Reverted back to using FIA_COND_unique instead of COND_unique because the PLT_CN IDs in the refresh don't match the PLT_CN IDs in the original version, making COND_unique and Organism incompatible
- 08:27 AM Revision 7495: inputs/FIA/import_order.txt: Removed FIA_COND_unique, which is superseded by COND_unique
- 08:26 AM Revision 7494: inputs/FIA/import_order.txt: Fixed bug where need to import COND_unique before Organism because the plot entries need to be created before they can be linked to by organisms
- 07:25 AM Revision 7493: redmine_synonyms: sed pattern: Match <h# directly at the beginning of the line rather than after ^.*, which greatly speeds up the pattern matching because the first character is a literal character. (If <h# were not located at the left margin, the ^.* would unfortunately still be needed because the beginning of the line needs to be matched in order to be removed by the replacement operation.)
- 07:22 AM Revision 7492: mappings/VegCore.csv: Regenerated from wiki. Alternatives are now able to use h3 instead of h4 (which had display problems). realLatitude/Longitude is now no longer needs the ? prefix to have its replacement (PRIVATE) interpreted as an alternative, and thus is properly able to be included in the vocabulary.
- 07:16 AM Revision 7491: mappings/Makefile: VegCore.vocab.csv: Use the term's type label instead of its header level to determine if it's a synonym or alternative. This allows header levels to be chosen for presentational reasons rather than being constrained by being parsable.
- 07:05 AM Revision 7490: redmine_synonyms: Don't require ambiguous terms to start with ?, because the ambiguous term for an alternative can be identified simply by choosing the last term that didn't have a type label (previously, this would have been the last term that wasn't h3 or h4)
- 07:01 AM Revision 7489: redmine_synonyms: Use the term's type label instead of its header level to determine if it's a synonym or alternative. This allows header levels to be chosen for presentational reasons rather than being constrained by being parsable.
- 06:26 AM Revision 7488: mappings/VegCore.csv: Regenerated from wiki. The data dictionary has been reformatted to be much more vertically compact, by placing the term type (Synonym, Alternative, etc.) and sources (From:) on the same line as the term. Note that globalUniqueIdentifier_SpeciesLink has been removed from the vocabulary because a definition entry has been added for it (when this entry is missing, the term is incorrectly identified as a primary term).
- 06:21 AM Revision 7487: mappings/Makefile, redmine_synonyms: Updated for new VegCore data dictionary format, which prefixes the term type (Synonym, Alternative, etc.) to the term instead of including it as a section label. This ensures that the term type of a non-primary term is shown next to the term when it is visited via a permalink, which causes the term header to appear at the top of the screen and obscures the section header containing the type.
- 06:00 AM Revision 7486: mappings/Makefile: VegCore.thesaurus.csv: removal of tables: ignore errors if grep found no match
- 02:06 AM Revision 7485: Renamed mappings/VegCore.csv to VegCore.vocab.csv and Veg+-VegCore.csv to VegCore.thesaurus.csv for clarity
- 02:03 AM Revision 7484: mappings/Makefile, input.Makefile: Renamed $(dict) to $(thesaurus) because Veg+-VegCore.csv is actually a thesaurus, not a dictionary
- 01:57 AM Revision 7483: mappings/Makefile: Replaced occurrences of VegCore.csv with $(vocab) and Veg+-VegCore.csv with $(dict)
02/06/2013
- 07:34 PM Revision 7482: README.TXT: Maintenance: VegCore data dictionary: When moving terms, check that no terms were lost: Updated steps now that VegCore.csv and Veg+-VegCore.csv are sorted by name, so that a comparison of added/deleted counts is not necessary and a simple `svn di` can be used
- 07:33 PM Revision 7481: mappings/Makefile: Veg+-VegCore.csv: Sort terms by name so that reordering terms in the VegCore data dictionary does not cause Veg+-VegCore.csv to change. This makes it much easier to identify synonyms and ambiguous terms that were accidentally deleted during a data dictionary refactoring. (Note that these are no longer included in VegCore.csv, so this is required in addition to sorting VegCore.csv by name.)
- 07:26 PM Revision 7480: mappings/Makefile: VegCore.csv: Sort terms by name so that reordering terms in the VegCore data dictionary does not cause VegCore.csv to change. This makes it much easier to identify terms that were accidentally deleted during a data dictionary refactoring.
02/05/2013
- 06:19 PM Revision 7479: mappings/VegCore.csv: Regenerated from wiki. This adds cf_aff.
- 06:18 PM Revision 7478: mappings/Makefile: VegCore.csv: Filter out namespaces by matching only terms whose header links within the data dictionary
- 06:08 PM Revision 7477: mappings/VegCore.csv: Regenerated from wiki. This causes TNRS's Annotations (cf/aff) to be mapped into VegBIEN.
- 06:05 PM Revision 7476: mappings/VegCore-VegBIEN.csv: matched*Fit_fraction: Remapped to taxonconfidence instead of taxonfit
- 05:56 PM Revision 7475: mappings/Makefile: VegCore.csv: Fixed bug where need to remove duplicates, which are no longer supported by canon, by removing alternatives of ambiguous terms when these occur separately from their definitions
- 05:29 PM Revision 7474: mappings/Makefile: VegCore.csv: Removed synonyms and ambiguous terms, since the canonicalization of them is handled by Veg+-VegCore.csv. This also reduces the time it takes canon to build the in-memory Python dict of replacements, which scales to all inputs and should speed up the build/test command.
- 05:22 PM Revision 7473: mappings/Makefile: VegCore.csv: Removed synonyms, since the canonicalization of them is handled by Veg+-VegCore.csv
- 05:10 PM Revision 7472: mappings/Makefile: VegCore.csv: Match terms by header # instead of matching all anchors, in order to include the leading ? before an ambiguous term
- 04:42 PM Revision 7471: mappings/Makefile: Veg+-VegCore.csv: Generate dynamically from VegCore.htm, which allows the VegCore thesaurus to be automatically kept up to date. More importantly, it allows terms in all map spreadsheets to be updated simultaneously when a term is renamed (e.g. by replacing a term with one of its synonyms).
- 04:40 PM Revision 7470: mappings/VegX-VegCore.csv: Applied term renamings from the new dynamically generated Veg+-VegCore.csv. Updates to VegCore term names that have occurred since the data dictionary was created are now able to take effect, which involves remapping several fields.
- 04:32 PM Revision 7469: mappings/VegCore-VegBIEN.csv, inputs/*/*/map.csv: Applied term renamings from the new dynamically generated Veg+-VegCore.csv, which reflects the current state of the data dictionary. (Permanently switching to the new Veg+-VegCore.csv will be a separate change.) Updates to VegCore term names that have occurred since the data dictionary was created are now able to take effect, which involves remapping and inferring units on several fields.
- 04:27 PM Revision 7468: mappings/VegCore-VegBIEN.csv: Mapped basalDiameter_in
- 04:15 PM Revision 7467: mappings/VegCore-VegBIEN.csv: Mapped diameterBreastHeightGentry_cm, basalDiameter_cm, precipitation_mm
- 04:14 PM Revision 7466: schemas/vegbien.sql: Added _mm_to_m()
- 03:56 PM Revision 7465: mappings/Makefile: Veg+-VegCore.csv: Fixed bugs where also need to filter out ambiguous tables, but shouldn't filter out acronyms (which are regular fields)
- 03:40 PM Revision 7464: mappings/VegCore-VegBIEN.csv: locationID->location.sourceaccessioncode: Removed restriction that this mapping can't occur if geovalidation information is present. The locationID is no longer mapped to the place.sourceaccessioncode, so this filter is not necessary.
- 03:38 PM Revision 7463: mappings/VegCore.csv: Regenerated from wiki
- 03:19 PM Revision 7462: mappings/Makefile: Veg+-VegCore.csv: Fixed bug where need to filter out table names to avoid applying table replacements to fields which have the same name as a table
- 03:03 PM Revision 7461: inputs/Madidi/map.csv: Fixed bug where needed to remove duplicate input names, now that translate doesn't allow them
- 01:59 PM Revision 7460: mappings/Makefile: VegX-VegCore.csv: Sort by the input column instead of the output column to keep the sort order stable across VegCore term renames
- 01:46 PM Revision 7459: mappings/Makefile: Veg+-VegCore.csv: Before running collapse_multimap, canonicalize alternatives of ambiguous terms using unambiguous mappings. This ensures that the alternatives lists contain only canonical VegCore terms rather than synonyms.
- 01:43 PM Revision 7458: mappings/VegCore.csv: Regenerated from wiki. All synonyms are now hyperlinked, allowing them to be matched by redmine_synonyms.
- 01:31 PM Revision 7457: mappings/Veg+-VegCore.csv: Removed Sources, Definition columns because source information is now in the VegCore data dictionary
- 01:25 PM Revision 7456: mappings/VegCore.csv: Regenerated from wiki. Ambiguous terms newly available to redmine_synonyms due to the bugfix now have multiple alternatives.
- 01:25 PM Revision 7455: redmine_synonyms: Ambiguous terms: Fixed bug where need to use header # instead of term name to determine whether a term is an alternative, because some alternatives (e.g. verbatimElevation) don't follow the units-suffix naming convention.
- 12:58 PM Revision 7454: mappings/VegCore.csv: Regenerated from wiki. All ambiguous terms now have multiple alternatives, preventing them from being automapped to a single alternative without prompting the user for confirmation
- 12:50 PM Revision 7453: mappings/Makefile: Veg+-VegCore.csv: translate: Fixed bug where need to run on $@ instead of $<
- 12:49 PM Revision 7452: mappings/VegCore.csv: Regenerated from wiki. All ambiguous terms now have multiple alternatives, preventing them from being automapped to a single alternative without prompting the user for confirmation
- 12:22 PM Revision 7451: mappings/VegCore.csv: Regenerated from wiki. All mappings/Veg+-VegCore.csv terms are now added as synonyms or separate terms.
- 10:26 AM Revision 7450: mappings/VegCore.csv: Regenerated from wiki. Most ambiguous terms are now split into alternatives, and most mappings/Veg+-VegCore.csv terms are now added as synonyms.
- 06:12 AM Revision 7449: canon: Raise an error if two input terms map to the same simplified string
- 04:34 AM Revision 7448: translate: Changed dictionary to thesaurus, since the map used actually has synonyms rather than definitions
- 04:31 AM Revision 7447: mappings/Makefile: Veg+-VegCore.csv: Translate the thesaurus's output terms using itself in order to map a synonym of an ambiguous term directly to its alternatives list rather than only to the ambiguous term itself
- 04:26 AM Revision 7446: mappings/Makefile: Veg+-VegCore.csv: Run collapse_multimap on the generated map so that all alternatives are included, rather than just the first alternative, when translate maps an ambiguous term
- 04:25 AM Revision 7445: redmine_synonyms: Fixed bug where need to output a CSV rather than TSV to be usable by other programs that use map spreadsheets
- 04:23 AM Revision 7444: Added collapse_multimap, which collapses multimap entries in a spreadsheet dictionary
- 03:45 AM Revision 7443: mappings/Veg+-VegCore.csv: Separate alternatives of ambiguous terms with , instead of ", " for easier machine-parsability
- 03:31 AM Revision 7442: redmine_synonyms: Added support for ambiguous terms, which unlike the synonyms format nests the term (the alternative) under the synonym (the ambiguous term) rather than the synonym under the term. Note that ambiguous terms must also be prefixed with ? to differentiate them from composites (e.g. recordedBy_givenName), which use the same _-based naming convention.
- 03:08 AM Revision 7441: mappings/VegCore.csv: Regenerated from wiki
- 02:49 AM Revision 7440: mappings/VegCore.csv: Regenerated from wiki
- 02:22 AM Revision 7439: schemas/vegbien.sql: analytical_stem_view: Renamed scientificNameWithMorphospecies to taxonNameWithMorphospecies because it does not contain the scientific name author, as required by DwC scientificName <http://rs.tdwg.org/dwc/terms/#scientificName>
- 01:56 AM Revision 7438: mappings/Makefile: VegCore.tables.csv: Exclude ambiguous table names, which should not be part of the tables summary (as neither are table synonyms)
- 01:51 AM Revision 7437: input.Makefile: $(translate?): Merged with $(translate), which is not used independently
- 01:50 AM Revision 7436: input.Makefile: Use new translate_ci instead of translate
- 01:47 AM Revision 7435: mappings/Makefile: Use new translate_ci instead of translate
- 01:39 AM Revision 7434: Added translate_ci
02/04/2013
02/02/2013
- 05:39 PM Revision 7432: mappings/Makefile: Added target to create Veg+-VegCore.csv from VegCore.htm, initially commented out until all the synonyms in the existing Veg+-VegCore.csv are added to the VegCore data dictionary <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore_data_dictionary>
- 05:38 PM Revision 7431: Added redmine_synonyms, which translates a Redmine HTML page to a thesaurus
- 04:37 PM Revision 7430: lockfile: Linux: Documented why newgrp and recursive invocation of lockfile are needed
- 04:33 PM Revision 7429: lockfile: Linux: Fixed bug where need to change primary group of the dotlockfile process to the group of the dir to contain the lockfile, because dotlockfile otherwise reports a "permission denied" error (even though the directory is actually writable, dotlockfile thinks it isn't). Running dotlockfile with a different primary group is complicated because newgrp, the command that does this, does not pass arguments to the new process, so they must instead be passed via environment variables and a recursive invocation of lockfile (with the $inner recursion flag set). Additionally, exec cannot be used to propagate the PPID (needed by dotlockfile) because newgrp creates a new process rather than using exec, so it must be manually entered into the lockfile after dotlockfile runs.
- 02:41 PM Revision 7428: lockfile: Linux: Fixed bug where need to lower retry count to avoid overflowing the retries variable
- 02:37 PM Revision 7427: lockfile: Linux: Added workaround for bug in dotlockfile where using -1 to retry indefinitely doesn't work, so need to use large integer instead
- 01:49 PM Revision 7426: lockfile: Linux: Use bin/dotlockfile instead of the system's dotlockfile, because the system's dotlockfile is SETGID mail, which prevents it from creating lockfiles in a directory owned by the bien user and group when being run by the login user
- 01:38 PM Revision 7425: bin/: svn:ignore: Added dotlockfile, which is copied from the system during installation
- 01:30 PM Revision 7424: bin/: svn:ignore: Removed no longer applicable test_output
- 01:26 PM Revision 7423: root Makefile: misc-Linux: Added command to copy dotlockfile to the bin/ dir, so that it can be used without being SETGID mail, which would prevent it from creating lockfiles in a directory owned by the bien user and group when being run by the user
- 01:24 PM Revision 7422: root Makefile: core: Added misc-* to install other dependencies
- 11:56 AM Revision 7421: schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Removed no longer needed canon_taxonverbatim.family alternative, since the family will be included in the canon_taxonlabel.taxonomicname by the mappings
- 11:49 AM Revision 7420: schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Fixed bug where need to use canon_*taxonlabel*.taxonomicname instead of canon_taxonverbatim.taxonomicname as one of the alternatives because only canon_taxonlabel.taxonomicname is guaranteed to be populated by the mappings, while canon_taxonverbatim.taxonomicname will only be populated if the datasource explicitly specifies that field. This distinction is only meaningful for data without a TNRS match, as TNRS supplies canon_taxonverbatim.taxonomicname.
- 11:28 AM Revision 7419: import_all: after_import(): Added wait on tnrs.make's lockfile to ensure that all background scrubbing processes are complete before creating the analytical DB
- 11:18 AM Revision 7418: import_all: Moved `waitpid $jobs` into after_import()
02/01/2013
- 04:57 PM Revision 7417: schemas/vegbien.ERD.mwb: Fixed table sizes
- 04:51 PM Revision 7416: schemas/vegbien.ERD.mwb: Regenerated exports
- 04:34 PM Revision 7415: schemas/vegbien.sql: removed all accessioncode fields, as VegBIEN does not use them
- 03:10 PM Revision 7414: Added inputs/FIA/_src/FIADB_version4.accdb and FIADB_version4.sql (created from it using Access To PostgreSQL and the additional transformations at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Tools#MS-Access-database-MDB>)
01/31/2013
- 08:20 PM Revision 7413: Added inputs/FIA/COND_unique/, generated from new FIA data
- 08:05 PM Revision 7412: inputs/FIA/FIA_COND_unique/create.sql: Fixed bug where need to remove `CREATE TABLE :table AS` at beginning because that is added by the make target
- 08:03 PM Revision 7411: inputs/FIA/geoscrub.~.clean_up.sql: Moved creation of FIA_COND_unique to FIA_COND_unique/create.sql
- 07:40 PM Revision 7410: README.TXT: Full database import: Updated time until import_all returns control to the shell to account for the TNRS names now being imported concurrently with the inputs rather than before them
- 07:31 PM Revision 7409: mappings/VegCore-VegBIEN.csv: Also include morphospecies in the accepted taxondetermination's taxonverbatim, so that it can easily be retrieved by the analytical DB views
- 07:15 PM Revision 7408: schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Fixed bug where need to use the taxonName or scientificName when the name components are not provided, as is the case when there is no scrubbed taxondetermination (because TNRS returns no match)
- 06:08 PM Revision 7407: mappings/VegCore.csv: Regenerated from wiki. This adds Brad's DwC ID terms and their definitions in <https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx>.
- 05:06 PM Revision 7406: schemas/vegbien.ERD.mwb: Regenerated exports
- 04:04 PM Revision 7405: join: Added support for direct mappings to VegBIEN by passing through outputs that start with / (indicating an XPath rather than a term)
- 04:01 PM Revision 7404: mappings/VegCore.csv: Regenerated from wiki
- 11:38 AM Revision 7403: schemas/vegbien.sql: analytical_stem_view: Added family_matched, taxonName_matched, scientificNameAuthorship_matched
- 11:02 AM Revision 7402: schemas/vegbien.sql: analytical_stem_view: Added family_verbatim, scientificName_verbatim, scientificNameAuthorship_verbatim from datasource taxondetermination
- 10:57 AM Revision 7401: mappings/VegCore.csv: Regenerated from wiki
- 10:30 AM Revision 7400: schemas/vegbien.sql: analytical_stem_view: Fixed bug where need to use identifiedBy and dateIdentified from the *datasource* taxondetermination rather than the canonical taxondetermination (whichever taxondetermination is most scrubbed)
- 10:23 AM Revision 7399: schemas/vegbien.sql: taxondetermination: taxondetermination_set_iscurrent(): is_datasource_current: Fixed bug where need to filter out determinationtypes for matched/accepted determinations, which are not datasource determinations
- 10:19 AM Revision 7398: schemas/vegbien.sql: taxondetermination: taxondetermination_set_iscurrent(): Fixed bug where need to also set existing datasource_current taxondetermination's is_datasource_current to false
- 08:52 AM Revision 7397: xml_dom.py: replace_with_text(): Added support for all scalar (non-Node) types, which will be stringified using strings.ustr()
- 03:52 AM Revision 7396: schemas/functions.sql: Added _fix_date()
- 02:49 AM Revision 7395: sql_io.py: put_table(): Documented that much of the complexity of the normalizing algorithm is due to PostgreSQL not having a native command for insert/on duplicate select
- 02:24 AM Revision 7394: sql_io.py: put_table(): Corrected "insert/if not exists get" to "insert/on duplicate select"
- 01:52 AM Revision 7393: sql_io.py: put_table(): Removed no longer applicable requirement that it be run at the beginning of a transaction, which was only required when the output table was locked during the function call
- 01:48 AM Revision 7392: sql_io.py: put_table(): Documented that the function's insert/if not exists get algorithm does not support database triggers that populate fields covered by a unique constraint
- 01:42 AM Revision 7391: inputs/FIA/_src/_README.TXT: Documented that FIA does not provide data for some states, e.g. HI
01/30/2013
- 10:48 PM Revision 7390: config/: Set svn:ignore to exclude *password files
- 10:41 PM Revision 7389: Removing config/bien_read_password from version control
- 10:30 PM Revision 7388: Removing config/bien_password from version control
01/29/2013
- 03:26 PM Revision 7387: inputs/FIA/: Added refreshed data (not yet mapped)
- 03:15 PM Revision 7386: input.Makefile: Existing maps discovery: $(exts): Also match uppercase versions of extensions
- 03:12 PM Revision 7385: lib/common.Makefile: Added $(ucase) and $(ci)
- 01:56 PM Revision 7384: inputs/FIA/_src/Makefile: Table bundling: $(tableCsvs): Fixed bug where need to replace % with $* in $(csvPattern)
- 01:15 PM Revision 7383: inputs/FIA/_src/Makefile: Table bundling: Fixed bug where need to remove trailing slashes from dirs that will match a target pattern
- 01:09 PM Revision 7382: inputs/FIA/_src/Makefile: Added Table bundling targets to regroup CSVs by tables
- 01:09 PM Revision 7381: lib/common.Makefile: Added $(mkdir)
- 11:02 AM Revision 7380: Added inputs/FIA/_src/_README.TXT with Bob's comments
- 11:02 AM Revision 7379: input.Makefile: SVN: $(_svnFilesGlob): Added README.TXT
- 10:33 AM Revision 7378: mappings/VegCore.csv: Regenerated from wiki. Synonym lists have now been translated to sections to create a web page anchor for each synonym, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore_refactoring#Index-synonyms-as-web-page-anchors>. This enables searching for VegCore synonyms in the data dictionary as well as terms, and makes it possible to swap a term and a synonym while still keeping both as indexed anchors.
- 06:19 AM Revision 7377: mappings/VegCore.csv: Regenerated from wiki. All uncategorized terms have now been moved to tables.
- 06:19 AM Revision 7376: README.TXT: Maintenance: VegCore data dictionary: Added steps to check that no terms were lost when moving terms
01/28/2013
- 05:13 PM Revision 7375: inputs/import.stats.xls: Updated import times
- 05:12 PM Revision 7374: mappings/VegCore.csv: Regenerated from wiki
01/25/2013
- 03:54 PM Revision 7373: schemas/vegbien.sql: analytical_stem_view: coordinates: Only use county_centroids coordinates when datasource coordinates are not provided, not also when datasource coordinates aren't geovalid. This also fixes a bug where (NULL) county_centroids coordinates were used for non-geovalid coordinates even when there was no county_centroids match, rather than including the non-geovalid coordinates.
- 03:34 PM Revision 7372: mappings/VegCore.csv: Regenerated from wiki
- 11:27 AM Revision 7371: schemas/vegbien.sql: taxondetermination: Added is_datasource_current, which is autopopulated to the most recent *datasource-provided* taxondetermination
- 11:07 AM Revision 7370: schemas/vegbien.sql: taxondetermination: Added taxondetermination_single_accepted_determination unique index to facilitate joining on the accepted determination
- 11:05 AM Revision 7369: schemas/vegbien.sql: taxondetermination: Added taxondetermination_single_matched_determination unique index to facilitate joining on the matched determination
- 10:32 AM Revision 7368: schemas/vegbien.sql: taxondetermination: Removed notespublic, notesmgt, which are not used by VegBIEN
- 09:30 AM Revision 7367: schemas/vegbien.sql: taxon_trait_view: scientificName: Use taxonverbatim.taxonname when taxonlabel/taxonverbatim.taxonomicname are not provided, to accommodate TNRS names. This is part of the workaround for the bug where the taxonlabel's taxonomicname (concatenated taxonomicname) is occasionally not populated.
- 09:10 AM Revision 7366: schemas/vegbien.sql: taxon_trait_view: Added workaround for bug where the taxonlabel's taxonomicname (concatenated taxonomicname) is occasionally not populated due to a taxonlabel constraint violation, by using the taxonverbatim's taxonomicname instead in these cases. This bug, which appeared in the r7317 import, is so far not reproducible (tested on Mac OS X), so its cause is unknown, but may be caused by a bug in functions._merge_prefix(), which is run on the taxonlabel's taxonomicname but not the taxonverbatim's taxonomicname.
01/24/2013
- 09:51 PM Revision 7365: schemas/vegbien.sql: analytical_stem_view: Added dateIdentified, identificationRemarks per Brad's request (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#E-mail-on-2013-1-16)
- 09:40 PM Revision 7364: inputs/FIA/_src/Makefile: Added extraction targets to extract zip archives
- 09:07 PM Revision 7363: inputs/FIA/_src/download: Use new Makefile, which uses make logic to determine if a file needs to be downloaded
- 09:05 PM Revision 7362: Added inputs/FIA/_src/Makefile, with targets to download each zip archive
- 08:00 PM Revision 7361: schemas/vegbien.sql: analytical_stem_view: derived terms: Added _bien suffix per Brad's request (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#Brad-Boyles-comments)
- 03:22 PM Revision 7360: Added inputs/FIA/_src/FIADB_version4.accdb.url
- 03:18 PM Revision 7359: inputs/FIA/_src/download: Only run wget on files that don't yet exist
- 03:16 PM Revision 7358: inputs/FIA/_src/download: Run wget in same directory as script to ensure files get downloaded there
- 03:06 PM Revision 7357: inputs/FIA/_src/download: Set svn:executable
- 03:04 PM Revision 7356: Added inputs/FIA/_src/download to download archives of CSVs for each state
- 03:03 PM Revision 7355: to_do/timeline.2013.xls: Updated with changes during conference call
- 09:46 AM Revision 7354: schemas/vegbien.sql: taxon_trait_view: Renamed datasource_taxonverbatim to taxonverbatim because there is now only one taxonverbatim
- 09:31 AM Revision 7353: schemas/vegbien.sql: taxon_trait_view: Moved the taxondetermination.iscurrent filter to the join condition to allow using the taxondetermination_single_current_determination index
- 09:24 AM Revision 7352: schemas/vegbien.sql: taxon_trait_view: Join only on the primary taxonlabel, not the accepted taxonlabel, because the scrubbed name is now available directly via the taxonlabel attached to the scrubbed taxondetermination
- 09:11 AM Revision 7351: schemas/vegbien.sql: analytical_stem_view: Added locality
- 08:18 AM Revision 7350: inputs/UNCC/Specimen/map.csv: accession: Remapped to catalogNumber per Bob's corrections
01/23/2013
- 10:31 PM Revision 7349: schemas/vegbien.ERD.mwb: Regenerated exports
- 10:25 PM Revision 7348: mappings/VegCore.csv: Regenerated from wiki
- 10:01 PM Revision 7347: README.TXT: Schema changes: Added instructions to run the appropriate sync function when changing the analytical views
- 09:56 PM Revision 7346: schemas/vegbien.sql: analytical_stem_view: Added georeferenceProtocol, which is set to 'county centroid' when county centroid coordinates are used
- 08:12 PM Revision 7345: make_analytical_db: Don't run export_analytical_db if the SQL script exits with an error
- 08:04 PM Revision 7344: README.TXT: Full database import: record the import times in inputs/import.stats.xls: Added `export version=<version>` because import_times may be run in a shell different from the one that the import was run in
- 08:03 PM Revision 7343: inputs/import.stats.xls: Updated import times
01/22/2013
- 07:43 PM Revision 7342: schemas/vegbien.sql: taxonverbatim: taxonverbatim_unique: Added morphoname for cases when there is just a morphoname, and to distinguish taxonverbatims with the same taxonlabel but different morphonames
- 07:43 PM Revision 7341: schemas/vegbien.sql: stemobservation: Added stemobservation_non_empty CHECK constraint to prevent creating an empty stemobservation for plantobservation rows without stem *data* but with stem *mappings*
- 07:36 PM Revision 7340: schemas/vegbien.sql: stemobservation: Added stemobservation_non_empty CHECK constraint to prevent creating an empty stemobservation for plantobservation rows without stem *data* but with stem *mappings*
- 07:34 PM Revision 7339: schemas/vegbien.sql: stemobservation: Added stemobservation_non_empty CHECK constraint to prevent creating an empty stemobservation for plantobservation rows without stem *data* but with stem *mappings*
- 07:16 PM Revision 7338: schemas/vegbien.sql: taxonverbatim: taxonverbatim_unique: Added morphoname for cases when there is just a morphoname, and to distinguish taxonverbatims with the same taxonlabel but different morphonames
- 07:11 PM Revision 7337: schemas/vegbien.sql: taxonverbatim: Allow taxonlabel_id to be NULL when morphoname is provided
- 07:09 PM Revision 7336: schemas/vegbien.sql: taxonverbatim: Allow taxonlabel_id to be NULL when morphoname is provided
- 07:04 PM Revision 7335: schemas/vegbien.sql: taxonverbatim: Added source_id to allow creating taxonverbatims without a (scoping) taxonlabel
- 05:34 PM Revision 7334: schemas/vegbien.sql: analytical_stem_view: Removed speciesBinomialWithMorphospecies now that it's duplicated by scientificNameWithMorphospecies
- 05:28 PM Revision 7333: schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Create it using the speciesBinomialWithMorphospecies formula, per Brad's request at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#2013-1-18>
- 05:05 PM Revision 7332: schemas/vegbien.sql: analytical_stem_view: Added coordinateSource to indicate whether coordinates are from county_centroids (georeferencing) or the source data
- 05:00 PM Revision 7331: schemas/vegbien.sql: Added coordinatesource enum
- 04:50 PM Revision 7330: mappings/VegCore.csv: Regenerated from wiki
- 04:34 PM Revision 7329: schemas/vegbien.sql: analytical_stem_view: coordinates: Also use the county_centroids coordinates when the datasource coordinates are not geovalid. (Note that canon_place.geovalid will be NULL, i.e. not true, when the datasource coordinates are NULL.)
- 04:28 PM Revision 7328: schemas/vegbien.sql: scientificName: Set to taxonverbatim.taxonname instead per Brad's changes at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#2013-1-18>. Renamed to taxonName since this now doesn't include the author, which is part of DwC's scientificName field.
- 03:55 PM Revision 7327: schemas/vegbien.sql: sync_analytical_stem_to_view(): Support running the function when dependent views do not exist. This allows using the sync function when changing column names of the analytical_stem_view, which sometimes requires manually dropping and re-creating the analytical_aggregate_view.
- 02:49 PM Revision 7326: backups/Makefile: %.md5/test: Added comment to run with `make -s` to avoid echoing make commands
- 02:42 PM Revision 7325: README.TXT: Full database import: Added steps to scrub unscrubbed taxondeterminations (if they are not scrubbed automatically)
- 02:06 PM Revision 7324: inputs/.geoscrub/_src/README.TXT: Added e-mails from Jim about how the county_centroids data was generated
- 01:18 PM Revision 7323: schemas/vegbien.sql: analytical_stem_view: coordinates: Use new county_centroids coordinates and uncertainty when the datasource's coordinates are not available
- 01:10 PM Revision 7322: Added inputs/.geoscrub/county_centroids/ from Jim
- 01:09 PM Revision 7321: inputs/.geoscrub/import_order.txt: Added geoscrub_output
- 12:24 PM Revision 7320: inputs/import.stats.xls: Updated import times
- 12:19 PM Revision 7319: README.TXT: Full database import: In PostgreSQL: Added step to check that there are TNRS taxondeterminations
- 12:17 PM Revision 7318: README.TXT: Full database import: In PostgreSQL: Added step to check that unscrubbed_taxondetermination_view returns no rows
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