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.
input.Makefile: Staging tables installation: %/cleanup: Documented that this removes any index comments, due to a PostgreSQL bug. (This occurs because ALTER TABLE recreates the index but not its comment.)
inputs/.TNRS/schema.sql: Removed hardcoded schema name
inputs/.TNRS/tnrs/map.csv: Changed Name_matched_accepted_family comment to match analogous Name_matched_author comment
inputs/.TNRS/tnrs/map.csv: Remapped Author_matched as the scientificNameAuthorship instead of Name_matched_author, because Name_matched_author contains the author based on the matched name, not the author in the original string, so it's not strictly from the original name
mappings/VegCore.csv: Added acceptedBinomial, originalBinomial
mappings/VegCore.csv: Added binomial
inputs/.TNRS/tnrs/map.csv: Mapped Specific_epithet_matched
Added inputs/test_taxonomic_names/
mappings/VegCore-VegBIEN.csv: taxonoccurrence.authortaxoncode: Only populate if needed to distinguish the taxonoccurrence within a plot
schemas/vegbien.sql: placepath: Removed no longer used placepath_unique constraint on place_id. Removed place_id from placepath_unique_within_datasource_by_name unique index because otherranks is now used to store custom ranks.
schemas/vegbien.sql: taxonpath, placepath: Added *_required_key check constraints to ensure that empty entries are not created when a row does not have taxonpath/placepath data
import_all: Use new dedicated cleanup make target to clean up TNRS.tnrs
tnrs.py: encode_map: Added hidden minus sign, which TNRS removes
csvs.py: tsv_encode_map: Escape \n as \n (instead of as a \ followed by a newline) for clarity. Added escape for \r by using strings.json_encode_map. TsvReader: Decode all escapes in tsv_encode_map.
tnrs.py: encode_map: Added × (times), which TNRS replaces with x
tnrs.py: encode_map: Added " and ', which TNRS removes when at the beginning or end
tnrs.py: encode_map: Documented why each character needs to be encoded
tnrs.py: encode_map: Removed '&', which is actually not a special character for TNRS (although ';' is)
tnrs.py: encode_map: Added '_', which TNRS replaces with space
sql_io.py: append_csv(): In INSERT mode, print # rows read (different from # lines read if some fields contained embedded newlines) and # rows inserted (different from # rows read if some violated a constraint)
sql.py: insert(): Explicitly return None if the insert failed and a DuplicateKeyException or NullValueException was suppressed
input.Makefile: Staging tables installation: $(logInstall*Add): Fixed bug where the existing install log would be overwritten in quiet mode, even though this function should append its output to the log. Note that plain $(logInstall*) always overwrites the existing install log because it is used by the first install command.
strings.py: json_encode(): Fixed bug where '\n' and '\r' also needed to be encoded
tnrs.py: repeated_tnrs_request(): Also retry request in debug mode if an HTTPError is thrown, so that debugging info can also be obtained if there is a bug in the TNRS client
tnrs_db: Updated query for new three-level taxonpath hierarchy, where the concatenated name is now stored in identifyingtaxonomicname instead of taxonomicnamewithauthor
root map: Removed no longer needed public schema override, which is now handled by vegbien_dest
vegbien_dest: Allow user to specify a custom public schema in the $public env var. This makes custom public schema functionality available to all VegBIEN-accessing scripts, not just map.
tnrs_db: Adjusted pause, max_pause so the daemon waits longer before exiting, because after the initial TNRS run, most names have already been scrubbed and new names may not be added until the end of the import (in the case of a very large new datasource)
input.Makefile: Staging tables installation: Added cleanup, %/cleanup to clean up already-installed tables
tnrs.py: encode(): Also prepend special padding string to empty and whitespace-only strings because these names are otherwise ignored by TNRS (no response row)
tnrs_db: pause: Increased to 30 min because if no new names are available in TNRS.tnrs, there is no need to check every minute for new names (which clutters up the log file output). The pause feature is designed to allow tnrs_db to run in parallel with the import process, and process new names as they are made available, which only happens once for each partition of each datasource.
tnrs_db: Fixed bug where the new filtering out of already-scrubbed names caused names to be skipped, because the loop would both advance by the number of rows found and those rows would no longer be returned by the query, causing only every other set of rows to be processed
tnrs.py: tnrs_request(): Rewrapped lines (became >80 chars after adding profiling)
tnrs.py: tnrs_request(): Use new encode() and TnrsOutputStream to escape TNRS-invalid characters
tnrs.py: Added encode(), decode(), decode_for_tsv(), and TnrsOutputStream to handle escaping TNRS-invalid characters
strings.py: Added regexp_repl_esc()
strings.py: Added replace_all() and replace_all_re(), as well as flip_map() for use with maps for these functions
csvs.py: Added tsv_encode_map for use in creating TSVs parsed by TsvReader
csvs.py: TsvReader: Also interpret '\t' as a tab, to provide a mechanism for encoding embedded tabs
tnrs.py: gwt_encode(): Escape special characters in the string instead of removing them, so that TNRS receives the original name rather than a modified version. This will help make the submitted names match up with the returned Name_submitted.
strings.py: Added json_encode()
strings.py: Added esc_quotes()
schemas/vegbien.sql: placepath.canon_placepath_id: Changed hierarchy comment to match the taxonpath.canon_taxonpath_id comment, but with a two-level hierarchy of datasource name -> accepted name. This may later be changed to a three-level hierarchy like taxonpath.canon_taxonpath_id depending on how GNRS works.
schemas/vegbien.sql: taxonpath.canon_taxonpath_id: Changed comment to specify that taxonpaths should now be linked in a three-level hierarchy of datasource name -> concatenated name -> accepted name
schemas/vegbien.sql: taxonpath, placepath: Changed "scrubbed" to "accepted" to emphasize that the name is the accepted name returned by TNRS or GNRS, rather than merely the matched name
mappings/VegCore-VegBIEN.csv: non-TNRS taxonpaths: Store the concatenated identifyingtaxonomicname in a separate taxonpath owned by the TNRS datasource, so that it will match up with (and create a link to) the corresponding submitted TNRS name's taxonpath. This in turn is linked to the TNRS-determined accepted name, thus creating a three-level hierarchy of datasource name -> concatenated name -> accepted name.
mappings/VegCore-VegBIEN.csv: taxonomic terms: Remapped the concatenated taxonomic name to new identifyingtaxonomicname to use it directly to match up with the TNRS submitted name. Continue to map scientificNameWithAuthorship to taxonomicnamewithauthor.
schemas/vegbien.sql: taxonpath: Renamed plantcode to identifyingtaxonomicname so that it can be used to store the concatenated taxonomicname that gets scrubbed. This enables ignoring the name components when the full name is specified, so that when a TNRS submitted name's matched components are included in its taxonpath, this will not prevent a datasource's concatenated name (without the matched components) from matching up with the corresponding TNRS submitted name.
schemas/vegbien.sql: taxonpath: Made taxonomicnamewithauthor optional again and include all columns in the taxonpath_unique_within_datasource_by_name unique index so that the original name components can be stored in a separate taxonpath from the taxonpath with the concatenated taxonomic name. (The datasource's taxonpath would not always contain an entry for taxonomicnamewithauthor, so the other columns also need to be used in the unique index.)
schemas/vegbien.sql: taxonpath: Added back datasource_id, plantcode to make taxonpath datasource-specific again. This way, the original name components can still be stored in taxonpath, in addition to storing the concatenated name in a datasource-general taxonpath for use by TNRS.
