Activity
From 11/04/2012 to 12/03/2012
12/03/2012
- 07:37 PM Revision 6569: inputs/VegBank/plot_/map.csv: Mapped confidentialitystatus to coordinateUncertaintyInMeters, overriding locationaccuracy when the confidentialitystatus indicates fuzzing
- 07:24 PM Revision 6568: inputs/NVS/*/map.csv: Mapped Taxon Growth Form values to growthform enum
- 07:08 PM Revision 6567: Added inputs/NVS/Source/
- 07:05 PM Revision 6566: inputs/NVS/import_order.txt: Specified import order
- 07:02 PM Revision 6565: inputs/input.Makefile: Staging tables installation: $(allInstalls): Exclude the Source table, which contains only (metadata) mappings, not data
- 06:54 PM Revision 6564: Regenerated vegbien.ERD exports
- 06:46 PM Revision 6563: Added inputs/NVS/TaxonOccurrence.Understory/
- 06:38 PM Revision 6562: Added inputs/NVS/Coordinates/
- 06:38 PM Revision 6561: inputs/NVS/Plot/map.csv: Mapped Plot
- 06:33 PM Revision 6560: mappings/VegCore-VegBIEN.csv: Mapped verbatimCoordinates
- 06:27 PM Revision 6559: mappings/Veg+-VegCore.csv: Removed type->dcterms:type automapping because this term can have many different meanings
- 06:07 PM Revision 6558: inputs/NVS/: Renamed Organism to AggregateOccurrence because this actually contains aggregated samplings
- 06:04 PM Revision 6557: inputs/NVS/StemObservation/map.csv: Mapped Item ID, Item Obs ID
- 05:58 PM Revision 6556: Added inputs/NVS/StemObservation/
- 05:52 PM Revision 6555: Added inputs/NVS/TaxonOccurrence/
- 05:51 PM Revision 6554: Added inputs/NVS/map.csv (global mappings)
- 05:47 PM Revision 6553: inputs/NVS/Project/map.csv: Remapped Project Abbreviation to projectName instead of Name, because Project Abbreviation is what's used throughout the tables to link to the project
- 05:34 PM Revision 6552: inputs/NVS/Plot/map.csv: Mapped Physiography
- 05:31 PM Revision 6551: inputs/NVS/Plot/map.csv: Mapped Area
- 05:29 PM Revision 6550: inputs/NVS/Plot/map.csv: Altitude: Provided rationale for units determination
- 05:25 PM Revision 6549: Added inputs/NVS/Organism/
- 05:06 PM Revision 6548: Added inputs/NVS/Project/
- 05:05 PM Revision 6547: mappings/VegCore-VegBIEN.csv: Mapped projectStartDate, projectEndDate
- 05:02 PM Revision 6546: mappings/VegCore.csv: Added projectStartDate, projectEndDate
- 05:02 PM Revision 6545: mappings/VegCore.csv: Renamed plotName to locationName because this term also applies to the location of a specimen. This replaces CTFS's definition of locationName as locality.
- 04:37 PM Revision 6544: root Makefile: apt-get: Use --yes to allow unattended installations
- 03:58 PM Revision 6543: schemas/vegbien.sql: analytical_*: Renamed plotName to locationName to match the new VegCore term name
- 03:51 PM Revision 6542: mappings/VegCore.csv: Renamed plotName to locationName because this term also applies to the location of a specimen. This replaces CTFS's definition of locationName as locality.
- 03:30 PM Revision 6541: mappings/VegCore.csv: Added subInstitutionCode
- 03:25 PM Revision 6540: schemas/vegbien.sql: analytical_stem_view: locationevent info: Fixed bug where need to use project.sourceaccessioncode instead of locationevent.project_id for the projectID
- 03:21 PM Revision 6539: schemas/vegbien.sql: analytical_stem_view: locationevent info: Fixed bug where need to use the parent locationevent's obsstartdate instead when the subevent does not provide it
- 03:19 PM Revision 6538: schemas/vegbien.sql: analytical_stem_view: locationevent info: Fixed bug where need to use the parent locationevent's project and method instead when the subevent does not provide them, because they are often attached to it instead
- 03:07 PM Revision 6537: schemas/vegbien.sql: analytical_stem_view: geolocation info: Fixed bug where need to use the parent location instead when provided, because lat/long and placenames are attached to it instead of the subplot's location
- 02:47 PM Revision 6536: backups/Makefile: %.md5: Fixed bug where md5sum does not have a -q option like md5
- 02:43 PM Revision 6535: backups/Makefile: %.md5: Fixed bug where need to use md5sum instead of md5 on Linux
- 02:39 PM Revision 6534: schemas/vegbien.sql: analytical_stem_view: Filter out non-current taxondeterminations (occurrences with no taxondetermination are preserved)
- 02:10 PM Revision 6533: schemas/vegbien.sql: Removed no longer needed darwin_core table. Use analytical_stem instead, which is now identical.
- 02:02 PM Revision 6532: schemas/vegbien.sql: sync_analytical_*_to_view(): Creating analytical_* table: Fixed bug where need LIMIT 0 so that it can be used on a full DB, which will have data in the tables used by analytical_stem_view
- 01:40 PM Revision 6531: schemas/vegbien.sql: Merged darwin_core into analytical_stem
- 01:21 PM Revision 6530: schemas/vegbien.sql: darwin_core_view, analytical_stem_view: Updated now that newWorldCountries.isoCode is a text field
- 12:35 PM Revision 6529: README.TXT: Data import: backups: Step to copy backups to jupiter: Added full path to aaronmk/ (/data/dev/aaronmk)
- 12:00 PM Revision 6528: inputs/newWorld/geoscrub.schema.~.changes.sql: Reversed order of adding unique constraints and changing types
- 11:57 AM Revision 6527: inputs/newWorld/geoscrub.schema.~.changes.sql: Changed isoCode type to text. Added unique constraint on isoCode.
- 11:06 AM Revision 6526: backups/Makefile: Added md5s target to generate .md5 files for all backups
- 11:05 AM Revision 6525: inputs/import.stats.xls: Updated import times
- 10:48 AM Revision 6524: backups/Makefile: %.md5: Run with `nice -n +5` to avoid slowing down the UI
- 10:46 AM Revision 6523: backups/: svn:ignore: Added *.md5. Removed no longer applicable *.log.
- 10:42 AM Revision 6522: backups/Makefile: Changed paths to be relative to the Makefile rather than the current directory, so this Makefile can be used in other directories as well (such as jupiter:/aaronmk/VegBIEN.backups/)
- 10:34 AM Revision 6521: backups/Makefile: %.backup: Also create MD5 of backup
- 10:31 AM Revision 6520: backups/Makefile: Added %.md5 target to create checksums of each backup
- 10:17 AM Revision 6519: README.TXT: Data import: backups: Added step to copy backups to jupiter in /aaronmk/VegBIEN.backups/ . The jupiter folder, which has several TB of space available, will replace local backup drives as the location for archived backups.
- 10:00 AM Revision 6518: README.TXT: Data import: Removed additional backup of just the public schema, which is not needed because the public schema is included in the full DB backup. The additional public schema backup increased the total backup size by 60-70%, so this will help conserve limited disk space on vegbiendev as well as on local archives of the backups.
- 09:52 AM Revision 6517: README.TXT: Backups: Full DB: Updated steps to match Data import steps, which add the date to the backup filename when it's created rather than afterwards
- 09:42 AM Revision 6516: README.TXT: Backups: Archived imports: Back up: Added instructions for archiving the last import before backing it up
- 09:10 AM Revision 6515: Regenerated vegbien.ERD exports
- 09:08 AM Revision 6514: schemas/vegbien.sql: analytical_*: Removed NOT NULL constraint on dateCollected
- 09:07 AM Revision 6513: schemas/vegbien.sql: source: Added sampletype field to indicate a plot or specimen datasource
- 09:00 AM Revision 6512: schemas/vegbien.sql: analytical_*: Removed NOT NULL constraint on dateCollected
- 08:55 AM Revision 6511: schemas/vegbien.sql: sync_analytical_*_to_view(): Added NOT NULL constraints
11/30/2012
- 05:20 PM Revision 6510: make_analytical_db: Added step to create darwin_core materialized view
- 05:09 PM Revision 6509: inputs/*/Source/map.csv for non-herbaria: Mapped sampleType
- 05:02 PM Revision 6508: inputs/.herbaria/herbaria/map.csv: Set sampleType to "specimen"
- 05:02 PM Revision 6507: mappings/VegCore-VegBIEN.csv: Mapped sampleType
- 05:00 PM Revision 6506: mappings/VegCore.csv: Added sampleType
- 04:57 PM Revision 6505: schemas/vegbien.sql: source: Added sampletype field to indicate a plot or specimen datasource
- 04:55 PM Revision 6504: schemas/vegbien.sql: Added sampletype enum
- 04:46 PM Revision 6503: root Makefile: $(postgresReload-*): Confirm the operation before continuing, since it involves changing PostgreSQL config files in nontrivial ways. Added instructions for setting kernel.shmmax to at least 4GB minus 1 byte on Linux, to work with the shared_buffers setting in postgresql.conf.
- 04:03 PM Revision 6502: schemas/postgresql.conf: shared_buffers: Documented that it must be less than ~95% of SHMMAX
- 03:58 PM Revision 6501: schemas/vegbien.sql: analytical_stem_view: identifiedBy: Fixed bug where need to use party.fullname instead of name components because the name is now mapped to fullname
- 03:28 PM Revision 6500: schemas/vegbien.sql: analytical_stem_view, darwin_core_view: dateCollected: Use the parent plot event's obsstartdate when the subplot event does not have its own obsstartdate
- 01:56 PM Revision 6499: schemas/vegbien.sql: analytical_stem_view: Don't filter out rows without a date or non-current taxondeterminations
- 01:54 PM Revision 6498: schemas/vegbien.sql: analytical_stem_view: Don't filter out rows without a date
- 01:28 PM Revision 6497: schemas/vegbien.sql: Added darwin_core_view
- 12:56 PM Revision 6496: schemas/vegbien.sql: analytical_stem_view: identifiedBy: Fixed bug where need to use party.fullname instead of name components because the name is now mapped to fullname
- 12:40 PM Revision 6495: schemas/vegbien.sql: sync_analytical_*_to_view(): Added CREATE INDEX statements
- 12:31 PM Revision 6494: README.TXT: Data import: Added steps to publish analytical DB on nimoy.bien_web
- 10:46 AM Revision 6493: schemas/vegbien.sql: analytical_stem_view: Changed JOINs to LEFT JOINs to include occurrences without taxondeterminations
- 10:21 AM Revision 6492: export_analytical_db: Use 'NULL' as the NULL value instead of \N, because MySQL has problems with \N
- 09:57 AM Revision 6491: publish_analytical_db: Load to bien3_adb instead of bien_web
11/29/2012
- 05:41 PM Revision 6490: README.TXT: Data import: Added step to export analytical DB
- 01:11 PM Revision 6489: root Makefile: $(postgres-Linux): Fixed bug where need $(asAdmin) before commands to rename existing *.conf
- 01:01 PM Revision 6488: root Makefile: $(postgres-Linux): Also install postgresql-contrib, which contains the hstore extension
11/28/2012
- 06:18 PM Revision 6487: Added inputs/NVS/
- 06:04 PM Revision 6486: inputs/CVS/Organism/map.csv: Mapped accordingTo to "Weakley 2006"
- 06:02 PM Revision 6485: inputs/NY/Specimen/map.csv: Omit UniqueNYInternalRecordNumber to avoid confusion since this is an internal-only ID. This makes InstitutionCode+CollectionCode+CatalogNumber the globally unique identifier instead.
- 06:00 PM Revision 6484: README.TXT: Added Datasource refreshing section with instructions for refreshing VegBank
- 05:57 PM Revision 6483: schemas/vegbien.sql: Renamed taxonconcept.concept_source_id back to concept_reference_id
- 05:52 PM Revision 6482: schemas/vegbien.sql: Renamed soilobs to soilsample per working group discussion
- 05:27 PM Revision 6481: input.Makefile: SVN: add: verify: Fixed bug where need to use $ prefix before string to parse newline
- 05:27 PM Revision 6480: input.Makefile: SVN: add: verify: Fixed bug where need to use $ prefix before string to parse newline
- 05:25 PM Revision 6479: inputs/NY/verify/: svn:ignore .csv files
- 05:25 PM Revision 6478: input.Makefile: SVN: add: Also svn:ignore .csv files
- 02:47 PM Revision 6477: export_analytical_db: Export NULL as \N to work with MySQL
- 01:22 PM Revision 6476: schemas/vegbien.sql: analytical_*: Added index on NOT NULL columns, starting with institutionCode
- 01:19 PM Revision 6475: schemas/vegbien.sql: analytical_*: Removed primary keys and NOT NULL constraints on columns that sometimes have NULL values
- 01:08 PM Revision 6474: publish_analytical_db: Added CSV dialect information
- 12:42 PM Revision 6473: root Makefile: PostgreSQL: $(postgresReload-*): Rename existing *.conf to *.conf.old
11/27/2012
- 06:44 PM Revision 6472: publish_analytical_db: Use LOAD DATA *LOCAL* INFILE instead of LOAD DATA INFILE to avoid needing FILE permissions on bien_web
- 01:17 PM Revision 6471: Added publish_analytical_db
- 12:43 PM Revision 6470: export_analytical_db: Append the public schema version to the CSV filename
- 12:27 PM Revision 6469: backups/Makefile: $(rsyncBackups): Added *.csv
11/26/2012
- 06:12 PM Revision 6468: Added export_analytical_db
- 06:10 PM Revision 6467: backups/: Ignore _* and *.csv
- 01:35 PM Revision 6466: make_analytical_db: mk_analytical_table(): Use explicit schema references everywhere. This fixes a bug where the TRUNCATE/INSERT steps on the public schema's table would reference the analytical_db view instead because they were not schema-scoped.
- 01:33 PM Revision 6465: make_analytical_db: mk_analytical_table(): Factored table references in different schemas out into vars
11/25/2012
- 09:31 PM Revision 6464: schemas/vegbien.sql: analytical_stem_view: recordNumber: Combine identifying fields in taxonoccurrence, plantobservation, and stemobservation to ensure that this field is unique within the plot and not NULL
- 09:13 PM Revision 6463: Regenerated vegbien.ERD exports
- 08:52 PM Revision 6462: make_analytical_db: Moved set -x () around just psql_verbose_vegbien so embedded $() expressions wouldn't also be in set -x (verbose) mode
- 08:49 PM Revision 6461: make_analytical_db: Fixed bug where need to use bash instead of sh because vegbien_dest requires it
- 08:37 PM Revision 6460: make_analytical_db: Factored analytical_* table creation code out into mk_analytical_table() function
- 08:28 PM Revision 6459: make_analytical_db: Create analytical_db views pointing to the analytical_* versions in the public schema
- 08:21 PM Revision 6458: vegbien_dest: $schemas: Removed analytical_db because views that will be added to it were shadowing public schema tables with the same names during population of those tables in make_analytical_db
- 07:47 PM Revision 6457: vegbien_dest: Export $public, to make sure it's available to any invoked scripts as an env var
- 07:45 PM Revision 6456: vegbien_dest: $schemas: Added analytical_db
- 07:38 PM Revision 6455: inputs/import.stats.xls: Added separate tab with stats for 2012-6~9. The Excel format apparently only supports 255 columns, so previous imports had been silently truncated off. Note that once the 2012-10 imports reach column 255, a new tab will need to be created with the 2012-10+ imports.
- 07:20 PM Revision 6454: bin/map: in_is_db: by_col: Clearing errors table: Skip this if the table has been set to None because it didn't exist (and thus was a metadata-only map spreadsheet)
- 06:54 PM Revision 6453: schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Fixed bug where need to use the specific_epithet from the accepted_taxonverbatim rather than the parsed_taxonverbatim
- 06:45 PM Revision 6452: schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Include the family any time the genus is not specified, instead of just when accepted_taxonlabel.rank = 'family'. These should have the same effect since TNRS includes the rank, but using COALESCE() is clearer.
- 06:41 PM Revision 6451: schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Changed to also include morphospecies when just the family is specified
- 06:35 PM Revision 6450: schemas/vegbien.sql: analytical_stem_view: Fixed bug where location.authorlocationcode needed to be used as the plotName when location.sourceaccessioncode was not provided, to ensure that plotName would be NOT NULL
- 06:20 PM Revision 6449: inputs/FIA/import_order.txt: Fixed bug where FIA_COND_unique needed to be explicitly included in import_order.txt now that we're using import_order.txt to import the Source metadata table before the data tables
- 06:15 PM Revision 6448: inputs/import.stats.xls: Updated import times
11/24/2012
- 03:07 PM Revision 6447: root Makefile: PostgreSQL: $(postgresReload-Linux): Try chmoding both as your user and as the bien user
- 02:46 PM Revision 6446: input.Makefile: Testing: $(runTest): Ignore failed diffs when the test is compared to another test's output (e.g. in by_col mode)
- 02:41 PM Revision 6445: bin/map: in_is_db: If table does not exist, set table to None so that db_xml.put_table() doesn't try to access it. This fixes a bug in metadata-only map spreadsheets under column-based import.
- 02:40 PM Revision 6444: db_xml.py: put_table(): Support None in_table by calling put() directly
- 02:29 PM Revision 6443: Removed no longer used geoscrub.*.sql. Use geoscrub_output instead.
- 02:27 PM Revision 6442: Removed no longer used geoscrub_cleaned_unique. Use geoscrub_output instead.
- 02:25 PM Revision 6441: Removed no longer used geoscrub_cultivated. Use analytical_stem_view.cultivated instead.
- 02:25 PM Revision 6440: Removed no longer used geoscrub_cultivated. Use analytical_stem_view.cultivated instead.
- 02:23 PM Revision 6439: schemas/vegbien.sql: analytical_stem_view: cultivated: Removed BIEN2's geoscrub_cultivated, which has now been replaced by the primary corresponding scripts (and never had particularly many matches to the locations in any case)
- 02:14 PM Revision 6438: schemas/vegbien.sql: analytical_stem_view: cultivated: Use OR instead of _or() to combine cultivated_family_locations.country IS NOT NULL with the other values, because this field's false value should not be used in place of NULL if all the other values are NULL, as it would be with _or(). (cultivated_family_locations.country IS NOT NULL can indicate presence, but not absence, of cultivated status.)
- 02:06 PM Revision 6437: schemas/functions.sql, vegbien.sql: _and(), _or(): Added comment comparing the function and the corresponding logical operator
- 01:50 PM Revision 6436: schemas/vegbien.sql: public: Added _or(), for use by analytical_stem_view
- 01:48 PM Revision 6435: schemas/vegbien.sql: analytical_stem_view: cultivated: Also set if family/country combination found in cultivated_family_locations
- 01:39 PM Revision 6434: schemas/vegbien.sql: cultivated_family_locations: Added data from nimoy:/home/boyle/bien2/geoscrub/cultivated/cult_by_taxon/flag_by_taxa.inc
- 01:33 PM Revision 6433: schemas/vegbien.sql: Added cultivated_family_locations to store locations where various taxon families are considered cultivated
- 01:24 PM Revision 6432: mappings/VegCore-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()
- 01:23 PM Revision 6431: xml_func.py: Simplifying functions: Added passthru entries for _and, _or
- 01:06 PM Revision 6430: schemas/vegbien.sql: Added _locationnarrative_is_cultivated()
- 12:57 PM Revision 6429: lib/PostgreSQL-MySQL.csv: Change text to varchar(255) because text columns can't be used in indexes in MySQL
- 12:51 PM Revision 6428: lib/PostgreSQL-MySQL.csv: Resaved in Excel, which removed unnecessary quotes around fields
- 12:22 PM Revision 6427: schemas/vegbien.sql: analytical_aggregate: Added identifiedBy, which is no longer a scoping field (which would prevent scientificNameWithMorphospecies from being unique) now that there is only one taxondetermination for each taxonoccurrence
- 12:05 PM Revision 6426: schemas/vegbien.sql: analytical_stem_view: dateCollected: For plots data, use the locationevent obsstartdate instead of the collectiondate in order to group taxonoccurrences/stems from the same locationevent together
- 11:59 AM Revision 6425: schemas/vegbien.sql: analytical_* pkeys: Added dateCollected because the records are actually unique within the location*event*, not the location
- 11:57 AM Revision 6424: schemas/vegbien.sql: analytical_stem_view: Exclude records with no collectiondate or obsstartdate, which is required to uniquely identify a record
- 11:54 AM Revision 6423: analytical_stem_view: dateCollected: Use locationevent.obsstartdate when aggregateoccurrence.collectiondate is not provided
- 11:37 AM Revision 6422: schemas/vegbien.sql: analytical_stem_view: Include only the current taxondetermination for each taxonoccurrence, to avoid cross-joining taxondeterminations with stems and thus multiplying the number of rows for datasources that have multiple taxondeterminations per taxonoccurrence
- 11:33 AM Revision 6421: schemas/vegbien.sql: taxondetermination: Added AFTER trigger to set the current taxondetermination for the taxonoccurrence
- 11:11 AM Revision 6420: lib/PostgreSQL-MySQL.csv: Statements ending in ";": When matching any character, use .*? (with the (?s) flag) instead of [^;]* in order to allow embedded ; to be matched. This fixes a bug where a CREATE VIEW statement was not removed because it contained an embedded ; .
- 11:06 AM Revision 6419: schemas/vegbien.sql: taxondetermination: Added unique index to ensure that there is only one current determination for each taxonoccurrence
- 11:05 AM Revision 6418: lib/PostgreSQL-MySQL.csv: Remove indexes with WHERE clauses
- 10:34 AM Revision 6417: schemas/vegbien.sql: analytical_aggregate: Added primary key on institutionCode, plotName, scientificNameWithMorphospecies, recordNumber. Note that this makes these fields NOT NULL, which should not be a problem because there are inner joins instead of LEFT JOINs on most of the tables which provide them, and LEFT JOINed tables have their identifying fields combined to create a NOT NULL value.
- 10:27 AM Revision 6416: schemas/vegbien.sql: analytical_stem_view: recordNumber: Combine identifying fields in taxonoccurrence, plantobservation, and stemobservation to ensure that this field is unique within the plot and not NULL
- 10:23 AM Revision 6415: lib/PostgreSQL-MySQL.csv: Only match a statement-terminating ; when it's at the end of a line
- 10:02 AM Revision 6414: schemas/vegbien.sql: analytical_aggregate: Added primary key on institutionCode, plotName, scientificNameWithMorphospecies. Note that this makes these fields NOT NULL, which should not be a problem because there are inner joins instead of LEFT JOINs on the tables which provide them.
- 09:21 AM Revision 6413: db_xml.py: put(): _setDefault(): Delay the evaluation of each col_default's value until the col_default is actually retrieved. This fixes a bug in the source table mappings where the explicit source entry was being created *after* the col_default source entry, causing the initial entry, which did not have the additional fields populated, to be used instead.
- 09:14 AM Revision 6412: dicts.py: Added WrapDict, a dict that runs a function on each value retrieved
- 08:59 AM Revision 6411: db_xml.py: put(): _setDefault(): Fixed bug where need to copy col_defaults before calling update() on it, to avoid modifying the input value (which may be reused by the caller, expecting it to be unmodified)
- 08:54 AM Revision 6410: db_xml.py: put(): col_defaults param: Fixed bug where need to use None as default value, because col_defaults will be modified by put() and the {} default value is a global instance
- 08:29 AM Revision 6409: mappings/VegCore-VegBIEN.csv: source table mappings: Set shortname to env var $source when it's not explicitly specified, because shortname is a required field of source
- 08:16 AM Revision 6408: db_xml.py: put(): Pass through the values of nodes which are text nodes
- 08:15 AM Revision 6407: db_xml.py: put(): put_(): Support _setDefault() values which are text nodes, by passing text strings through when put_() is run on all col_defaults entries
- 07:50 AM Revision 6406: db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names
- 07:47 AM Revision 6405: dicts.py: DictProxy: Implemented __delitem__()
- 07:32 AM Revision 6404: bin/map: update_in_label(): Removed hardcoded source_id col_default, which is now set in mappings/VegCore-VegBIEN.csv's output root
- 07:29 AM Revision 6403: mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()
- 07:25 AM Revision 6402: db_xml.py: put(): Added _setDefault() built-in function, which adds an entry to col_defaults
- 07:23 AM Revision 6401: xml_func.py: _env(): Fixed bug where need to retrieve actual string value of name param using xml_dom.NodeTextEntryIter instead of NodeEntryIter
- 07:20 AM Revision 6400: xml_func.py: _env(): Fixed bug where need to use xml_dom.replace_with_text() instead of xml_dom.replace() because replace() requires a DOM node
- 06:44 AM Revision 6399: bin/map: update_in_label(): Set $source env var to the in_label (datasource name), to make it available to _env()
- 06:43 AM Revision 6398: xml_func.py: Simplifying functions: Added _env()
- 06:05 AM Revision 6397: Added inputs/VegBank/Source/, containing referenceType metadata
- 06:00 AM Revision 6396: Added inputs/SpeciesLink/Source/, containing referenceType metadata
- 05:55 AM Revision 6395: Added inputs/SALVIAS*/Source/, containing referenceType metadata
- 05:47 AM Revision 6394: Added inputs/REMIB/Source/, containing referenceType metadata
- 05:41 AM Revision 6393: Added inputs/GBIF/Source/, containing referenceType metadata
- 05:34 AM Revision 6392: Added inputs/TEAM/Source/, containing referenceType metadata
- 05:33 AM Revision 6391: Placed inputs/TEAM/_src/Vegetation-Tree-and-Liana-Metadata-1.5.pdf under version control
- 05:27 AM Revision 6390: inputs/FIA/import_order.txt: Added Source, which needs to come before Organism
- 05:22 AM Revision 6389: Added inputs/Madidi/Source/, containing referenceType metadata
- 05:19 AM Revision 6388: Added inputs/FIA/Source/, containing referenceType metadata
- 05:14 AM Revision 6387: Added inputs/CVS/Source/, containing referenceType metadata
- 05:07 AM Revision 6386: Added inputs/CTFS/Source/, containing referenceType metadata
- 05:05 AM Revision 6385: bin/map: Support map spreadsheets containing only metadata mappings (with no corresponding staging table), by falling back to an empty table when the named table does not exist
- 04:19 AM Revision 6384: mappings/VegCore-VegBIEN.csv: institutionCode: Also map to the sourcename's matched source, which identifies whether the source is a herbarium
- 04:08 AM Revision 6383: schemas/vegbien.sql: source: Made shortname NOT NULL to ensure that all datasources have a globally-unique short name
- 03:33 AM Revision 6382: import_all: Added import of inputs/.herbaria/ before the main import
- 03:28 AM Revision 6381: Added inputs/.herbaria/
- 03:25 AM Revision 6380: input.Makefile: SVN: add: Also run %/add on all data subdirs
- 03:21 AM Revision 6379: input.Makefile: Existing maps discovery: Moved tables discovery to its own section, above SVN so it can be used by SVN
- 03:11 AM Revision 6378: mappings/VegCore.csv: referenceType: Fixed sort order
- 03:09 AM Revision 6377: mappings/VegCore-VegBIEN.csv: Mapped referenceType
- 03:06 AM Revision 6376: mappings/VegCore.csv: Added referenceType
- 02:10 AM Revision 6375: mappings/VegCore-VegBIEN.csv: institutionCode: Remap to source.shortname when specimen information is not provided, as is the case for geoscrub.herbaria on nimoy
- 01:47 AM Revision 6374: inputs/bien_web/observation/map.csv: Mapped observationID->occurrenceID
- 01:20 AM Revision 6373: README.TXT: Datasource setup: Add input data for each table present in the datasource: Added step to run `make inputs/<datasrc>/<table>/install` if the table is in a .sql export
- 01:17 AM Revision 6372: README.TXT: Datasource setup: MySQL inputs: Added step to install the export, which needs to happen before mapping individual tables
- 01:13 AM Revision 6371: README.TXT: Datasource setup: Add input data for each table present in the datasource: Replaced "CSV" with "CSV(s)" because there can be multiple CSV part files for one table
- 01:11 AM Revision 6370: README.TXT: Datasource setup: Add input data for each table present in the datasource: Don't add a CSV or create.sql file for tables that are in a .sql export
- 01:06 AM Revision 6369: README.TXT: Schema changes: Sync ERD with vegbien.sql schema: Changed instructions to just select tables with arrows next to them rather than all tables, because each table that's updated will have its lines reset and the number of lines that need to be fixed should be minimized
- 01:02 AM Revision 6368: README.TXT: Datasource setup: Accept the test cases: `make inputs/<datasrc>/test by_col=1`: Clarified that errors could indicate bugs in the *VegBIEN* unique constraints
- 12:59 AM Revision 6367: README.TXT: Data import: To remake analytical DB: Added explicit public schema setting since the analytical DB is often manually remade *after* the public schema has been renamed. Removed warnings that certain commands must be run after running make_analytical_db, because the "remake analytical DB" instructions no longer require this.
- 12:48 AM Revision 6366: README.TXT: Datasource setup: MySQL inputs: Added steps to export the database to a PostgreSQL-compatible .sql file, which can be directly used by the install process without the need to export each table as CSV
- 12:36 AM Revision 6365: README.TXT: Datasource setup: Choosing a table name: Documented that for .sql exports, you must use the name of the table in the DB export, not a suggested or custom name
- 12:34 AM Revision 6364: input.Makefile: Staging tables installation: $(dbExports): Also include the files that would be generated by running _MySQL/*.make and creating the corresponding PostgreSQL translations
- 12:18 AM Revision 6363: input.Makefile: Staging tables installation: Moved .sql export downloading and translation to separate Input data retrieval section
11/23/2012
- 11:41 PM Revision 6362: Added lib/MySQL.{data,schema}.sql.make templates to use in datasources' _MySQL/ dirs
- 10:38 PM Revision 6361: inputs/import.stats.xls: Updated import times
11/21/2012
- 11:13 PM Revision 6360: schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Changed to use Brad's formula, which concatenates genus and specific_epithet/morphospecies, and uses family if just the family is present, rather than using the full taxonomic name
- 11:05 PM Revision 6359: mappings/VegCore-VegBIEN.csv: Concatenated taxonlabel: Don't prepend family if the taxonName/scientificName itself is the family, so that the family is not duplicated in the concatenated taxonomic name
- 10:19 PM Revision 6358: schemas/functions.sql: _nullIf(): Removed NOT NULL constraint on null param, to support use a (nullable) column rather than a literal as the null-equivalent value
- 09:08 PM Revision 6357: xml_func.py: Simplifying functions: Added _nullIf(), to remove calls with no null value
- 09:00 PM Revision 6356: xml_dom.py: Added prune_parent()
- 08:51 PM Revision 6355: schemas/functions.sql: Added _or()
- 08:20 PM Revision 6354: schemas/functions.sql: Added _merge_words()
- 08:04 PM Revision 6353: schemas/vegbien.sql: analytical_*: Renamed geosourceValid to geovalid. (It had gotten renamed in the reference -> source rename.)
- 08:00 PM Revision 6352: mappings/VegCore.csv: Renamed georeferenceValid to geovalid
- 07:48 PM Revision 6351: inputs/import.stats.xls: Updated import times. This now includes the Canadensys plants-related datasources HIBG, JBM, QFA, TRT, TRTE, UBC, VASCAN, and WIN.
11/20/2012
- 09:59 PM Revision 6350: inputs/import.stats.xls: Updated import times
- 09:42 PM Revision 6349: Added inputs/HIBG/
- 09:33 PM Revision 6348: Added inputs/JBM/
- 09:29 PM Revision 6347: Added inputs/VASCAN/
- 09:22 PM Revision 6346: Added inputs/WIN/
- 09:18 PM Revision 6345: Added inputs/UBC/
- 09:14 PM Revision 6344: Added inputs/TRTE/Specimen/
- 09:11 PM Revision 6343: Added inputs/QFA/
- 09:06 PM Revision 6342: Added inputs/TRT/
- 08:21 PM Revision 6341: schemas/vegbien.sql: Allow bien_read to SELECT from all tables in the public schema
- 08:10 PM Revision 6340: schemas/vegbien.sql: Allow bien_read to SELECT from analytical_aggregate, analytical_stem
- 08:09 PM Revision 6339: lib/PostgreSQL-MySQL.csv: Removed GRANT/REVOKE because SCHEMA GRANTs are not supported in MySQL
- 07:57 PM Revision 6338: pg_dump_vegbien: non-$owners mode: Removed --no-privileges in order to include GRANTs to other users
- 07:49 PM Revision 6337: root Makefile: PostgreSQL: $(postgresReload-Linux): Making schemas/*.conf world-readable: Fixed bug where need to do this as the bien user, which owns the files
- 07:46 PM Revision 6336: root Makefile: PostgreSQL: $(postgresReload-*): Make schemas/*.conf world-readable so it's readable by the postgres user, which the .conf installation is run as
- 07:43 PM Revision 6335: root Makefile: PostgreSQL: $(postgresReload-*): Also install pg_hba.conf
- 07:36 PM Revision 6334: root Makefile: PostgreSQL: Added postgres_reload to reload postgresql.conf and restart the DB
- 07:30 PM Revision 6333: root Makefile: PostgreSQL: postgres-*: Factored postgresql.conf installation out in to $(postgresReload-*)
- 07:15 PM Revision 6332: schemas/: Synced pg_hba.conf and pg_hba.Mac.conf's bien entries, which adds phpPgAdmin support (template1 access) on the Mac and bien_read access on Linux
- 06:56 PM Revision 6331: root Makefile: VegBIEN DB: DB and users: Also create bien_read user for read-only access to the DB
- 06:53 PM Revision 6330: schemas/pg_hba.Mac.conf: Allow access to the bien group rather than just the bien user, which will include bien_read
- 06:35 PM Revision 6329: schemas/pg_hba.Mac.conf: Fixed bug where also need to allow password-based logins from the same machine, in order to work with pgAdmin
- 06:06 PM Revision 6328: schemas/vegbien.ERD.poster.pdf: Updated to 33x51in poster size and 0.25in margins
- 05:35 PM Revision 6327: README.TXT: Schema changes: Creating a poster of the ERD: Added section with the State St FedEx Kinkos' rates for posters ($10.25/sq ft laminated)
- 05:29 PM Revision 6326: README.TXT: Schema changes: Creating a poster of the ERD: Changed "Measure the fractional height of the text onscreen" to "Determine the poster size"
- 05:19 PM Revision 6325: Added schemas/vegbien.ERD.poster.pdf
- 04:10 PM Revision 6324: Added schemas/vegbien.ERD.poster.core.print_options.png
- 04:01 PM Revision 6323: Added schemas/vegbien.ERD.poster.core.pdf
- 03:29 PM Revision 6322: schemas/pg_hba.Mac.conf: Fixed bug where needed ident entry for postgres superuser
- 03:18 PM Revision 6321: Added config/bien_read_password
- 02:53 PM Revision 6320: README.TXT: Schema changes: Added instructions to calculate the minimum VegBIEN poster size (to make the text as least as big as on the VegBank ERD poster), which is 35x54in portrait
11/19/2012
- 08:01 PM Revision 6319: schemas/vegbien.sql: analytical_stem_view: cultivated: Use location.iscultivated when taxonoccurrence.iscultivated is not available
- 07:55 PM Revision 6318: Added inputs/FIA/FIA_COND_unique/, which contains the oldgrowth flag
- 07:53 PM Revision 6317: mappings/VegCore-VegBIEN.csv: Mapped oldGrowth
- 07:48 PM Revision 6316: schemas/functions.sql: Added _not()
- 07:43 PM Revision 6315: mappings/VegCore.csv: Added oldGrowth
- 07:36 PM Revision 6314: mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot
- 07:35 PM Revision 6313: mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot
- 07:25 PM Revision 6312: schemas/vegbien.sql: location: Added iscultivated for cases when entire plots rather than individual taxonoccurrences are marked as cultivated
- 07:17 PM Revision 6311: inputs/FIA/: Added FIA_COND table from nimoy.geoscrub and code to generate a unique plot table from it, including the oldgrowth calculated field
- 06:46 PM Revision 6310: Added inputs/FIA/Organism/postprocess.sql to cast PlotCD to a bigint
- 06:22 PM Revision 6309: my2pg: Also remove (#) after bigint
- 06:05 PM Revision 6308: Regenerated vegbien.ERD exports
- 06:03 PM Revision 6307: schemas/vegbien.ERD.mwb: Fixed lines
- 05:54 PM Revision 6306: schemas/vegbien.ERD.mwb: Fixed lines
- 05:54 PM Revision 6305: schemas/vegbien.sql: source: Renamed fulltext to citation because according to the VegBank data dictionary <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=reference&entity=dba_tabledescription&where=where_tablename#fulltext> this is actually the full text *of the reference citation*, not of the reference itself (it would be unusual to store that in VegBank)
- 05:48 PM Revision 6304: schemas/vegbien.sql: Removed no longer needed sourcejournal, which can be stored in source and pointed to via parent_id instead of sourcejournal_id. sourcejournal.journal maps to source.fulltext, issn to isbn, and abbreviation to shortname.
- 05:48 PM Revision 6303: mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place
- 05:41 PM Revision 6302: schemas/vegbien.sql: source: Added matched_source_id
- 05:34 PM Revision 6301: sql.py: parse_exception(): function MissingCastException: If 1st param is hstore, only perform the cast on the value param. This fixes a bug in _map() calls whose value is a non-text type, such as SALVIAS.plotMetadata.AccessCode.
- 05:32 PM Revision 6300: sql_io.py: cast(): Use sql_gen.Cast() to generate the cast, in order to take advantage of its support for casts to unknown
- 05:30 PM Revision 6299: sql_gen.py: Cast: Support casts to unknown by casting to text first
- 04:59 PM Revision 6298: schemas/postgresql.conf: Turn on the error log
- 04:58 PM Revision 6297: schemas/pg_hba.conf: Also grant the bien user access to template1, which is accessed by phpPgAdmin
- 04:24 PM Revision 6296: schemas/vegbien.sql: source: Added parent_id for nested sources, e.g. an article in a journal
- 04:23 PM Revision 6295: lib/forwarding.Makefile: $(subdirs): Also exclude .archive/
- 04:09 PM Revision 6294: mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place
- 04:08 PM Revision 6293: schemas/vegbien.ERD.mwb: Fixed lines
- 03:54 PM Revision 6292: Renamed inputs/_archive/ to .archive/ so it wouldn't be treated as a datasource
- 03:49 PM Revision 6291: README.TXT: Documentation: Redmine-formatted list of steps for column-based import: Use ACAD instead of QMOR, which was removed
- 03:45 PM Revision 6290: inputs/Makefile: Import logs: $(rsyncLogs): Include log files at any depth in the directory tree rather than just 1-2 levels deep. This adds log files whose containing directories have been moved to _archive/ directories.
- 03:29 PM Revision 6289: Added inputs/_archive/
- 03:27 PM Revision 6288: Removed inputs/QMOR/ because it's an insect collection
- 03:25 PM Revision 6287: schemas/vegbien.sql: projectcontributor: Removed surname, since this information is stored in party_id->party.surname
- 03:23 PM Revision 6286: schemas/vegbien.sql: projectcontributor: Removed cheatrole, since there is already a role field and this field was unused in VegBank
- 03:21 PM Revision 6285: schemas/vegbien.sql: role: Added values from projectcontributor.ROLE_ID <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=projectcontributor&entity=dba_tabledescription&where=where_tablename#ROLE_ID>
- 03:17 PM Revision 6284: schemas/vegbien.sql: sourcecontributor: role: Changed type to role
- 03:15 PM Revision 6283: schemas/vegbien.sql: role enum: Added VegBank data dictionary values from <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1331&entity=dba_fielddescription¶ms=1331>
- 03:03 PM Revision 6282: schemas/vegbien.sql: sourcecontributor: Renamed position to order for consistency with the ERD definition <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=referencecontributor&entity=dba_tabledescription&where=where_tablename#position> and disambiguation from other meanings of position which are similar to role
- 03:00 PM Revision 6281: schemas/vegbien.sql: sourcecontributor: Renamed roletype to role for consistency with the ERD definition <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=referencecontributor&entity=dba_tabledescription&where=where_tablename#roleType>
- 02:53 PM Revision 6280: inputs/.geoscrub/geoscrub_output/map.csv: Mapped to county, acceptedCounty
- 02:52 PM Revision 6279: mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place
- 02:50 PM Revision 6278: mappings/VegCore.csv: Added acceptedCounty
- 02:42 PM Revision 6277: schemas/pg_hba.Mac.conf: Changed to match schemas/pg_hba.conf
- 02:37 PM Revision 6276: schemas/pg_hba.conf: Fixed bug where also need an IPv6 bien entry with md5 authentication, because the IPv4 md5 authentication does not apply to "localhost", which is translated to the IPv6 address ::1
- 02:27 PM Revision 6275: schemas/pg_hba.conf: Fixed bug where also need a *local* bien entry with md5 authentication, because the host-based md5 authentication applies only to literal IP addresses, not "localhost"
- 02:08 PM Revision 6274: Added schemas/pg_hba.Mac.conf
- 02:01 PM Revision 6273: schemas/pg_hba.conf: Restrict all accesses to the server except the bien user accessing vegbien using ident or a password, and the postgres superuser logging in using ident
- 01:25 PM Revision 6272: inputs/.geoscrub/geoscrub_output/map.csv: Mapped countyvalidity to latLongInCounty
- 01:24 PM Revision 6271: schemas/functions.sql: _map(): Fixed bug where entries that map to NULL were incorrectly being treated as if the entry didn't exist. Note that -> returns NULL both if the entry's value is NULL and if the entry doesn't exist, so ? must be used to recheck the presence of the key in the hstore.
- 12:48 PM Revision 6270: mappings/VegCore-VegBIEN.csv: Mapped latLongInCounty
- 12:46 PM Revision 6269: mappings/VegCore.csv: Added latLongInCounty
- 12:43 PM Revision 6268: schemas/vegbien.sql: Added distance_to_county_m. Note that this can also be used to store latLongInCounty by mapping true to 0 and false to -1.
- 12:22 PM Revision 6267: schemas/pg_hba.conf: Changed trust authentication back to ident/md5. Not sure how it got set to trust since I used md5 when enabling remote access to the DB for the bien user.
- 12:08 PM Revision 6266: Added schemas/pg_hba.conf
- 11:48 AM Revision 6265: schemas/vegbien.sql: place: Removed placecode to prevent datasources from creating duplicate entries for the same place, with different placecodes. This was a problem with the original BIEN2 geoscrub dataset, which contained duplicates.
- 10:54 AM Revision 6264: inputs/import.stats.xls: Updated import times
11/16/2012
- 07:06 PM Revision 6263: Regenerated vegbien.ERD exports
- 07:03 PM Revision 6262: schemas/vegbien.sql: analytical_stem_view: Fixed bug where need to join taxonoccurrence.collector_id to party because it's now an fkey rather than a literal name
- 06:58 PM Revision 6261: schemas/vegbien.sql: analytical_*: Added coordinateUncertaintyInMeters
- 06:34 PM Revision 6260: schemas/vegbien.sql: analytical_stem_view: Join to newWorldCountries on 2-digit ISO code instead of country name, to increase (BIEN2) newWorldCountries and GADM overlap
- 06:29 PM Revision 6259: psql_vegbien: Run with sh because it no longer needs bash support
- 06:28 PM Revision 6258: psql_script_vegbien: Fixed bug where needs to be run with bash instead of sh
- 06:27 PM Revision 6257: Added inputs/newWorld/iso_code_gadm/
- 06:16 PM Revision 6256: Added inputs/newWorld/_src/
- 06:15 PM Revision 6255: inputs/XAL/Specimen/map.csv: darwin:FieldNumber: Removed command to determine that field is unused, because UNUSED is a factual assertion that does not need a reason to be specified each time
- 06:11 PM Revision 6254: inputs/XAL/Specimen/map.csv: Remapped darwin:CoordinatePrecision to UNUSED
- 06:08 PM Revision 6253: inputs/NY/Specimen/map.csv: Remapped CoordinatePrecision to coordinateUncertaintyInMeters, assuming units of m based on the range and precision of values
- 06:03 PM Revision 6252: mappings/VegCore.csv: coordinatePrecision: Added units (degrees) to form coordinatePrecision_deg
- 06:00 PM Revision 6251: mappings/VegCore-VegBIEN.csv: Removed mapping for coordinatePrecision, which is not the same as coordsaccuracy_m. coordinatePrecision is instead "the precision of the coordinates" themselves in degrees (<http://rs.tdwg.org/dwc/terms/#coordinatePrecision>).
- 05:53 PM Revision 6250: schemas/vegbien.sql: coordinates: Changed coordinates.coordsaccuracy_deg units to m
- 05:51 PM Revision 6249: Regenerated inputs/bien_web/observation/test.xml.ref
- 05:17 PM Revision 6248: schemas/vegbien.ERD.mwb: Added projectcontributor, locationeventcontributor to ERD
- 05:02 PM Revision 6247: schemas/vegbien.sql: higher_plant_group_nodes: Added root->NULL mapping to store all the families that don't match any higher plant group
- 04:58 PM Revision 6246: schemas/vegbien.sql: higher_plant_group_nodes: Allow NULL values for higher_plant_group, to allow mapping all remaining families to NULL in family_higher_plant_group
- 04:09 PM Revision 6245: psql_vegbien: Fixed bug where did not display command prompt when run from command line, by moving automatic setting of search_path to psql_script_vegbien. psql_script_vegbien is now used instead of psql_vegbien wherever the search_path needs to be set, so removing this functionality from psql_vegbien is not a problem.
- 04:03 PM Revision 6244: input.Makefile: BIEN commands: $(psqlAsBien): Use psql_script_vegbien, which automatically adds the $(psqlOpts), instead of psql_vegbien
- 03:54 PM Revision 6243: schemas/functions.sql: _map(): Support any entry having the value '*' (not just the '*' entry), which passes through that value. Support an entry having the value '!', which raises an exception.
- 03:40 PM Revision 6242: inputs/SALVIAS/plotMetadata_/map.csv: AccessCode: Removed _map entry for 4, which does not apply to plots
- 03:07 PM Revision 6241: schemas/vegbien.ERD.mwb: Fixed lines
- 01:00 PM Revision 6240: schemas/vegbien.sql: locationevent: Added accesslevel
- 12:54 PM Revision 6239: inputs/SALVIAS/plotMetadata_/map.csv: Mapped AccessCode to dcterms:accessRights with appropriate _map filter
- 12:49 PM Revision 6238: Added inputs/.geoscrub/geoscrub_cleaned_unique/_no_import to disable geoscrub_cleaned_unique, since the new geoscrub_output supersedes it
- 12:47 PM Revision 6237: Added inputs/.geoscrub/geoscrub_output/
- 12:46 PM Revision 6236: Added inputs/.geoscrub/_src/README.TXT
- 12:29 PM Revision 6235: Regenerated inputs/bien_web/observation/VegBIEN.csv
- 12:24 PM Revision 6234: Added inputs/.geoscrub/_src/ to store Jim's geoscrub CSV
- 12:21 PM Revision 6233: schemas/functions.sql: _map(): Changed error message for an unmapped value to "Value not in map" rather than "Invalid map value", because an unmapped value is not necessarily explicitly invalid
- 12:16 PM Revision 6232: inputs/VegBank/plot_/map.csv: confidentialitystatus filter: Merged mappings for 0 with other public-equivalent fields. Note that fuzzed plots are still public, because the private columns have been removed.
11/15/2012
- 11:16 PM Revision 6231: inputs/VegBank/plot_/map.csv: Mapped confidentialitystatus to dcterms:accessRights with an appropriate _map filter
- 11:16 PM Revision 6230: mappings/VegCore-VegBIEN.csv: Mapped dcterms:accessRights
- 11:14 PM Revision 6229: schemas/functions.sql: _map(): Raise data_exception if value not in map and no default provided (not the same as a NULL default value)
- 10:54 PM Revision 6228: mappings/VegCore-VegBIEN.csv: verbatimGrowthForm: Removed _map filter, which applied only to SALVIAS and has now been moved to the applicable SALVIAS tables
- 10:51 PM Revision 6227: inputs/SALVIAS*/plotObservations/map.csv: Remapped Habit to growthForm with _map filter applied
- 10:43 PM Revision 6226: sql_io.py: put_table(): Special handling for functions with hstore params: Fixed bug where need to unwrap literal values of mapping, which might be sql_gen.Literal objects
- 10:43 PM Revision 6225: sql_gen.py: Added get_value()
- 10:42 PM Revision 6224: dicts.py: join(): Added support for unhashable types, which are passed through. This adds support for SQL literal values which are dicts (hstores).
- 10:25 PM Revision 6223: xml_func.py: Removed no longer used _map(), which has been replaced by a corresponding DB function
- 10:22 PM Revision 6222: schemas/functions.sql: Added _map(), which uses the new hstore functionality. This expands _map() functionality to column-based import.
- 10:20 PM Revision 6221: root Makefile: VegBIEN DB: DB and bien user: mk_db: hstore extension: Fixed bug where need to use `CREATE EXTENSION hstore SCHEMA pg_catalog` instead of createlang, because hstore must be explicitly created in pg_catalog or else it will be created in the public schema instead, causing it to get deleted every time the public schema is reinstalled and cascading the delete to everything (including in other schemas) that uses hstore
- 10:04 PM Revision 6220: sql_io.py: put_table(): Added special handling for functions with hstore params. Note that although _map() doesn't exist yet as a DB function, this code must be in place before _map() is created to avoid param type mismatch errors.
- 08:57 PM Revision 6219: root Makefile: PostgreSQL: postgres-Linux: Changed plpython to plpython3 in order to install plpython3u
- 08:30 PM Revision 6218: schemas/py_functions.sql: _date(): Removed features that require dateutil, which is not available under plpython3u. This includes removing the now-unused date string parameter.
- 08:26 PM Revision 6217: mappings/VegCore-VegBIEN.csv: Removed _date/date, because _date using a string date argument is no longer supported under plpython3u (dateutil is missing). Note that PostgreSQL's own date parsing is sufficient for most dates, so this use of _date is not strictly necessary and removing it will improve import times.
- 08:12 PM Revision 6216: schemas/py_functions.sql: Replaced xrange() with range() for plpython3u
- 08:05 PM Revision 6215: root Makefile: Python: python-Linux: Also install python3, needed by plpython3u
- 08:04 PM Revision 6214: schemas/py_functions.sql: Updated except clause syntax for PostgreSQL 9.1.6
- 08:03 PM Revision 6213: schemas/*.sql: Updated for PostgreSQL 9.1.6, which has standard_conforming_strings = on (which affects \-escapes in string literals), escape_string_warning not explicitly set, and uses ALTER TABLE ONLY instead of ALTER TABLE
- 07:49 PM Revision 6212: README.TXT: Removed step to manually run make_analytical_db, now that this is done automatically by import_all. Added separate instructions to remake the analytical DB.
- 07:45 PM Revision 6211: import_all: Change to main directory make targets are run from. Use relative paths to bin/ commands, which is possible now that the current dir is set.
- 07:41 PM Revision 6210: import_all: Create a background process that waits until the import is done and then runs make_analytical_db
- 07:36 PM Revision 6209: Added waitpid
- 06:52 PM Revision 6208: import_all: Documented that `wait %1` waits for asynchronous commands
- 06:40 PM Revision 6207: root Makefile: VegBIEN DB: DB and bien user: mk_db: Also install hstore extension. Note that this is only supported by PostgreSQL 9.1+.
- 06:33 PM Revision 6206: input.Makefile: Editing import: Updated queries for current schema
- 06:27 PM Revision 6205: inputs/.geoscrub/geoscrub_cultivated/create.sql: Fixed bug where need to filter out NULL lat/longs because primary keys can't contain NULL values
- 06:17 PM Revision 6204: schemas/py_functions.sql: Changed function languages to plpython3u to match the new installed version. Note that plpythonu is not available on Mac under PostgreSQL 9.1.6.
- 05:59 PM Revision 6203: reinstall_all: Fixed bug where also need to include datasources starting with . such as .TNRS/, by using with_all's new $all option
- 05:58 PM Revision 6202: with_all: Added $all option to also include datasources starting with . such as .TNRS/. This is necessary for reinstall_all, which needs to install *all* datasources.
- 05:18 PM Revision 6201: root Makefile: PostgreSQL: $(pg_ctl-*): Fixed bug where need to pause for a few seconds after restarting PostgreSQL, to wait for the server to be ready to accept connections
- 05:12 PM Revision 6200: root Makefile: Installation: uninstall: Removed inputs/uninstall because the DB will be uninstalled anyway, so the inputs don't need to be individually removed first
- 05:11 PM Revision 6199: schemas/postgresql.Mac.conf: Added back unix_socket_directory setting, which is apparently still needed in PostgreSQL 9.1.6
- 05:06 PM Revision 6198: root Makefile: PostgreSQL: postgres-Linux: Also install postgresql.conf
- 04:54 PM Revision 6197: root Makefile: PostgreSQL: postgres-Darwin: Also install postgresql.Mac.conf
- 04:40 PM Revision 6196: root Makefile: PostgreSQL: $(macUsePostgresLib): Factored out PostgreSQL dir to $(macPostgresDir)
- 04:38 PM Revision 6195: schemas/postgresql.Mac.conf: Updated to PostgreSQL 9.1.6's postgresql.conf
- 04:29 PM Revision 6194: root Makefile: Datasources: inputs/install: Fixed bug where need to `wait` after `. bin/reinstall_all` to wait for inputs to finish installing before installing the public schema. This is necessary because views in the public schema now have dependencies on some datasources, such as TNRS.
- 04:25 PM Revision 6193: root Makefile: PostgreSQL: $(psqlAsAdmin): Use new $(asAdmin)
- 04:25 PM Revision 6192: root Makefile: VegBIEN DB: Schemas: schemas/public/install: Use $(psqlNoSearchPath) instead of $(psqlAsBien) because the search_path is set by vegbien.sql
- 04:16 PM Revision 6191: root Makefile: Datasources: Added inputs/install override which runs `. bin/reinstall_all` instead, in order to install all datasources simultaneously
- 04:03 PM Revision 6190: root Makefile: Python: python-Darwin: Added instructions to install Python 3.2 (Python 2 comes with Mac OS X, but Python 3.2 is needed for plpython3u)
- 03:55 PM Revision 6189: root Makefile: VegBIEN DB: DB and bien user: mk_db: Updated for PostgreSQL 9.1.6 on the Mac, which only provides plpython3u (Python 3)
- 03:54 PM Revision 6188: root Makefile: VegBIEN DB: DB and bien user: mk_db: Updated for PostgreSQL 9.1.6, which requires the DB name to be specified on the command line instead of in the $PGDATABASE env var set by postgres_vegbien. Fixed bug where need to run createlang as postgres superuser, because plpythonu is an untrusted language (with unrestricted access to the entire DB).
- 03:51 PM Revision 6187: root Makefile: PostgreSQL: postgres-Darwin: Updated for PostgreSQL 9.1.6, which requires some /usr/lib/ symlinks to be changed to newer versions installed in the PostgreSQL lib/ dir
- 03:49 PM Revision 6186: input.Makefile: $(psqlAsBien), csv2db: Turn off the automatic search_path where needed, because when the input is installed, the schemas in it may not exist yet
- 02:16 PM Revision 6185: schemas/vegbien.sql: place: Renamed geosource_valid to geovalid. (It had gotten renamed in the reference -> source rename.)
- 02:12 PM Revision 6184: schemas/vegbien.sql: location: Renamed confidentialitystatus->accesslevel, confidentialityreason->accessconditions to match the corresponding fields in source. Note that accessconditions stores more than confidentialityreason did, because it can contain details about the accesslevel in addition to the reason for it.
- 02:07 PM Revision 6183: schemas/vegbien.sql: source.accesslevel, location.confidentialitystatus: Changed type to accesslevel
- 02:03 PM Revision 6182: schemas/vegbien.sql: Added accesslevel enum
- 01:51 PM Revision 6181: inputs/import.stats.xls: Updated import times
11/14/2012
- 06:37 PM Revision 6180: Regenerated vegbien.ERD exports
- 06:30 PM Revision 6179: schemas/vegbien.sql: Renamed reference -> source to make this table more broadly applicable, and because this now stores the datasource metadata
- 06:19 PM Revision 6178: schemas/vegbien.sql: referencename: Scope it by top-level datasource, because institutionCodes (which map to this field) are not globally unique. This involves renaming the previous reference_id field, which was for the matched reference, to matched_reference_id, to allow a scoping reference_id field.
- 06:16 PM Revision 6177: mappings/VegCore-VegBIEN.csv: Made taxonoccurrence.verbatimcollectorname an fkey to party, and renamed it to collector_id
- 05:57 PM Revision 6176: inputs/VegBank/taxonobservation_/map.csv: Mapped new givenname, surname (from collector_id's party) to recordedBy
- 05:54 PM Revision 6175: inputs/VegBank/taxonobservation_/create.sql: Also join to collector_id's party to include collector name
- 05:53 PM Revision 6174: inputs/VegBank/vegbank.~.clean_up.sql: Rename taxoninterpretation.party_id to taxoninterpretation_party_id to make it globally unique when joining taxoninterpretation to other tables
- 05:48 PM Revision 6173: inputs/VegBank/vegbank.~.clean_up.sql: Rename party.d_obscount to party_d_obscount to make it globally unique when joining with other tables
- 05:43 PM Revision 6172: inputs/VegBank/vegbank.~.clean_up.sql: Rename taxoninterpretation.party_id to taxoninterpretation_party_id to make it globally unique when joining taxoninterpretation to other tables
- 05:35 PM Revision 6171: mappings/VegCore-VegBIEN.csv: Made taxonoccurrence.verbatimcollectorname an fkey to party, and renamed it to collector_id
- 05:32 PM Revision 6170: input.Makefile: Existing maps discovery: $(allTables): Fixed bug where need to remove extra whitespace before $(tables) when there are no $(joinedTables)
- 05:32 PM Revision 6169: lib/mappings.Makefile: Checking if $(termsSubdirs) defined: Fixed bug where can't use ifndef because that checks if the variable is *empty*, not undefined. Need to use `ifeq ($(origin var),undefined)` instead.
- 05:11 PM Revision 6168: inputs/TEAM/V*/map.csv: Omit *Method, because it just contains "Derived" for a small fraction of the rows
- 04:47 PM Revision 6167: inputs/SALVIAS/: Updated to new salvias_plots export on nimoy, which has a different schema
- 04:03 PM Revision 6166: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Moved Ensure globally unique column names to end to match VegBank order
- 03:54 PM Revision 6165: my2pg: *int types: Added mediumint
- 03:30 PM Revision 6164: Placed inputs/SALVIAS/_archive/ under version control
- 03:18 PM Revision 6163: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Remove private data that should not be publicly visible, indicated by plotMetadata.AccessCode = 1
- 03:17 PM Revision 6162: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Enable cascading deletes by adding the necessary fkeys
- 03:17 PM Revision 6161: Added inputs/SALVIAS/_src/salvias_data_access_controls.txt
- 02:26 PM Revision 6160: inputs/import.stats.xls: Updated import times
- 02:25 PM Revision 6159: inputs/.geoscrub/import_order.txt: Fixed bug where geoscrub_cultivated needs to be installed *after* geoscrub_cleaned_unique, not before as it would be with the default alphabetical sort order
- 02:24 PM Revision 6158: inputs/.geoscrub/geoscrub_cultivated/: Use _no_import file to exclude geoscrub_cultivated from the import, because it's used directly as a lookup table by analytical_stem rather than being imported. This ensures that there is no import log or input row count for geoscrub_cultivated in the import times, which would skew the import row count because the row count would be included even though no columns are mapped.
- 02:18 PM Revision 6157: input.Makefile: $(tables): Fixed bug where need to use $(importTables) instead of $(tables) in all places that should use only imported tables, rather than just in the import process itself
- 02:13 PM Revision 6156: input.Makefile: Import to VegBIEN: Added support for tables which should be installed but not imported, but which must be installed *after* tables which are imported rather than before. This currently applies to geoscrub.geoscrub_cultivated, which depends on geoscrub_cleaned_unique (and therefore must be installed after it), but which should not be imported because it's used directly as a lookup table by analytical_stem.
- 10:02 AM Revision 6155: inputs/VegBank/vegbank.~.clean_up.sql: Documented that plots with confidentialitystatus >= 4 are not deleted if their embargos have already expired. This applies to the Shenandoah NP data, which has confidentialitystatus = 5 but is no longer embargoed according to the embargo table
11/13/2012
- 08:10 PM Revision 6154: inputs/SALVIAS/: Mapped unmapped fields with a VegCore/VegBIEN equivalent. plotMetadata_/: Remapped life_zone to communityID because it is now _alt-ed together with vegetation_*, and thus not just a description with life_zone_code as its globally unique name.
- 07:35 PM Revision 6153: Regenerated vegbien.ERD exports
- 07:10 PM Revision 6152: schemas/vegbien.sql: referencetype: Added terms from reference.referencetype closed list in VegBank data dictionary. Cited sources in comment.
- 06:39 PM Revision 6151: schemas/vegbien.sql: reference.referencetype: Changed type to referencetype enum
- 06:38 PM Revision 6150: schemas/vegbien.sql: Added referencetype enum, containing VegBank's values in reference.referencetype as well as values for bien_web.datasource.aggregatorOrPrimary and bien_web.dataSourceNormalized.isHerbarium,isAggregator
- 06:23 PM Revision 6149: specimenreplicate: Made institution_id an fkey to referencename instead of party, to later be matched up with reference entries for each aggregator's subprovider
- 06:15 PM Revision 6148: schemas/vegbien.sql: referencename: Added referencename_unique unique index on name
- 06:00 PM Revision 6147: schemas/vegbien.sql: referencename: Made reference_id optional so it can be populated later when referencenames are scrubbed
- 05:58 PM Revision 6146: schemas/vegbien.sql: referencename: Renamed identifier to name because it is specifically any name for the reference, not necessarily an ID
- 05:53 PM Revision 6145: schemas/vegbien.sql: Renamed referencealtident to referencename to allow any verbatim reference name to go here, with reference containing the corresponding accepted reference name
- 05:50 PM Revision 6144: schemas/vegbien.sql: reference: Added accesslevel, accessconditions from bien_web.datasource
- 05:41 PM Revision 6143: schemas/vegbien.sql: address: Added street2 from bien_web.party.address2
- 05:38 PM Revision 6142: schemas/vegbien.sql: address: Renamed fields to bien_web.party names
- 05:12 PM Revision 6141: schemas/vegbien.sql: party: Added department from bien_web.party
- 05:06 PM Revision 6140: inputs/SALVIAS/plotMetadata_/map.csv: Mapped lookup_MethodCode_Description to new observationMeasure
- 05:06 PM Revision 6139: schemas/vegbien.sql: method: Made name optional when description or observationmeasure is specified
- 05:03 PM Revision 6138: schemas/vegbien.sql: method: method_unique: Include observationmeasure since the method name sometimes is not globally unique (e.g. in SALVIAS)
- 04:58 PM Revision 6137: mappings/VegCore-VegBIEN.csv: Mapped observationMeasure
- 04:57 PM Revision 6136: mappings/VegCore.csv: observationMeasure: Added source to DwC samplingProtocol
- 04:54 PM Revision 6135: mappings/VegCore.csv: Added observationMeasure
- 04:40 PM Revision 6134: schemas/vegbien.ERD.mwb: Added family_higher_plant_group
- 04:28 PM Revision 6133: schemas/vegbien.sql: Removed VegBank-internal fields starting with d_
- 04:19 PM Revision 6132: schemas/vegbien.ERD.mwb: Moved tables so commclass would have more room. Moved revision back to original spot.
- 04:07 PM Revision 6131: schemas/filter_ERD.csv: Display referencecontributor->party connection in ERD
- 03:56 PM Revision 6130: schemas/vegbien.sql: Removed no longer used table referenceparty
- 03:54 PM Revision 6129: schemas/vegbien.sql: referencecontributor: Point to party instead of referenceparty, which duplicates party
- 03:51 PM Revision 6128: schemas/vegbien.sql: party: Added new suffix field to party_unique unique index
- 03:49 PM Revision 6127: schemas/vegbien.sql: party: Added fields from referenceparty. Note that referenceparty.type is named partytype.
- 03:25 PM Revision 6126: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Rename lookup_MethodCode.Description to lookup_MethodCode_Description to make it globally unique when joined with plotMetadata
- 03:24 PM Revision 6125: input.Makefile: SVN: $(svnFilesGlob): Added root-level .sql files containing ~, which run additional commands after the original data is imported
- 03:22 PM Revision 6124: inputs/SALVIAS/_MySQL/: Updated svn:ignore from running `make inputs/SALVIAS/add`
- 02:30 PM Revision 6123: mappings/VegCore-VegBIEN.csv: matched place's coordinates: Fixed bug where coordinates entry itself needed to have its datasource (reference) set to geoscrub, in addition to the place entry that uses it, in order to match up properly with geoscrub's corresponding input place (whose coordinates as well as place are owned by the geoscrub datasource)
- 02:22 PM Revision 6122: mappings/VegCore-VegBIEN.csv: matched place's coordinates: Fixed bug where coordinates mappings with and without matched_place_id=0 need to sort together in order to be merged, by prepending ".," to the place attrs list
- 02:22 PM Revision 6121: inputs/VegBank/plot_/test.xml.ref: Updated inserted row count
- 12:00 PM Revision 6120: inputs/import.stats.xls: Updated import times
11/09/2012
- 08:30 PM Revision 6119: Regenerated vegbien.ERD exports
- 08:20 PM Revision 6118: inputs/Makefile: Input data: $(rsyncLogs): Also include logs from the datasource's top-level logs/ dir, which contains make_analytical_db.log.sql
- 08:09 PM Revision 6117: inputs/VegBank/vegbank.~.clean_up.sql: Remove still-embargoed plots
- 08:07 PM Revision 6116: inputs/VegBank/vegbank.~.clean_up.sql: Enable cascading deletes by setting all foreign keys to ON DELETE CASCADE
- 07:49 PM Revision 6115: Added inputs/VegBank/_src/vegbank.schema.sql.make and vegbank.schema.sql
- 07:48 PM Revision 6114: input.Makefile: Staging tables installation: sql/install: Use new pg_dump_limit to remove security and schema-setting commands
- 07:46 PM Revision 6113: Added pg_dump_limit to filter a PostgreSQL DB dump to remove security and schema-setting commands
- 06:37 PM Revision 6112: inputs/.geoscrub/geoscrub_cleaned_unique/create.sql: Removed no longer needed index on latitudeDecimalVerbatim, longitudeDecimalVerbatim, which is now on geoscrub_cultivated instead
- 06:32 PM Revision 6111: schemas/vegbien.sql: analytical_stem_view: Fixed bug where needed to join on new geoscrub_cultivated, not geoscrub, for all geoscrub-related information. geoscrub contains many duplicate records, causing one input row to match many rows in geoscrub, when there should only be one entry for each coordinate pair.
- 06:26 PM Revision 6110: Added inputs/.geoscrub/geoscrub_cultivated/
- 06:04 PM Revision 6109: inputs/.geoscrub/geoscrub_cleaned_unique/create.sql: Added index on latitudeDecimalVerbatim, longitudeDecimalVerbatim for use by analytical_stem_view
- 05:34 PM Revision 6108: inputs/newWorld/geoscrub.schema.~.changes.sql: Change countryNameStd type to text to allow merge-joining with place.country in analytical_stem_view
- 05:28 PM Revision 6107: inputs/newWorld/geoscrub.schema.~.changes.sql: ALTER TABLE ... ALTER COLUMN statement: Reformatted to allow adding additional ALTER COLUMN clauses
- 05:25 PM Revision 6106: inputs/.geoscrub/geoscrub_cleaned_unique/create.sql: Change latitudeDecimalVerbatim, longitudeDecimalVerbatim types to double precision to allow merge-joining with coordinates.latitude_deg, longitude_deg in analytical_stem_view
- 05:12 PM Revision 6105: README.TXT: Data import: Instead of using `make schemas/rotate` and then renaming the public schema to the correct name, just rename directly to the correct name using `make schemas/rename/...`. Use new import_name to determine the import name instead of manually finding the date in the first datasource's log file name.
- 05:06 PM Revision 6104: Added import_name, which gets the name of an import based on its log file names
- 04:50 PM Revision 6103: README.TXT: Data import: Moved checking that imports were successful before running make_analytical_db
- 04:41 PM Revision 6102: root Makefile: Installation: Fixed bug where schemas/install needed to happen *after* inputs/install because some of the public schema's views now depend on inputs
- 04:07 PM Revision 6101: schemas/vegbien.sql: analytical_stem_view: cultivatedBasis: Concatenate ''::text to geoscrub.isCultivatedReason so it will be cast to a text field both on PostgreSQL 9.1.1 (local machine), which removes any explicit cast to text when creating the view, and 9.1.6 (vegbiendev), which requires an explicit cast to text
- 03:49 PM Revision 6100: schemas/vegbien.sql: analytical_stem_view: cultivatedBasis: Use geoscrub.isCultivatedReason instead when geoscrub.isCultivated is used as the source for cultivated
- 12:53 PM Revision 6099: schemas/vegbien.sql: analytical_stem_view: Use geoscrub.isCultivated when taxonoccurrence.iscultivated is not provided (joining to geoscrub on the coordinates)
11/08/2012
- 06:38 PM Revision 6098: root Makefile: VegBIEN DB: Schemas: Run all schema installs and uninstalls using no_search_path=1, so that the schemas in the automatic search_path are not required for the command to run
- 06:37 PM Revision 6097: psql_vegbien: Added $no_search_path option to turn off the automatic SET search_path directive
- 06:11 PM Revision 6096: schemas/vegbien.sql: taxonverbatim: Added growthform for growthform based on the taxon name rather than provided with the input data's taxonoccurrence
- 06:00 PM Revision 6095: schemas/vegbien.ERD.mwb: Fixed lines
- 05:47 PM Revision 6094: inputs/SALVIAS/plotMetadata/: LEFT JOINed with lookup_MethodCode to create plotMetadata_
- 04:52 PM Revision 6093: schemas/vegbien.sql: threatened_taxonlabel_view: Fixed bug where needed DISTINCT on resulting taxonlabel_id because some descendants apparently appear in multiple threatened taxonlabels' subtrees
- 04:42 PM Revision 6092: schemas/vegbien.sql: analytical_*: Added threatened, using new threatened_taxonlabel lookup table
- 04:12 PM Revision 6091: schemas/vegbien.sql: reference_by_shortname(): Fixed bug where need to use $-syntax to reference params in sql-language functions
- 04:07 PM Revision 6090: schemas/vegbien.sql: threatened_taxonlabel_view: Use new reference_by_shortname()
- 03:45 PM Revision 6089: root Makefile: VegBIEN DB: Schemas: public: schemas/public/uninstall: Fixed bug where need to run psql_vegbien without public in the search_path because it may have already been deleted
- 03:44 PM Revision 6088: root Makefile: VegBIEN DB: Schemas: public: schemas/public/install: Fixed bug where need to run psql_vegbien without public in the search_path because it doesn't exist, by setting public to the empty string (deleting it)
- 03:42 PM Revision 6087: vegbien_dest: $schemas: Don't include the , before $public if it has been set to the empty string (deleted)
- 03:27 PM Revision 6086: schemas/vegbien.sql: Added reference_by_shortname(). Using this function instead of the manual query should force the query planner to evaluate this expression first, rather than complexly reordering joins to place this nested select as a filter condition.
- 03:00 PM Revision 6085: schemas/vegbien.sql: Added threatened_taxonlabel derived table with generating view threatened_taxonlabel_view
- 02:48 PM Revision 6084: Updated inputs/UNCC/Specimen/test.xml.ref inserted row count
- 01:38 PM Revision 6083: mappings/VegCore.csv: Added threatened
- 01:21 PM Revision 6082: inputs/VegBank/vegbank.~.clean_up.sql: Remove private columns (plot.reallatitude, reallongitude) that should not be publicly visible
- 01:13 PM Revision 6081: inputs/CVS/Organism/map.csv: Removed now-dropped realLatitude, realLongitude
- 01:12 PM Revision 6080: inputs/CVS/Organism/map.csv: Removed now-dropped realLatitude, realLongitude
- 01:12 PM Revision 6079: Added inputs/CVS/Organism/postprocess.sql to drop private realLatitude, realLongitude columns
- 01:10 PM Revision 6078: input.Makefile: Staging tables installation: Added back postprocess.sql, which is now used for one-time dropping of private columns that should not be publicly visible
- 12:47 PM Revision 6077: input.Makefile: Maps building: %/.map.csv.last_cleanup: $(dict) canon/translate: Use new $(translate?)
- 12:45 PM Revision 6076: input.Makefile: Maps building: %/.map.csv.last_cleanup: Added $(srcDict) as a prerequisite, so that .last_cleanup will be re-run if it changes. Added empty $(srcDict) target in case it doesn't exist.
- 12:39 PM Revision 6075: inputs/bien_web/observation/map.csv: Omit *_index because they are placeholder columns created by the MySQL to PostgreSQL translation
- 12:37 PM Revision 6074: input.Makefile: Maps building: %/.map.csv.last_cleanup: Fixed bug where can only canon/translate using $(srcDict) if it exists for the datasource
- 12:26 PM Revision 6073: inputs/bien_web/observation/: Regenerated from actual bien_web.observation schema on nimoy, which has additional columns
- 12:24 PM Revision 6072: input.Makefile: SVN: $(svnFilesGlob): Added top-level map.csv, which can be used to apply a datasource-global data dictionary to all tables
- 12:18 PM Revision 6071: input.Makefile: Maps building: %/.map.csv.last_cleanup: Also apply any map.csv at the top level of the datasource directory. This can be used to apply a datasource-global data dictionary to all tables.
- 12:01 PM Revision 6070: my2pg: Also remove column comments. Note that these cannot be translated by sed, because PostgreSQL only allows setting column comments in a separate statement, not inline with the column's entry in the CREATE TABLE statement, and sed can only make replacements contiguous with the input line.
- 11:28 AM Revision 6069: mappings/VegCore.csv: Removed incorrect duplicate entry for verbatimSubgenus
- 10:58 AM Revision 6068: schemas/vegbien.sql: _taxon_family_require_std(): Fixed bug where name needed to be lowercased before checking if it ended in -aceae, to support family names that are uppercase. Note that this resulted in the family not being prepended to the TNRS input name for datasources with uppercase family names, so the next DB import will likely produce a number of unscrubbed TNRS input names which now have the uppercase family prepended.
- 10:17 AM Revision 6067: inputs/.TNRS/tnrs/tnrs.make: Fixed bug where need to reference the log file path relative to the make script itself, because otherwise the log file would go in inputs/.TNRS/logs/tnrs.make.log.sql
- 10:07 AM Revision 6066: inputs/.TNRS/tnrs/tnrs.make: Fixed bug where need to use just the basename of $0 as the log file name
- 09:51 AM Revision 6065: Added inputs/IUCN/
- 09:51 AM Revision 6064: input.Makefile: SVN: add: Added _src/ (when it exists). $(_svnFilesGlob): Added .url, .pdf files in _src/.
- 07:47 AM Revision 6063: psql_vegbien: Use bash because it supports substitutions
- 07:46 AM Revision 6062: psql_vegbien: Set the search_path to $out_schemas set by vegbien_dest. This will enable running any psql_vegbien script on a schema other than public.
- 07:07 AM Revision 6061: schemas/vegbien.sql: analytical_stem_view: Changed inner joins on non-datasource taxonlabels to LEFT JOINs, to ensure that an entry is included in the analytical DB even if there was no matched taxonlabel. In theory, this shouldn't be necessary, because every taxonlabel should have a canonical taxonlabel since canon_label_id is auto-populated to the taxonlabel_id if there is no matched_label_id; there should be a taxonverbatim for every datasource and accepted taxonlabel because datasources link to taxonlabel via taxonverbatim and TNRS populates a taxonverbatim for every accepted taxonlabel; and there should be a parsed taxonlabel for every datasource taxonlabel because the mappings populate it.
- 06:56 AM Revision 6060: schemas/vegbien.sql: analytical_stem_view: Removed join on specimenreplicate, because it isn't used in the analytical DB. Each specimen will still get an entry in analytical_*, because it gets its own location.
- 06:45 AM Revision 6059: README.TXT: Data import: Before starting import, added step to run `make inputs/upload` and reinstall newly-uploaded datasources
- 03:22 AM Revision 6058: README.TXT: Schema changes: Remember to update the following files with any renamings: Added mappings/verify.*.sql
- 02:21 AM Revision 6057: README.TXT: Data import: make_analytical_db: Documented how to view progress in log file
- 02:18 AM Revision 6056: make_analytical_db: Run all commands synchronously so the log file output doesn't become jumbled
- 02:16 AM Revision 6055: make_analytical_db: Fixed bug where log file needed to be appended to instead of overwritten
- 02:15 AM Revision 6054: make_analytical_db: Wrap each individual command in `set -x` to avoid echoing low-level commands such as sleep, wait
- 02:02 AM Revision 6053: make_analytical_db: Moved log file to inputs/analytical_db/logs/make_analytical_db.log.sql so it would be synced along with the other import logs
- 01:57 AM Revision 6052: inputs/.TNRS/tnrs/tnrs.make: Output the time at which it's run, so this is included in the log file
- 01:53 AM Revision 6051: inputs/.TNRS/tnrs/tnrs.make: Moved log file to logs/tnrs.make.log.sql so it would automatically be synced along with the other import logs
- 01:49 AM Revision 6050: make_analytical_db: Moved log file to inputs/analytical_db/logs/make_analytical_db.log.sql so it would be synced along with the other import logs
- 01:40 AM Revision 6049: inputs/Makefile: Import logs: $(rsyncLogs): Always download the TNRS daemon log, rather than requiring tnrs_log=1 to be specified to download it
- 01:37 AM Revision 6048: make_analytical_db: Output the time at which it's run, so this is included in the log file
- 01:36 AM Revision 6047: make_analytical_db: Store output in schemas/make_analytical_db.log
- 01:24 AM Revision 6046: schemas/vegbien.sql: Removed no longer used make_analytical_db(). Use bin/make_analytical_db instead.
- 01:23 AM Revision 6045: make_analytical_db: Use new psql_verbose_vegbien
- 01:22 AM Revision 6044: Added psql_verbose_vegbien
- 01:18 AM Revision 6043: make_analytical_db: Use psql_script_vegbien, which contains the necessary psq options, instead of setting those options manually
- 01:15 AM Revision 6042: make_analytical_db: Run the SQL commands directly with psql instead of using the make_analytical_db() function. This provides incremental results and avoids running all commands in one transaction, thus preventing pgAdmin from freezing when the user attempts to access a table used in analytical DB creation (because the TRUNCATE statement fully locks the table until the entire analytical DB is built).
- 12:46 AM Revision 6041: schemas/vegbien.sql: make_analytical_db(): Added make_family_higher_plant_group()
- 12:17 AM Revision 6040: inputs/import.stats.xls: Updated import times. Fixed input row counts and import times to include derived data, such as TNRS and geoscrub, which adds to the import time and therefore should be considered in the import's speed. (TNRS was already being included in the import time for some, but not all, imports.)
11/06/2012
- 05:02 PM Revision 6039: schemas/vegbien.sql: analytical_*: Added higherPlantGroup
- 04:06 PM Revision 6038: pg_dump_vegbien: When not in data mode, use --inserts so the INSERT statements generated can be run directly in pgAdmin, they can be directly translated to MySQL, and an empty COPY FROM statement isn't generated for every table
- 04:05 PM Revision 6037: schemas/vegbien.sql: Added family_higher_plant_group lookup table, generated with make_family_higher_plant_group() using the contents of higher_plant_group_nodes
- 03:40 PM Revision 6036: schemas/vegbien.sql: Added family_higher_plant_group lookup table, generated with make_family_higher_plant_group() using the contents of higher_plant_group_nodes
- 03:23 PM Revision 6035: mappings/VegCore-VegBIEN.csv: Always map taxonNameOrEpithet to taxonomicname, now that it's globally unique at all ranks in the datasource that provides it (NCBI)
- 03:18 PM Revision 6034: inputs/.NCBI/nodes/create.sql: Make name_txt completely globally unique by removing all duplicates, not just duplicate genera
- 03:17 PM Revision 6033: inputs/.NCBI/nodes/create.sql: Make name_txt (mostly) globally unique by removing several other kingdoms/superkingdoms, not just Animalia
- 02:56 PM Revision 6032: inputs/.NCBI/nodes/create.sql: Making genus globally unique: Moved comment with kingdom name to line with DELETE, and put "delete cascades to descendants" comment on its own line
- 01:57 PM Revision 6031: schemas/vegbien.sql: Added higher_plant_group_nodes lookup table
- 01:57 PM Revision 6030: schemas/vegbien.sql: Added higher_plant_group_nodes lookup table
- 01:49 PM Revision 6029: schemas/Makefile: DDLs: $(pg_dump): Turn off schema-only mode so that lookup table contents are included as well
- 01:47 PM Revision 6028: pg_dump_vegbien: Except in (raw) data mode, filter out pg_catalog.setval() statements (only lookup table contents should be preserved)
- 01:39 PM Revision 6027: lib/PostgreSQL-MySQL.csv: Remove SELECT pg_catalog.setval() statements
- 01:27 PM Revision 6026: lib/PostgreSQL-MySQL.csv: Remove COPY statements
- 01:18 PM Revision 6025: pg_dump_vegbien: $schema flag defaults to on to export only schema
- 01:08 PM Revision 6024: pg_dump_vegbien: Fixed bug where schema name var can't be named $schema because that would conflict with the $schema flag
- 01:03 PM Revision 6023: root Makefile: VegBIEN DB: DB and bien user: db: Run inputs/.TNRS/install before schemas/install because public.tnrs_input_name depends on TNRS.tnrs
- 12:33 PM Revision 6022: pg_dump_vegbien: Only include just the schema if new $schema flag is set. This causes constant lookup tables to automatically be exported for DB schemas, which was not fully supported by the $data flag because it also forced $owners to be enabled.
- 12:17 PM Revision 6021: schemas/vegbien.sql: Added higher_plant_group enum
- 11:25 AM Revision 6020: mappings/VegCore.csv: Added higherPlantGroup
- 10:40 AM Revision 6019: schemas/vegbien.sql: analytical_*: Added isNewWorld
- 10:32 AM Revision 6018: mappings/VegCore.csv: Added isNewWorld
- 10:21 AM Revision 6017: inputs/newWorld/: Added geoscrub.schema.~.changes.sql to add a unique constraint on countryNameStd and change isNewWorld's type to boolean
- 09:59 AM Revision 6016: Added inputs/newWorld/
- 09:55 AM Revision 6015: README.TXT: Datasource setup: Moved Auto-create the map spreadsheets after Install the staging tables, because for DB-only tables, creating the map spreadsheets requires the header.csv generated by the staging tables install
- 09:48 AM Revision 6014: input.Makefile: SVN: add: Also set _MySQL/'s svn:ignore
- 09:30 AM Revision 6013: inputs/SALVIAS/_MySQL/salvias_plots.*.sql.make: Use new my2pg_export
- 09:27 AM Revision 6012: inputs/.geoscrub/_MySQL/geoscrub.*.sql.make: Use new my2pg_export
- 09:25 AM Revision 6011: Added my2pg_export
11/05/2012
- 11:16 PM Revision 6010: Regenerated vegbien.ERD exports
- 11:14 PM Revision 6009: schemas/vegbien.ERD.mwb: Added analytical_stem, analytical_aggregate to ERD
- 10:49 PM Revision 6008: schemas/vegbien.sql: analytical_*: Added georeferenceValid, distanceToCountry_km, distanceToStateProvince_km
- 10:34 PM Revision 6007: schemas/vegbien.sql: Added _m_to_km()
- 10:06 PM Revision 6006: inputs/.geoscrub/geoscrub_cleaned_unique/map.csv: Removed geoscrubID->locationID mapping because it allowed multiple occurrences of the same placename/coordinates combination, which was causing problems when datasources try to link up to the geoscrub places (and end up matching multiple output rows for each input row)
- 09:54 PM Revision 6005: sql_io.py: put_table(): Removed assertion that into's row count be at least full_in_table's row count, because now that DISTINCT ON is used to satisfy the into table pkey, this is no longer necessarily true
- 09:15 PM Revision 6004: schemas/vegbien.sql: method: method_unique: Added reference_id to make method unique within the datasource instead of globally unique within VegBIEN
- 09:12 PM Revision 6003: mappings/VegCore.csv: Added samplingProtocolID
- 08:48 PM Revision 6002: mappings/VegCore-VegBIEN.csv: subplot locationevent: Only populate parent locationevent's location unique IDs if a subplot #/subplotID is actually specified. (The lack of a location unique ID will cause the parent locationevent's location to be removed, as well as the parent locationevent itself if there is no parent locationevent unique ID.) This fixes a bug where top-level plots in datasources that provide a nullable subplot #/subplotID were incorrectly getting connected to parent locationevents.
- 08:34 PM Revision 6001: mappings/verify.plots.sql: Added # locations, # location events, which also include subplots
- 08:17 PM Revision 6000: inputs/SALVIAS/verify/plots.ref.sql: Standardized line wrapping to put ; on its own line in multi-line queries and at the end of the line in one-line queries
- 08:13 PM Revision 5999: mappings/verify.plots.sql: Added "top-level" to # locations, # location events names because these queries do not include all locations
- 07:52 PM Revision 5998: inputs/SALVIAS/verify/plots.ref.sql: # locations: Fixed count to include all plotMetadata entries instead of just unique coordinates, because each plotMetadata entry now gets its own location
- 07:34 PM Revision 5997: mappings/VegCore-VegBIEN.csv: matched place: When any of the accepted* names is specified, set matched_place_id=0 (self-reference) to indicate that the matched place is an accepted (scrubbed) place
- 05:30 PM Revision 5996: schemas/vegbien.sql: analytical_stem_view: Use the canonical (scrubbed) place instead of the datasource's place where available. Note that canon_place_id is always populated (with a self-reference if needed), to enable using a just a LEFT JOIN for this.
- 05:14 PM Revision 5995: schemas/vegbien.sql: analytical_stem_view: Use datasource_* prefix instead of reference_* prefix that tables had gotten when datasource_id was renamed to reference_id
- 05:04 PM Revision 5994: inputs/SALVIAS/verify/plots.ref: Regenerated on vegbiendev using the PostgreSQL 9.1 pg_catalog.default collation
- 04:49 PM Revision 5993: sql_io.py: put_table(): Setting pkeys of missing rows: Fixed bug in column-based import where when input rows match multiple output rows in one of this iteration's input tables, the into table's pkey constraint is violated because full_in_table contains multiple entries for an input pkey
- 04:42 PM Revision 5992: schemas/vegbien.sql: place: Added index on matched_place_id to facilitate looking up places by matched_place_id in place_set_canon_place_id()
- 04:26 PM Revision 5991: schemas/vegbien.sql: Added geoscrub_input derived table with associated view. Build geoscrub_input as part of make_analytical_db().
- 03:56 PM Revision 5990: sql.py: Added table_has_pkey()
- 03:13 PM Revision 5989: sql.py: table_pkey_col(): For PostgreSQL DBs, use pg_catalog via index_cols() and table_pkey_index(), in order to use the search_path to look up the table. This fixes a bug where the pkey would be selected from information_schema.table_constraints in random order, and this order sometimes returned the corresponding table in the public schema but sometimes in other schemas, such as VegBank. This became a problem now that VegBIEN has a place table, which conflicts with VegBank's place table. (Most other VegBank tables that are mapped to have been renamed in VegBIEN.)
- 02:41 PM Revision 5988: sql.py: add_pkey_or_index(): Use new add_pkey_index()
- 02:41 PM Revision 5987: sql.py: Added add_pkey_index()
- 02:29 PM Revision 5986: inputs/import.stats.xls: Updated import times
- 02:15 PM Revision 5985: import_times: Use $'' quoting to expand tab, in order to also work on Mac OS X
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