schemas/vegbien.ERD.mwb: Fixed lines

schemas/tree_cross-links.sql: Synced with schema, updating with new table names

schemas/vegbien.sql: Removed no longer used taxon table. Use taxonconcept instead.

schemas/vegbien.sql: taxonconcept.taxonname: comment: Stated that this is the name of the taxon within its parent taxon

schemas/vegbien.sql: taxonconcept: comment: Removed no longer accurate comment that an accepted taxonconcept points to the identified taxon in the tree of life, because it is the identified taxon in the tree of life

schemas/filter_ERD.csv: Changed the table with the visible fkey from plant* to taxon* to be plantstatus rather than plantusage, since it contains more core fields

schemas/vegbien.sql: taxonconcept: Removed taxon_id, since taxonconcept now contains all the information needed to represent a taxonomic hierarchy, including both conceptual and nomenclature information

schemas/vegbien.sql: plantusage: Point just to taxonconcept instead of both to taxonconcept and taxon

schemas/vegbien.sql: taxonconcept: rank, verbatimrank comments: Added info from corresponding fields in taxon that also applies to taxonconcept

schemas/vegbien.sql: taxonconcept: comment: Added info from taxon that also applies to taxonconcept

schemas/vegbien.sql: Added taxonconcept_ancestor cross-link table

schemas/vegbien.sql: taxonconcept: Added description field

mappings/VegCore-VegBIEN.csv: Remapped taxon hierarchy for accepted taxonconcepts to taxonconcept parent_id hierarchy

schemas/vegbien.sql: Fixed bug where taxonconcept.parent_id was missing a foreign key constraint

schemas/vegbien.sql: taxonconcept: Changed instructions for including a taxon name at a rank with no explicit column to create a parent taxonconcept for it and point to it using parent_id instead of using otherranks. Removed no longer used otherranks field.

schemas/vegbien.sql: taxonconcept: taxonconcept_required_key check constraint: Added taxonname

schemas/vegbien.sql: taxonconcept: taxonconcept_unique_within_creator_by_name unique index: Removed duplicate entry for creator_id

schemas/vegbien.sql: taxonconcept: Added parent_id to point to the parent taxonconcept

sql_gen.py: null_sentinels: Added 'unknown' for taxonrank

schemas/vegbien.sql: taxonrank: Added 'unknown'

mappings/VegCore-VegBIEN.csv: Also map *taxonRank to taxonconcept.rank, so that if it's in the taxonrank enum, it will automatically populate this field

mappings/VegCore-VegBIEN.csv: Remapped *infraspecificEpithet to new taxonconcept.taxonname rather than placing it in subspecies prefixed with the taxonRank, because it isn't necessarily the subspecies and because taxonname is defined to contain the lowest-rank portion of the taxonomic name. Note that when both morphospecies and infraspecificEpithet are provided, infraspecificEpithet takes priority for the taxonname field, because if TNRS leaves unmatched terms (which are tentatively mapped to morphospecies) but also matches an infraspecificEpithet, then the unmatched terms can't be for a morphospecies (because an infraspecificEpithet and therefore also a specificEpithet was matched, so the species is definite and formally named).

schemas/vegbien.sql: taxonconcept: Renamed morphospecies to taxonname since it's used in the same way as taxon.taxonname: to store the lowest-rank portion of the taxonomic name, such as the morphospecies suffix

inputs/.TNRS/tnrs/map.csv: Mapped *_matched terms that are both matched in the input name and which correspond to the matched taxonconcept (Genus_matched, Specific_epithet_matched, etc.) to both the input and matched taxonconcepts

inputs/.TNRS/tnrs/map.csv: Mapped terms matched in the original string (rather than deduced from the matched taxonconcept) to new verbatim* taxonomic terms

mappings/VegCore-VegBIEN.csv: Mapped verbatim* taxonomic terms to the TNRS input taxonconcept

mappings/VegCore-VegBIEN.csv: TNRS input taxonconcept: Split single _if statement controlling where morphospecies goes into two _if statements for each case, so that other verbatim* terms don't need to have an _if statement in their mapping to the input taxonconcept

mappings/VegCore.csv: Added back verbatim* taxonomic terms, which will now be used for the TNRS input taxonconcept. Note that they will have a different meaning than the original* taxonomic terms that they were renamed to in r5062.

mappings/VegCore-VegBIEN.csv: In TNRS mode, remapped morphospecies (Unmatched_terms) to the input name's taxonconcept, because this does not relate to the matched taxon concept

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

Makefiles: .last_cleanup targets: Also make the file that's being cleaned up .PRECIOUS so it doesn't get deleted if the .last_cleanup target has an error

Makefiles: .last_cleanup targets: Make each individual target .PRECIOUS (don't delete on error) because just making %.last_cleanup precious doesn't seem to prevent deletion

mappings/VegCore-VegBIEN.csv: Mapped *taxonRank to new taxonconcept.verbatimrank

schemas/vegbien.sql: taxonconcept: Added rank, verbatimrank analogous to those fields in taxon

Makefiles: Don't delete %.last_cleanup on error because it's a mod time record rather than a generated file, and so that it's left at the last successful cleanup time when a cleanup operation is cancelled

input.Makefile: Maps building: %/.map.csv.last_cleanup: Removed no longer accurate comment about mappings being autoremoved

inputs/.TNRS/tnrs/map.csv: Remapped Name_submitted to new verbatimScientificNameWithAuthorship to create an additional level of taxonconcept for the concatenated (TNRS input) name separate from the parsed (TNRS output) name

mappings/VegCore-VegBIEN.csv: Mapped verbatimScientificNameWithAuthorship as an additional level of taxonconcept for the concatenated (TNRS input) name separate from the parsed (TNRS output) name

schemas/vegbien.sql: taxonconcept.canon_taxonconcept_id: comment: Changed three-level hierarchy to four-level hierarchy which separates the concatenated (TNRS input) name from the parsed (TNRS output) name

mappings/VegCore.csv: Added back verbatimScientificNameWithAuthorship, which will now be used to store the TNRS input name

schemas/filter_ERD.csv: Removed no longer used table taxonscope

schemas/vegbien.sql: voucher: Removed accessioncode because this table has no sourceaccessioncode which it would be generated from (it just links a taxonoccurrence to a vouchering specimenreplicate)

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.

schemas/vegbien.sql: taxonconcept: Renamed definer_id to creator_id to allow merging with datasource_id when datasource_id is renamed to creator_id

mappings/VegCore-VegBIEN.csv: Populated new taxonconcept.definer_id from identifiedBy, or when no identifiedBy is specified, from the datasource itself (using _simplifyPath:[next=datasource_id])

sql_io.py: put_table(): Resolve default value column after the main loop (inserts and selects), so that the default value column can refer to an output column that is not in the original mapping but is added to the mapping from a col_defaults entry. This requires deferring the "Missing mapping for NOT NULL column" warning until the default value column is resolved, and including all columns in the full_in_table since the default value input column is not yet known.

schemas/vegbien.sql: taxonconcept: comment: Changed definition to "A taxon concept defined by an entity" to correspond with the table's new name and usage

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: party: Fixed bug where needed separate unique index for roots (datasources), whose organizationnames must be globally unique rather than unique within a datasource

schemas/vegbien.sql: taxonconcept: Renamed concept_reference_id to definer_id because this is a clearer name and because this will allow merging with datasource_id, which serves the same purpose

schemas/vegbien.sql: party: Made it datasource-scoped. Since this creates a recursive fkey, a datasource (a root party) should point to itself in this field, which will happen automatically by setting it to the special value 0.

lib/PostgreSQL-MySQL.csv: Changed translation of fulltext to quote the identifier instead of appending characters to make it not a reserved word

schemas/vegbien.sql: taxonconcept: Moved concept_reference_id to the top of the table because it is now a key scoping field

schemas/vegbien.sql: concept_reference_id: Made it an fkey to party instead of taxonscope, because this is now the entity that defined the taxon concept, and is no longer specific to morphospecies. Removed no longer used table taxonscope.

schemas/vegbien.sql: taxonconcept: Documented that it's equivalent to VegBank's plantConcept table

schemas/filter_ERD.csv: taxonconcept inward fkeys: Removed not applicable taxon filtered table, since the fkey points in the opposite direction and thus is not part of this filter

schemas/vegbien.sql: taxonconcept: Renamed scope_id -> concept_reference_id as part of taxonomic schema refactoring at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/2012-10-03_conference_call#Taxonomic-schema-refactoring>

README.TXT: Schema changes: Moved "update the following files with any renamings" out of "Sync ERD with vegbien.sql schema" because this is needed for any schema changes, not just as part of syncing the ERD

README.TXT: Schema changes: Added Refactoring tips section with steps to rename a table and a column

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>

README.TXT: Schema changes: Syncing ERD with vegbien.sql schema: Added step to update mappings/VegCore-VegBIEN.csv with any renamings

README.TXT: Schema changes: Syncing ERD with vegbien.sql schema: Added step to update schemas/filter_ERD.csv with any table renamings

inputs/import.stats.xls: Updated import times. This now includes the half-hour-long pre-import of the TNRS taxonomic names (which the datasources then match up with), as well as the concatenation of the datasource's taxonomic name components to create or match up with the TNRS input name.

README.TXT: Data import: make backups/TNRS.backup/restore: Run it in the background because it takes awhile

README.TXT: Data import: Added steps to sync the TNRS schema to the latest version on vegbiendev

README.TXT: Data import: make inputs/download-logs: Added tnrs_log=1 so the TNRS daemon log is downloaded as well

Added inputs/test_taxonomic_names/Taxon/testNames.txt since this is test data, and thus can be under version control

Added inputs/test_taxonomic_names/README.TXT with Bob's comments

schemas/vegbien.sql: taxonpath.taxon_id: Changed comment to indicate that this used for parsed, not just accepted names. Parsed names have been standardized by TNRS but may be synonyms.

README.TXT: Documentation: To import and scrub just the test taxonomic names: Added `yes|` before make schemas/public/reinstall so the user isn't prompted to confirm the reinstallation a second time, and can just copy and paste the set of 5 commands directly into the terminal

tnrs_db: Made wait option default to off to facilitate running tnrs_db by itself, rather than as part of an import

tnrs_db: Added wait option to have tnrs_db exit as soon as no more names are available. This is useful for running tnrs_db when there is no concurrent import running, and therefore no need to wait for new data.

tnrs_db: Fixed the time of the "Waited" message so it that the total_pause (containing the next wait) would be incremented after the message was displayed. Split the "Waited" and "Waiting" messages into two separate messages.

README.TXT: Data import: Added steps to back up the TNRS cache, since it takes a long time to recreate. This also enables syncing it with a local machine when `make backups/download` is run.

README.TXT: Documentation: Added instructions to import and scrub just the test taxonomic names

input.Makefile: Staging tables installation: uninstall: For the TNRS datasource, prompt the user before deleting the schema, since the data in it is not easily reconstructible from a flat file

sql.py: map_expr(): When matching without quotes, support names containing spaces by not matching words when preceded or followed by quotes

sql.py: Expressions: bool_re: Also match parentheses surrounding the boolean value

README.TXT: Data import: import_all: Don't run with & because this prevents the created jobs from being owned by the calling shell. Instead, import the TNRS names as a separate backgrounded step and wait for it to finish before starting import_all. Removed TNRS import steps from import_all since these are now invoked separately.

README.TXT: Data import: Run import_all in the background, because it needs to import all the taxonomic names synchronously before it can start the datasource import in the background

Regenerated vegbien.ERD exports

inputs/.TNRS/tnrs/map.csv: Mapped Unmatched_terms to morphospecies because the morphospecies is what's left once named ranks are matched

mappings/VegCore-VegBIEN.csv: Mapped morphospecies

mappings/VegCore.csv: Added morphospecies

schemas/vegbien.sql: taxonpath: Added morphospecies

inputs/.TNRS/tnrs/test.xml.ref: Updated for latest TNRS output

inputs/.TNRS/tnrs/map.csv: Infraspecific_rank_2, Infraspecific_epithet_2_*: Mapped to UNUSED because they do not appear to be provided by TNRS (it just puts additional infraspecific names in Unmatched_terms)

inputs/.TNRS/tnrs/map.csv: Omit Infraspecific_rank because Name_matched_rank contains the unabbreviated rank and is provided more often

mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed infraspecificEpithet (Infraspecific_epithet_matched) to taxon at the infraspecies rank

mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed taxonomic ranks to the tree of life in the taxon table

schemas/vegbien.sql: taxon: Added comment that this table stores the tree of life

mappings/VegCore-VegBIEN.csv: accepted taxonomic terms: Use new _set_canon_taxonpath() to set the canon_taxonpath_id after the taxonpath has been inserted, so that if the taxonpath is an accepted name (scrubs to itself), it will link up to the just-inserted taxonpath with the taxonomic ranks parsed out, rather than to a new taxonpath containing only the few taxonomic ranks of the accepted name that TNRS provides. In particular, this (together with the tnrs_accepted_names sorting index on TNRS.tnrs) ensures that an accepted name is imported with its genus and species parsed out by TNRS instead of concatenated together in the Accepted_name_species field (genus+species). This enables the individual taxonomic ranks to be used in constructing the leaves of the tree of life (the taxon table).

sql_io.py: put_table(): Fixed bug where row_ct_ref was incorrectly being incremented when the iteration is a function call. This bug only occurred in row-based mode, because the DB cursor for a function call is not stored in column-based mode.

inputs/.TNRS/tnrs/map.csv: Use Name_matched_author/Name_matched_accepted_family instead of Author_matched/Family_matched because these fields are provided more often, due to being determined from the matched name itself rather than from the original string. This helps to fill in as many fields as possible. For accepted names (which scrub to themselves), this is especially important, because it adds the accepted name's family, which is not present in the input taxonomic name.

xml_func.py: process(): Fixed bug where need to preserve complex functions that have unevaluated XML nodes as arguments, because XML nodes are not accepted by sql_io.put() (they are handled by db_xml.put())

schemas/vegbien.sql: Renamed set_canon_taxonpath() to _set_canon_taxonpath() (adding _ prefix) so that db_xml.put() treats its arguments as arguments rather than as children with fkeys to parent

schemas/vegbien.sql: Added set_canon_taxonpath() to set a taxonpath's canon_taxonpath_id after it has been created

Added inputs/.TNRS/tnrs/cleanup.sql to cluster TNRS.tnrs on tnrs_accepted_names. This keeps TNRS.tnrs sorted with the accepted names first.

input.Makefile: Staging tables installation: %/cleanup: Also run any custom cleanup.sql provided in the subdir. %/install: Removed processing of postprocess.sql because no datasources are using it and because cleanup.sql can now be used for this purpose.

inputs/.TNRS/schema.sql: tnrs: Added tnrs_accepted_names index, which sorts accepted names first, and cluster the table on this index. This ensures that the component-parsed entries for accepted names are created before any verbatim names that point to them.