README.TXT: Maintenance: system updates that affect PostgreSQL: list of things that could break if PostgreSQL is not restarted: Added that you may not be able to access the database as the postgres superuser
backups/fix_perms: Removed world read permissions from backups dir. Note that this will require superuser permissions to view archived backups on jupiter, because the bien group is not set up with the same members as on vegbiendev. (On jupiter, it contains only stri,regetz,donoghue,naiamh.)
inputs/CVS/taxonObservation_/map.csv: Mapped plantname, plantNameWithAuthority
inputs/CVS/cvs.~.utils.sql: plantconcept_plantnames(): Use CVS's taxonLevel values, which are different from the VegBank plantLevel values that the original version of this function used
inputs/CVS/cvs.~.utils.sql: plantconcept_*(): Use plantConcept.lowestParentConcept_ID,taxonLevel instead of plantStatus.plantParent_ID,plantLevel to find the plantConcept's ancestors, because CVS does not use plantStatus except in very few cases and instead puts the parent link directly in plantConcept
inputs/VegBank/vegbank.~.utils.sql: plantconcept_plantnames(): Made function STABLE instead of VOLATILE because it does not modify any tables
inputs/CVS/cvs.~.utils.sql: plantconcept_plantnames(): Made function STABLE instead of VOLATILE because it does not modify any tables
mappings/VegCore.csv: Removed no longer used verbatimGrowthForm. Use growthForm instead.
mappings/VegCore-VegBIEN.csv: Removed no longer used verbatimGrowthForm. Map to growthForm instead and translate growth form values to VegBIEN's growthform enum.
inputs/Madidi/Organism/map.csv: Habit: Mapped growth form values
inputs/Madidi/Organism/map.csv: Remapped Habit from verbatimGrowthForm to growthForm, which points to the same place
inputs/CVS/taxonObservation_/map.csv: Use denorm_* denormalized taxonomic ranks in place of the normalized ranks when both are provided
input.Makefile: Maps validation: %/new_terms.csv: Fixed bug where need to filter unmapped_terms.csv's terms out of the output column, not the input column, because that's what the unmapped terms are generated from. Usually these columns are the same for unmapped terms, but sometimes an output term is changed from the original column's name but still doesn't match a VegCore term in mappings/VegCore-VegBIEN.csv.
input.Makefile: SVN: add: Added comment with instructions to update all inputs with these settings, using `make inputs/add`
input.Makefile: SVN: add: verify: Also ignore *.xlsx
README.TXT: Data import: Creating enough disk space: Added instructions for removing archived backups to free up space
inputs/CVS/taxonObservation_/map.csv: Fixed bug where taxonLevel, not taxonRank, needs to be mapped to taxonRank, because CVS's taxonRank is actually a number, while taxonLevel contains the corresponding text string
README.TXT: Data import: Before import, added step to make sure there is at least 100GB of disk space
sql_io.py: put_table(): is_function: Fixed bug where need to add the pkeys table's test pkey constraint after the data is added rather than when the empty table is created, to avoid adding a pkey constraint that will later be violated by data which returns multiple output rows for an input row (such as calls to _split())
sql_io.py: put_table(): insert_into_pkeys(): Allow callers to override run_query_into()'s add_pkey_ param in case the initial version of the pkeys table should not yet have the test pkey constraint (e.g. because data is added after the table is created)
README.TXT: Data import: Checking for errors: Search for "Command exited with non-zero status" to find errors, which is faster than checking that each input's log ends in "Encountered 0 error(s)"
inputs/import.stats.xls: Updated import times
README.TXT: Data import: import_all: Corrected text of note about time until control is returned to the shell
README.TXT: Data import: Moved download of logs to right after the import is done, because this is a quick step that doesn't depend on the backup- and export-creation steps
mappings/VegCore-VegBIEN.csv: institutionCode: Removed mapping to sourcename.matched_source_id, which is now autopopulated. Split any list of institutionCodes apart using new _split().
schemas/vegbien.sql: sourcename: Added sourcename_set_matched_source_id() trigger
schemas/functions.sql: Added _split()
schemas/vegbien.sql: sourcelist_unique: Removed COALESCE around name because it's NOT NULL
schemas/vegbien.sql: Allow multiple institutionCodes for each specimenreplicate by linking new sourcelist table many-to-many to source via sourcename (which is now a linking table)
schemas/vegbien.sql: sourcename: Removed system, which has been replaced by source_id as the scoping field
schemas/vegbien.sql: party: Added sourceaccessioncode and uniquify on it instead when provided. vegbien.ERD.mwb: Rearranged party-related tables to allow the tables to be fully expanded.
schemas/vegbien.sql: Renamed sampletype to observationtype to match the VegCore term
Added inputs/SALVIAS/salvias_users.~.clean_up.sql
inputs/SALVIAS/: Added salvias_users tables
my2pg: Translate blob to bytea
my2pg: Also remove UNIQUE and FULLTEXT inline indexes
mappings/VegCore.csv: UNUSED: Comments: Added Redmine formatting
mappings/VegCore.csv: OMIT: Changed "is omitted" to "should be omitted", because the mappings specify suggestions rather than requirements as to how a field should be used
mappings/VegCore.csv: Removed no longer used subInstitutionCode. Use datasource, institutionCode instead.
schemas/vegbien.sql: analytical_*: Renamed subInstitutionCode to institutionCode because this is the institution storing the specimen, as defined by DwC
schemas/vegbien.sql: analytical_*: Renamed institutionCode to datasource because this is actually the top-level datasource providing the record, not the institution storing the specimen
mappings/VegCore.csv: Added datasource
mappings/VegCore.csv: referenceType: Added closed list values
mappings/VegCore.csv: observationMeasure: Re-sourced to SALVIAS:observation_type, since SALVIAS comes before VegBIEN in the source precedence
mappings/VegCore.csv: Renamed sampleType to observationType to match the SALVIAS term it's derived from
inputs/SALVIAS-CSV/Plot/map.csv: Mapped observation_type
mappings/VegCore.csv: Added individualCount_*cm_or_more used by analytical_aggregate
mappings/VegCore.csv: subplotX/Y: Added definition
mappings/VegCore.csv: subplot*: Sources: Put SALVIAS:subplot last, because the specific field is closer in meaning to the term than the category
mappings/VegCore.csv: project*Date: Added definition
mappings/VegCore.csv: parentPlotName: Added definition
mappings/VegCore.csv: parent*: Sources: Put VegBank:PARENT_ID last, because the specific field is closer in meaning to the term than the category
mappings/VegCore.csv: locationName: Added definition
mappings/VegCore.csv: eventDate/startDate/endDate: Added definition
mappings/VegCore.csv: locationName: Sources: Put VegX:plotName first because it is closest in meaning to the term
mappings/VegCore.csv: recordedBy*: Added definition
mappings/VegCore.csv: recordedBy.middleName: Added source to DwC:recordedBy
inputs/CVS/: Joined together stemCount and stemLocation tables to create stemLocation_, in order to include the stem size class's measurements in each tagged stem's stemobservation (in addition to in the stemobservation for the aggregateoccurrence as a whole)
inputs/CVS/: Joined together taxonImportance and stemCount tables to create stemCount_, because stemCount actually stores stem abundance by size, rather than grouping stems by organism (http://vegbankdev.nceas.ucsb.edu/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename), and is thus an AggregateOccurrence-related table along with taxonImportance
inputs/CVS/taxonObservation_/map.csv: Fixed bug where need to indicate that data is plots data to prevent the specimenreplicate ID from being forwarded to the location ID
inputs/VegBank/taxonobservation_/map.csv: Fixed bug where need to indicate that data is plots data to prevent the specimenreplicate ID from being forwarded to the location ID
mappings/VegCore-VegBIEN.csv: Don't forward specimenreplicate IDs to location for plots data (where the specimenreplicate IDs apply only to the specimen)
xml_func.py: Simplifying functions: Added _eq()
xml_func.py: Added is_scalar()
xml_func.py: process(): row-based mode: preserving complex funcs: Fixed bug where functions with no params would crash reduce() because it requires at least one value when no initial value is specified
Added scalar.py
Renamed inputs/NCU-NCSC/ to NCU because this is the primary herbarium contained in the data
inputs/VegBank/: Joined together stemcount and stemlocation tables to create stemlocation_, in order to include the stem size class's measurements in each tagged stem's stemobservation (in addition to in the stemobservation for the aggregateoccurrence as a whole)
inputs/VegBank/stemlocation/map.csv: Also mapped stemlocation_id to individualID to create one plantobservation for each stemobservation
inputs/VegBank/stemlocation/map.csv: Remapped stemcount_id to aggregateOccurrenceID to match stemcount_id's mapping in stemcount_
inputs/VegBank/: Joined together taxonimportance and stemcount tables to create stemcount_, because stemcount actually stores stem abundance by size, rather than grouping stems by organism (http://vegbankdev.nceas.ucsb.edu/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename)
Added inputs/VegBank/_archive
input.Makefile: Testing: Added `%/test: %/test.xml` to allow testing just a subdir
input.Makefile: General targets: Added `%/: %/map.csv` to allow remaking just a subdirectory
inputs/CVS/: Refreshed data with new export from Bob
inputs/CVS/cvs-archive-2012-12-04.schema.sql: Fixed types using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Tools#MS-Access-database-MDB>
bin/map: Removed column names simplification, which was causing columns with the same alphanumeric characters but different punctuation to be simplified to the same name. Name simplification is now performed by the mapping mechanism itself, and can be overridden in the mappings.
Regenerated inputs/VegBank/new_terms.csv
Added inputs/NCU/_src/NCU_specimens_public_2012-12-10.zip.url
inputs/NCU/: Refreshed data with new export from Bob
Added inputs/NCU-NCSC/_archive
input.Makefile: SVN: add: Also add _archive/ subdir
publish_analytical_db: Time the import of the data
export_analytical_db: Also create a .md5 for the export
export_analytical_db: Run commands in the root svn dir
mappings/VegCore.csv: soil composition terms: Removed ppm units from the definition, since units are actually fraction or percent
README.TXT: Data import: Moved On local machine steps after On nimoy steps, because the On nimoy steps are more important
mappings/VegCore.csv: Comments: Added quotes around quotations from other sources
mappings/VegCore.csv: Definitions: Added quotes around quotations from other sources
Added backups/fix_perms
backups/Makefile: Synchronization: %/download: Also download any .md5 file for the file
README.TXT: Data import: On nimoy: Added instructions to verify the export's MD5 sum
README.TXT: Data import: On nimoy: Replaced step to manually upload the analytical_aggregate export with the command to download it from jupiter
README.TXT: Data import: On nimoy: Removed step to rename any existing analytical_aggregate table, since the import is now done directly into the versioned table
mappings/VegCore.csv: VegX terms without definitions in VegX: Added definitions from non-VegX sources, etc.
