Factored OS section out from Makefile, input.Makefile into lib/common.Makefile

Makefile, input.Makefile: Use new $(version), which unlike $(date) also includes the svn revision, to version log files, etc. This way, the working copy can be put back to the way it was at the time of a given import (excluding changes to nonversioned files). This also makes it easier to get all the log files for a particular import when different tables' imports started at different times.

Makefile: Added $(root) for use with $(rootRevision)

lib/common.Makefile: Added $(version), to replace $(date) for versioning log files, etc., and helper function $(rootRevision)

lib/common.Makefile: Added $(revision)

input.Makefile: Removed no longer used $(SED)

lib/common.Makefile: Added $(sed)

Factored $(date) out from Makefile, input.Makefile into lib/common.Makefile

sql_io.py: put_table(): DuplicateKeyException: Fixed bug where indexes with conditions needed to have the input rows filtered by the condition, to prevent trying to retrieve an existing/inserted row using a join on the index columns when the index in fact does not apply. This fixes a bug in the import of taxonconcept where the taxonconcept_0_unique_identifying_name unique index has a condition which was not satisfied for input rows with no identifyingtaxonomicname, causing any input row with NULL in this column to match all taxonconcepts with a NULL identifyingtaxonomicname. This uses ignore_cond()'s new support for constraints that did not fail at least once.

sql_io.py: put_table(): ignore_cond(): Added support for constraints that did not fail at least once, and therefore should not be required to simplify to a non-false value. As part of this, only track the failed constraint in the errors table if it actually failed at least once based on the deleted row count or the `failed` param.

sql_gen.py: map_expr(): Fixed bug where names were being replaced when they were inside another name. This occurred with combined names created by sql_io.into_table_name().

sql.py: ConstraintException: message: Wrap condition in strings.as_tt()

sql.py: run_query(): DuplicateKeyException: Also retrieve the index's condition using new index_cond()

sql.py: Added index_cond()

sql_io.py: put_table(): insert_into_pkeys(): Take a query as the param instead of sql.mk_select()'s params, to allow the caller to pass in any query without needing insert_into_pkeys() to manually pass through those args

sql.py: constraint_cond(): Fixed NotImplementedError message to apply to this function

sql_io.py: put_table(): ignore_cond(): Log message: Replaced don't with do not so it wouldn't mess up syntax highlighting when viewing the log file in a text editor

input.Makefile: Staging tables installation: Don't delete %/header.csv on error, because header.csv is a byproduct rather than the primary output and is created roughly atomically

schemas/vegbien.sql: *_ancestor tables: Added descriptive comment that these are ancestor cross link tables

csvs.py: sniff(): Support multi-char delims using \t, such as \t|\t used by NCBI. Support custom line suffixes, such as \t| used by NCBI.

csvs.py: TsvReader.next(): Remove only the autodetected line ending instead of any standard line ending. Note that this requires all header override files to use the same line ending as the CSV they override, which is now the case.

csvs.py: is_tsv(): Support multi-char delimiters by checking only the first char of the delimiter

csvs.py: sniff(): Also autodetect the line ending

csvs.py: sniff(): Also autodetect the line ending

inputs/test_taxonomic_names/Taxon/+header.txt: Changed line endings to \r\n to match testNames.txt line endings. This will be necessary when the line ending is autodetected by csvs.sniff().

csvs.py: TsvReader.next(): Renamed raw_contents var to line, since this is just the line with the ending removed

strings.py: Replaced no longer used contains_any() with find_any(), which returns any found substring, or None if none of the substrings were found

csvs.py: Modify csv.Dialect._validate() to ignore "delimiter must be a 1-character string" errors, in order to support multi-char delimiters used by TsvReader

csvs.py: Modify csv.Dialect._validate() to ignore "delimiter must be a 1-character string" errors, in order to support multi-char delimiters used by TsvReader

csvs.py: TsvReader: Use str.split() instead of csv.reader().next() to parse the row, for efficiency and to support multi-char delimiters. This is possible because the TSV dialect doesn't use CSV parsing features other than the delimiter and newline-escaping (which is handled separately).

Regenerated vegbien.ERD exports

input.Makefile: $(exts): Added .dmp

csvs.py: delims: Added |

Removed no longer used inputs/.public/. Use inputs/.TNRS/ and inputs/.TNRS/tnrs/tnrs.make instead.

README.TXT: Documentation: To import and scrub just the test taxonomic names: Added steps to restore the original DB when the test scrub is complete

inputs/test_taxonomic_names/test_scrub: Also export the results to inputs/test_taxonomic_names/_scrub/

inputs/test_taxonomic_names/test_scrub: Use regular for .. in loop with a list of what's being processed in each iteration (match_input_names, parse_accepted_names)

inputs/.TNRS/tnrs/map.csv: Mapped Genus_score, Specific_epithet_score

mappings/VegCore-VegBIEN.csv: Mapped matchedGenusFit_fraction, matchedSpeciesFit_fraction. Reordered canon_concept_fit_fraction _maxs in the order they would be used if _alt were being used instead.

mappings/VegCore.csv: Added matchedSpeciesFit_fraction

mappings/VegCore.csv: matchedFamilyFit_fraction: Source the "matched" to Family_matched, which is a closer fit than Name_matched. matchedGenusFit_fraction: Fixed Genus_matched source to use #detailed_download instead of #simple_download.

mappings/VegCore.csv: Added matchedGenusFit_fraction

README.TXT: Removed extra trailing whitespace

README.TXT: Documentation: To import and scrub just the test taxonomic names: Use new inputs/test_taxonomic_names/test_scrub

Added inputs/test_taxonomic_names/test_scrub

schemas/vegbien.sql: taxonconcept: Renamed canon_taxonconcept_id to canon_concept_id to shorten the name, which is used often

schemas/vegbien.sql: taxonconcept: Added taxonconcept_canon_concept_min_fit() trigger to remove the canon_concept_id link from insufficient matches. These occur when e.g. a name in another language is approximated to a latin name or when the input name is not a proper taxon but TNRS provides a best-guess match anyway.

inputs/.TNRS/tnrs/map.csv: Mapped Family_score to new matchedFamilyFit_fraction

mappings/VegCore-VegBIEN.csv: Use matchedFamilyFit_fraction as canon_concept_fit_fraction when greater than matchedTaxonFit_fraction, because if there is at least a matched family, there is a valid taxonconcept to attach to

xml_func.py: Simplifying functions: Added _min, _max as passthroughs

schemas/functions.sql: Added _max(), _min()

mappings/VegCore.csv: Added matchedFamilyFit_fraction

mappings/VegCore-VegBIEN.csv: Remapped matchedTaxonFit_fraction to the verbatim* taxonconcept, because this is actually for the verbatim* concept's fit to the matched concept, not the matched concept's fit to the accepted concept

inputs/.TNRS/tnrs/map.csv: Restored *-prefixed output terms for unmapped terms that had initially been mapped to OMIT but could reasonably match to something in the future. Continue mapping Name_number to OMIT because it isn't globally unique (it identifies the name only within one TNRS batch).

inputs/.TNRS/tnrs/map.csv: Mapped Overall_score to new matchedTaxonFit_fraction

mappings/VegCore-VegBIEN.csv: Mapped matchedTaxonFit_fraction to _set_canon_taxonconcept(canon_concept_fit_fraction)

mappings/VegCore.csv: Added matchedTaxonFit_fraction

schemas/vegbien.sql: _set_canon_taxonconcept(): Also set the canon_concept_fit_fraction

schemas/vegbien.sql: taxonconcept: Added canon_concept_fit_fraction to store the closeness of fit of the canon_concept

schemas/vegbien.sql: taxonconcept: Renamed canon_taxonconcept_id to canon_concept_id to shorten the name, which is used often

sql.py: mk_update(): in_place: Convert columns of type character varying to text so that they can be merge-joined with text columns. Note that these two types are equivalent but not aliases of one another, so the explicit type change is needed.

sql_gen.py: Added canon_type()

sql.py: mk_update(): in_place: Factored retrieval of column type out into separate statement for clarity

schemas/functions.sql: _join*(): Fixed bug where was returning '' instead of NULL when only NULL inputs were provided, because array_to_string() always returns a non-NULL string. Functions must always return NULL in place of '' to ensure that empty strings do not find their way into VegBIEN, and to prevent inconsistencies between row-based and column-based import (row-based import folds empty strings to NULL while column-based import relies on having a clean input table).

sql_io.py: cleanup_table(): Use sql.table_pkey_col() instead of sql.pkey_col() so that only an actual pkey column is removed from the list of columns to clean. This fixes a bug where the first column in the table was not cleaned up if there was no pkey. Note that this bug only affected newly re-created staging tables, because staging tables previously had a special row_num pkey column added if they did not already have a pkey. The row_num column is now added by column-based import instead.

sql.py: table_pkey_col(): Raise a DoesNotExistException if the table has no pkey

sql.py: pkey_col(): Call table_pkey_col() directly rather than via pkey_name(). pkey_name(): Call pkey_col() instead of table_pkey_col() now that pkey_col() calls table_pkey_col().

sql.py: pkey_col(): Documented that if there is no pkey, returns the first column in the table

sql.py: pkey_col(): Specify recover directly as a kw_arg because it's the only kw_arg passed to pkey_name()

sql.py: Added table_pkey_col() and use it in pkey_name()

sql.py: Renamed pkey() to pkey_name()

sql.py: Renamed pkey_col_() to pkey_col()

sql.py: Removed no longer used pkey_col

db_xml.py: cleanup_table(): Inline sql.pkey_col ('row_num') because this is the only place it's used

cleanup_table(): Use new sql.table_cols() instead of sql.table_col_names()

sql.py: Added table_cols()

db_xml.py: put(): Fixed bug where needed to avoid truncating the pkeys_loc table, in case it's the same as one of the in_tables. This occurs now that sql_io.put_table() passes through the actual input column instead of the joined-together input table's column when ignoring all rows.

sql_io.py: put_table(): Resolving default value column: If ignoring all rows, use input cols directly instead of cols from joined-together input table. In addition to being simpler, this prevents the returned column's name from growing longer and longer as each iteration prepends its input table table name to the default value column name.

sql_io.py: put_table(): Moved changing the table of the default value column from Resolving the default value column to Setting pkeys of missing rows, because the table change is only needed in this section

sql_io.py: put_table(): Resolving default value column: Always call sql_gen.remove_col_rename() because it will just pass the value through if it's not a column

sql_gen.py: simplify_parens(): Removed extra simplify_parens() at end because it is done in the final iteration that performs no other replacements, so it is not necessary to also do it explicitly

sql_io.py: put_table(): Replaced limit_ref integer with ignore_all_ref boolean, because it is no longer used as a select statement limit

sql_io.py: put_table(): remove_all_rows(): Corrected "just create an empty pkeys table" comment to "just return the default value column"

sql_io.py: put_table(): mk_main_select(): Removed setting limit to limit_ref⁰, because an empty pkeys table is no longer created when ignoring all rows

sql_io.py: put_table(): Setting pkeys of missing rows: Removed "limit_ref⁰ == 0" check because this code is never reached in that case

sql_io.py: put_table(): Ignoring all rows for unrecoverable errors: Even in multi-row mode, just return whatever the default value or column was, instead of creating an output table containing the default value filled in for every row. This also assists the optimization to skip empty levels of taxonconcepts, because it folds the empty level to that level's parent level rather than creating a whole new temp table with ultimately the same contents.

sql_gen.py: not_false_re, not_true_re: Appended \b to ensure that true/false is only matched as a single word

sql_gen.py: simplify_expr(): Also simplify "NOT false" to true

sql_gen.py: simplify_expr(): Also simplify "NOT true" to false

sql_io.py: put_table(): ignore_cond(): Changed "Ignoring rows where" message with the negated (filter-out) condition to "Ignoring rows that don't satisfy" with the filter condition for clarity

sql_io.py: put_table(): ignore_cond(): If cond simplifies to false, remove all rows instead of filtering out individual rows which will all be filtered out. This optimization should improve import times of tables, such as taxonconcept, which use a check constraint instead of NOT NULL constraints to prevent empty rows. The taxonomic schema refactoring caused the creation of many more levels of taxonconcepts, many of which (such as variety, forma, cultivar) are empty for most datasources, so this optimization should also reduce overall import times for datasources that have any empty levels of taxonconcept. Note that this optimization is only possible now that sql_gen.simplify_expr() is able to simplify all the way to a single boolean value for the taxonconcept_required_key constraint.

Moved expression transforming functions from sql.py to sql_gen.py because they do not manipulate an actual database and merely generate SQL

sql.py: Added true_expr, false_expr and use them where their values are used

sql.py: simplify_expr(): Also simplify "AND true" expressions

sql.py: simplify_expr(): Also simplify "AND false" expressions

sql.py: Added atom_re and use it in simplify_parens()

sql.py: Added or_re and use it in simplify_expr()

sql.py: logic_op_re(): Added expr_re param for an expr on the other side of the operator

sql.py: simplify_parens(): Use bool_re

sql.py: Removed no longer needed paren_re()