bugfix: *.sql: public.source_by_shortname(): need to wrap it in a nested SELECT because Postgres incorrectly does not constant-fold (inline) it, leading to a slowdown when it is therefore run many times. this is done using the steps at wiki.vegpath.org/Postgres_queries#wrap-function-call-in-nested-SELECT .
moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).
fix: bin/map: put template: comment out the "Put template:" label so that the output is valid XML, and displays properly in a browser rather than showing a syntax error
bugfix: mappings/VegCore-VegBIEN.csv: nest all taxonoccurrences inside a stratum event, so that the parent locationevent is always fully populated before child locationevents point to it. (previously, a stub parent event was created when the child event was imported first, which blocked the fully-populated parent event from being inserted later on.) this uses auto-folding (for VegBank/CVS) and auto-forwarding (for other datasources) to prune empty stratum events for taxonoccurrences that don't have strata. (see wiki.vegpath.org/Auto-folding, wiki.vegpath.org/Auto-forwarding for more info about these normalization techniques.) note that the inserted row counts stay exactly the same for all datasources except VegBank (which was being fixed), indicating that this signficant change to the mappings did not change the semantics of the import of taxonoccurrences.
inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix
inputs/REMIB/Specimen/postprocess.sql: map_nulls() derived cols: documented total runtime (7.5 min on vegbiendev)
inputs/REMIB/Specimen/postprocess.sql: map_nulls() derived cols: updated runtimes for map_nulls() inlining, which created a speed improvement of 7x for the numeric columns and 2.5x for the text columns (292563.362->41929.772 ms and 83640.424->35690.797 ms, respectively). note that the map_nulls__coord__*() calls could be optimized further by combining the successive map_nulls() calls into one, with the hstores merged.
inputs/REMIB/Specimen/postprocess.sql: map_nulls__*(): turned off STRICT to allow dynamic inlining, which speeds up the mk_derived_col() statements by 5x (342799.823 ms -> 71533.252 ms (6 min -> 1 min) for latitude_sec)
inputs/REMIB/Specimen/postprocess.sql: runtimes: updated for vegbiendev, before dynamic inlining. the times are about twice as fast as on starscream, so vegbiendev is faster at whatever is the limiting speed factor (probably not CPU, based on other benchmarks).
inputs/REMIB/Specimen/postprocess.sql: runtimes: documented the machine the times are from
inputs/REMIB/: switched to new-style import, using the steps at wiki.vegpath.org/Switching_to_new-style_import#stage-I-source-specific > "run the following for each datasource"
bugfix: inputs/REMIB/Specimen/map.csv: state: changed output column name to stateProvince_verbatim to match the renaming in postprocess.sql
inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: removed out-of-date rerun time, which applied to doing all the deletes in the same statement (however, the current rerun time is approximately the same). note that index scans are not actually used (as the previous comment incorrectly stated) because the conditions for this filter are prefix-less regexps.
inputs/REMIB/Specimen/: translated single-column filters to postprocessing derived columns, using the steps at wiki.vegpath.org/Switching_to_new-style_import#stage-I-source-specific > "translate single-column filters to postprocessing derived columns". null-mapping filters now use wrappers around new util.map_nulls(). note that the verbatim columns input to the filters need to be renamed to avoid name collisions with their filtered columns, which must be VegCore terms for new-style import.
inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: also filter out non-numbers for long_sec, lat_min, lat_sec
inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: remove rows where long_min is not a number
inputs/REMIB/Specimen/postprocess.sql: change E'' to regular '' to avoid the need to double \ (instead ' would be doubled). E'' used to be necessary in previous versions of PostgreSQL to avoid a warning about escape string syntax.
inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: removed unnecessary () around `DELETE FROM :table WHERE long_deg ...`
inputs/REMIB/Specimen/postprocess.sql: removed coll_year, country, long_deg indexes because the frameshift filter conditions on these columns do not use index scans (because their regexp patterns do not contain a fixed prefix). eventually, some regexp patterns may be able to be modified to use prefixes.
bugfix: inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: can't OR together conditions to determine rows to delete, because if any condition is NULL instead of true/false, this will NULL out the entire WHERE condition and prevent any other true conditions from causing a deletion. the best way to fix this is to use a separate DELETE statement for each condition, so that NULLs only impact that particular condition's DELETE. unlike using a modified, NULL-insensitive OR, which would prevent the use of index scans, this allows indexes to be used for conditions that support them.
inputs/REMIB/Specimen/postprocess.sql: removed duplicate CREATE INDEX for the acronym column
bugfix: inputs/REMIB/Specimen/postprocess.sql: switched back to the input column names, since the renaming to *_verbatim is part of a later step
inputs/REMIB/Specimen/create.sql: moved filtering out of frameshifted rows to postprocess.sql, where it can happen in an idempotent DELETE. this allows filters to remove additional rows to easily be added on top of the existing filters, without needing to remake Specimen (which takes a long time, because of the many stage I derived columns that get added). the logical inversion inherent in the DELETE condition has been factored through rather than wrapped in NOT (...), because removal of frameshifted rows is more accurately specified as the detection of specific patterns that indicate frameshifting rather than the validation of all fields.
inputs/REMIB/Specimen/create.sql: also remove frameshifted rows with invalid long_deg values
bugfix: inputs/*/*/postprocess.sql: made all operations idempotent, so that postprocess.sql can be run repeatedly (e.g. by new-style import)
inputs/*/*/map.csv for CSV tables with a row_num column: added missing row_num entry, which is needed by the staging table column renaming to make the order of the map.csv columns match the order in the staging table
mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: filter out genera that contain numbers (using new _filter_genus()), which break TNRS and prevent it from matching any other parts of the name. later, these genera can instead be moved to the end of the name, where TNRS will correctly match them as Unmatched_terms.
inputs/GBIF/Specimen/postprocess.sql, inputs/REMIB/Specimen/postprocess.sql: updated for providers in r9459, which adds TEX
inputs/*/*/postprocess.sql: Remove institutions that we have direct data for: query to obtain list: updated for current schema
inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files
inputs/input.Makefile: %/.map.csv.last_cleanup: Run fix_line_endings after canon/translate to standardize Python's \r\n line endings back to \n. This prevents issues with mixed line endings because LibreOffice (and probably Excel) treat all cell-internal line endings as \n but row line endings as whatever the file had, while text editors like jEdit translate all line endings to whatever the autodetected line ending is. (This creates spurious line ending diffs when a map spreadsheet containing multiline cells is edited in a text editor.)
mappings/VegCore.htm: Regenerated from wiki. Renamed specimenHolders to specimenHolderInstitutions to make it obvious that this is a list of institutions, such as would be in institutionCode in a DwC export.
inputs/REMIB/Specimen/map.csv: Mapping NULL-equivalent lat/long to NULL: Fixed bug where need special *=* mapping to pass through values not in the map
inputs/REMIB/Specimen/map.csv: Map NULL-equivalent text fields (country, state, etc.) to NULL
inputs/REMIB/Specimen/map.csv: Map NULL-equivalent lat/long to NULL
inputs/REMIB/Specimen/map.csv: Remapped lat/long_deg,min,sec to new latitude/longitude_deg,min,sec, allowing the DMS coordinates to be translated
mappings/VegCore.htm: Regenerated from wiki. Documentation has been added on how to choose term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming) and how to form globally unique ID values (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Forming-IDs). Source and Specimen terms have been renamed to be self-explanatory and unambiguous (the DwC equivalents remain as synonyms). Short definitions of Source terms have been added to explain the differences between them. Source, Specimen, and Collection terms have been shortened according to the new instructions for choosing preferred term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming).
inputs/*/*/VegBIEN.csv: Regenerated from mappings/VegCore-VegBIEN.csv
mappings/VegCore.htm: Regenerated from wiki. Brad's new DwC ID terms spreadsheet has now been added, and a number of the ID terms clarified, disambiguated, and recategorized. In particular, institutionCode has now been split into the custodialInstitutions and collectingInstitution, to differentiate between which institution has the specimen vs. stamped the specimen. This distinction is important because the catalogNumber, stamped on the specimen, is only unique within the collectingInstitution. Most datasources don't unambiguously specify which institution their institutionCode is referring to, so it has been assumed to be custodialInstitutions unless a data dictionary says otherwise (as is the case for UNCC). In addition, a MatchedTaxonDetermination table has been added with the *_matched fields from TNRS.
mappings/VegCore-VegBIEN.csv: institutionCode list->sourcename mapping: _split(): Also match ; as a separator, and match separators with or without a following space
mappings/VegCore.csv: Regenerated from wiki. This adds Brad's DwC ID terms and their definitions in <https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx>.
mappings/VegCore-VegBIEN.csv: Don't create NCBI crosslinks for the matched taxonomic name. These crosslinks are no longer needed now that TNRS provides a separate accepted name on which crosslinks can be made.
inputs/REMIB/Specimen/postprocess.sql: Added back ARIZ, NY because some REMIB specimens for these datasources are not yet in the datasources themselves
Added inputs/REMIB/Specimen/postprocess.sql to remove institutions that we have direct data for
mappings/VegCore-VegBIEN.csv: Removed TNRS input taxonlabels meant to cross-link to taxonlabels added by the TNRS import, because TNRS taxondeterminations are now created instead
mappings/VegCore-VegBIEN.csv: taxonlabel.taxonomicname: Prepend the family to the rest of the name using new _merge_prefix() instead of _join_words()/_nullIf(), so that any input taxonomic name that includes the family will not have the family duplicated in the combined taxonomic name. Previously, the duplication was removed only when the rest of the input name was equal to the family. This change fixes a bug in the new TNRS import where a pre-concatenated taxonomic name (Accepted_scientific_name) which includes the family is now used instead of Accepted_name, which only includes it when it's equal to the family.
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: Allow multiple institutionCodes for each specimenreplicate by linking new sourcelist table many-to-many to source via sourcename (which is now a linking table)
mappings/VegCore-VegBIEN.csv: Don't forward specimenreplicate IDs to location for plots data (where the specimenreplicate IDs apply only to the specimen)
mappings/VegCore-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()
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
db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names
mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()
mappings/VegCore-VegBIEN.csv: institutionCode: Also map to the sourcename's matched source, which identifies whether the source is a herbarium
mappings/VegCore-VegBIEN.csv: institutionCode: Remap to source.shortname when specimen information is not provided, as is the case for geoscrub.herbaria on nimoy
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
mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place
schemas/vegbien.sql: Renamed reference -> source to make this table more broadly applicable, and because this now stores the datasource metadata
mappings/VegCore-VegBIEN.csv: Made taxonoccurrence.verbatimcollectorname an fkey to party, and renamed it to collector_id
specimenreplicate: Made institution_id an fkey to referencename instead of party, to later be matched up with reference entries for each aggregator's subprovider
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)
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
mappings/VegCore-VegBIEN.csv: decimalLatitude/Longitude->geoscrub input coordinates: Also set to NULL if 0 here, not just for the coordinates linked to the datasource's place instance
mappings/VegCore-VegBIEN.csv: matched place: Also map verbatim place's geoscrub-related fields to the matched place, to link up with geoscrub's corresponding input place
mappings/VegCore-VegBIEN.csv: Renamed creator_ids to reference_id since they are now fkeys to reference
schemas/vegbien.sql: Made creator_ids an fkey to reference instead of party, so that datasources are stored separately from people and to allow adding reference-type metadata (URL, copyright, etc.) for each datasource
mappings/VegCore-VegBIEN.csv: matched taxonlabel's ancestors: Only create the cross links to NCBI if the name is accepted (taxonIsCanonical)
mappings/VegCore-VegBIEN.csv: Mapped acceptedCountry, acceptedStateProvince, acceptedDecimalLatitude/Longitude. Mapped decimalLatitude/Longitude to matched place's coordinates when acceptedDecimalLatitude/Longitude not provided (as is the case for the geoscrub table).
mappings/VegCore-VegBIEN.csv: Remapped latitude/longitude to new coordinates table
schemas/vegbien.sql: Renamed placepath to place since this contains primary information about the place, including the reference to the canonical place
mappings/VegCore-VegBIEN.csv: Only prepend the family to the concatenated scientificName for TNRS if it ends in -aceae (using _taxon_family_require_std()), to avoid sending unsupported, nonstandard families to TNRS which it will place in Unmatched_terms
mappings/VegCore-VegBIEN.csv: Prepend the family to the concatenated scientificName input to TNRS, so that TNRS can use it to disambiguate the genus
schemas/vegbien.sql: taxonverbatim: Renamed species to specific_epithet to avoid confusion with the scientific meaning of species (genus+specificEpithet), since this field contains just the specific epithet
inputs/REMIB/Specimen/header.csv: Regenerated for new staging tables format
mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Do not include rank in the mapping because taxonomicname is globally unique, and thus it isn't used in looking up the NCBI taxonlabel
mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Also attach TNRS genus to NCBI backbone. This causes attachment to be made with as many of family and genus as are provided and have an entry in NCBI.
mappings/VegCore-VegBIEN.csv: Instead of connecting the acceptedFamily to the NCBI backbone, connect the family for the TNRS matched taxonlabel. This connects more families and also connects the same set of fields as will be connected for the genus.
inputs/*/*/header.csv: Regenerated for new staging tables format (which now includes a row_num column on every CSV table), as part of reinstalling staging tables
schemas/vegbien.sql: Link taxondetermination to taxonverbatim (which is a subclass of taxonlabel) instead of directly to taxonlabel. This will enable later having multiple taxonverbatims for one taxonlabel.
schemas/vegbien.sql: taxonlabel: Renamed identifyingtaxonomicname to taxonomicname because the taxonomicname provided by the datasource is now in taxonverbatim, so there is no name collision. Note that both of these fields store the same type of information, but taxonlabel's is autogenerated while taxonverbatim's is verbatim (and is only set if provided by the datasource).
schemas/vegbien.sql: taxonlabel: Moved non-scoping fields to new taxonverbatim subclass table, which contains the component parts of the taxonlabel
mappings/VegCore-VegBIEN.csv: Also create the identifyingtaxonomicname on the verbatim taxonlabel supplied by the datasource, in addition to on the TNRS input taxonlabel that the verbatim taxonlabel is matched up with
mappings/VegCore-VegBIEN.csv: Expanded brace expressions for putting together the identifyingtaxonomicname
mappings/VegCore-VegBIEN.csv: Always generate the concatenated identifyingtaxonomicname, even for higher taxa, to ensure that this field is always populated. Note that this will cause names of higher taxa to be scrubbed by TNRS, but this is usually not a problem because such names either have no match or not a close enough match based on the name only. Naming conventions generally cause names at different ranks to be different, so that collisions with lower ranks should not be a problem.
schemas/vegbien.sql: Renamed taxonconcept to taxonlabel per today's conference call, where it was decided that taxonconcept contained too many unrelated fields to be purely a taxon concept
schemas/vegbien.sql: taxonconcept: Renamed taxonname to taxonepithet for clarity and to be consistent with TCS's use of "epithet" to denote what the taxonname was intended to be (http://www.tdwg.org/standards/117/download/#/UserGuidev_1.3.pdf)
mappings/VegCore-VegBIEN.csv: identifyingtaxonomicname: Don't create if taxonconcept has an explicit parent, because the taxonName (which is generally only a component of the full taxonomic name, e.g. specificEpithet) is not globally unique. Datasources that provide name components in such a way that levels at or below family can't be directly concatenated cannot currently receive an identifyingtaxonomicname for input to TNRS.
schemas/vegbien.sql: taxonconcept: Renamed canon_concept_id to matched_concept_id, because this is actually the closest-match taxonconcept in the match hierarchy (datasource concept -> parsed concept -> matched concept -> accepted concept) rather than the accepted synonym, which goes in accepted_concept_id
schemas/vegbien.sql: taxonconcept: Renamed canon_taxonconcept_id to canon_concept_id to shorten the name, which is used often
schemas/vegbien.sql: taxonconcept: taxonconcept_required_key: Removed family and genus because these are now cached fields only, and are not used for scoping a taxonconcept. Instead, *taxonomicname and taxonname+parent_id are used for this purpose. This removes several leaf taxonconcepts with insufficient scoping information to create a taxonconcept separate from the main tree. With the upcoming population of creationdate, some of these taxonconcepts will reappear due to the date's additional distinguishing information.
mappings/VegCore-VegBIEN.csv: taxonconcept: Moved infraspecific taxonconcept to its own level, rather than combining it with the level that contains the full taxonomic name and author (as well as any morphospecies), for consistency with the storage of other ranked taxonomic name components, which each get their own taxonconcept. The infraspecific taxon concept is general to all parties making idenfitications (within a datasource), while the concatenated name and author and any morphospecies are specific to the person who defined the taxonconcept used by a taxondetermination.
mappings/VegCore-VegBIEN.csv: taxonconcepts: Also create the taxonconcept tree if datasource provided separated components of the taxonomic name and/or its own tree of life with higher classifications. This enables storing the datasource's own tree of life to supplement any official tree (TROPICOS, USDA, etc.).
mappings/VegCore-VegBIEN.csv: taxonconcept tree: Don't map infraspecificEpithet+taxonRank to a taxonconcept in the tree of parent concepts because it has already been mapped to the primary, lowest-level taxonconcept
mappings/VegCore-VegBIEN.csv: Remapped taxon hierarchy for accepted taxonconcepts to taxonconcept parent_id hierarchy
mappings/VegCore-VegBIEN.csv: TNRS-only mappings: Switch them on when verbatimScientificNameWithAuthorship is provided rather than when acceptedScientificNameWithAuthorship is provided, because it's the presence of a separate TNRS input name that really determines when TNRS is being mapped
schemas/vegbien.sql: Renamed datasource_id to creator_id so it can apply generally to any entity (such as a person), not just an aggregated datasource. This also enables taxonconcept.datasource_id to merge with creator_id, which now serves the same purpose.
mappings/VegCore-VegBIEN.csv: Fixed bug where needed to set datasource_id=0 on the TNRS party (which concatenated names/TNRS inputs are owned by) in order to make it a datasource (a root party)
schemas/vegbien.sql: Renamed taxonpath -> taxonconcept as part of taxonomic schema refactoring at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/2012-10-03_conference_call#Taxonomic-schema-refactoring>
mappings/VegCore-VegBIEN.csv: Mapped morphospecies
mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed infraspecificEpithet (Infraspecific_epithet_matched) to taxon at the infraspecies rank
