xml_dom.py: value(): Skip comment nodes. This fixes a bug where comments inside text elements would prevent the value from being retrieved.
inputs/CTFS/test: Accepted test outputs for new VegX_CTFS_row_120000_bci.0.test.organisms.xml instead of VegX_CTFS_row_180000.0.test.organisms.xml, which didn't have <taxonNameUsageConcepts> that match up with <individualOrganisms>
inputs/CTFS/maps/VegX.organisms.csv: Added taxonConcept mappings
mappings/VegX-VegBIEN.organisms.csv: Added species taxonConcept mapping for identifier role
Added expand_xpath to expand XPath abbreviations
VegX mappings: Renamed taxonNameUsageConceptsID to taxonNameUsageConceptID (no plural) to match VegX 1.5.3
inputs/CTFS/maps/VegX.organisms.csv: Corrected CensusNumber input mapping
mappings/Makefile: Generate self maps for all core maps
mappings/Makefile: VegX-VegBIEN.stems.csv: Removed $(rootAttrs) from out root because stems don't use tcs namespace elements (stems don't have taxonDeterminations separate from the main organism)
VegX mappings: taxonConcept mappings: Added "tcs:" namespace prefix to appropriate elements. This will make the taxonConcept XPaths compatible with CTFS VegX.
input.Makefile: Vars/functions: Make: $(subMake): When forwarding to another dir based off of $(root), forward to $(root) rather than directly to the dir of the target. This ensures that any special targets that are only defined in the root Makefile still get run, even when the target is in a subdir with its own Makefile.
inputs/CTFS/test: Accepted initial test outputs. A lot of leaves are still unmapped with the default mappings.
inputs/CTFS/maps: Added initial maps
input.Makefile: Maps building: full via maps (maps/$(via).%.full.csv): $(makeFullCsv): Sort all maps so that rows are re-ordered whether or not a core self map exists. This way, if a core self map is created, it will not cause the sort order of the generated via-format XMLs to change. This makes it easier to accept any changes to test outputs that result from adding a core self map.
mappings/Makefile: VegX: Added VegX.self.organisms.csv. Added root attrs to chRoot maps, commented out since it's not ready to be checked in yet.
xpath.py: get(): Run xml_dom.by_tag_name() with ignore_namespace=False (possibly later set to True)
xml_dom.py: Comments: Added clean_comment() and mk_comment(). Searching child nodes: by_tag_name(): Added ignore_namespace option to ignore namespace of node name.
root Makefile: Added %-remake target
mappings/Makefile: Renamed joinMaps to dwcMaps and chrootMaps to vegxMaps. Added commented-out code to create VegX.self.organisms.csv (not ready to check in yet because it affects many dependent maps).
input.Makefile: Removed no longer needed $(noEmptyMap)
xml_func.py: process(): Use new xml_dom.mk_comment()
xml_dom.py: Added clean_comment() and mk_comment() to properly sanitize comment contents (comments can't contain '--')
Added inputs/TRTE
inputs/QMOR/test: Added initial accepted test outputs
inputs/QMOR/maps: Added maps
Added inputs/QMOR
inputs/MT/test: Added initial accepted test outputs
inputs/MT/maps: Added maps
mappings/Makefile: DwC-VegBIEN.specimens.csv: Don't call remove_empty to produce it, because join now deals with empty mappings correctly by still raising a warning. Removed no longer needed intermediate DwC.ci-VegBIEN.specimens.csv.
join: Also print "No join mapping" warning if a join mapping was found but it was empty. The warning in that case is actually "No non-empty join mapping" to distinguish it from a mapping that's missing entirely. input.Makefile: missing_mappings: Support new "No join mapping" error message.
Added inputs/MT
Added disown_all to disown all running jobs
stop_imports: Call jobspecs relative to $selfDir, rather than assuming it will be run from the svn root dir
union: Call maps.merge_headers() using **dict(prefer=header_num) instead of just prefer=header_num in order to work on Python 2.5.2 (which nimoy is running)
inputs/ACAD/test: Accepted initial test outputs
Added inputs/ACAD/maps/ maps
Accepted new test outputs resulting from the addition of the id -> occurrenceID mapping in mappings/DwC1-DwC2.specimens.csv
inputs/SALVIAS*/maps: Cleaned up maps for the first time since all via maps became subject to cleanup
input.Makefile: Removed no longer needed default "maps/.$(via).%.csv.last_cleanup" rule
input.Makefile: Maps building: Via maps cleanup: Added `env ignore=1` since with the switch to subtracting $(coreMap), all inputs will attempt to subtract some map, even if it's not subtractable
input.Makefile: Don't clean src maps, only build them
inputs/ARIZ/maps/DwC.specimens.csv: Re-cleaned up to take advantage of additional entries now removed by subtract
input.Makefile: Maps building: Via maps cleanup: Subtract $(coreMap) instead of $(coreSelfMap) so that entries whose input and output maps to the same place are subtracted as well
subtract: Also remove mappings whose input and output maps to the same non-empty value in map_1
util.py: Added all_equal(), all_equal_ignore_none(), have_same_value()
mappings/DwC1-DwC2.specimens.csv: Added id -> occurrenceID mapping
inputs/SALVIAS-CSV/maps/VegX.%.full.csv: Regenerated using new src maps
mappings/DwC1-DwC2.specimens.csv: Added mappings from dcterms elements without namespace to with namespace
inputs/SALVIAS-CSV: Built maps/src.%.csv
Added inputs/ACAD/maps/src.specimens.csv
input.Makefile: Maps building: Autogen src maps with known table names. Sources: $(withCatSrcs): Fixed bug where substitution pattern did not contain %.
Added src_map to make a source map spreadsheet from a CSV header
input.Makefile: Split Maps section into "Existing maps discovery" and "Maps building" sections. Sources: Added cat, cat-% to cat out sources.
input.Makefile: Factored out sources-related code to new Sources section
input.Makefile: $(srcMaps): Removed `$(filter-out maps/src.join.%.csv,...)` because maps/src.join.%.csv are no longer created
README.TXT: Schema changes: Split updating graphical ERD exports into separate section. Update graphical ERD exports: Added schemas/vegbien.ERD.core.pdf .
README.TXT: Added Datasource setup section with instructions to add a new datasource
Added inputs/ACAD
input.Makefile: Only setSvnIgnore the input dir, since it already exists and doesn't need to be added (inputs/Makefile adds it)
inputs/*/maps/DwC.specimens.csv: Removed extranenous XML meta info from DwC column root, since it now just needs to be present in the core via map mappings/DwC-VegBIEN.specimens.csv
union: Use new maps.merge_headers() to write properly combined header
maps.py: join_combinable(): Fixed roots_combinable() to run on col names instead of roots, which were passed in. merge_mappings(): Factored out mapping column combining into merge_mapping_cols(), which handles an optional prefer param as well to take the header_num env var. Added merge_headers().
util.py: Added sort_by_len(), shortest(), longest()
join: Use new maps.join_combinable() to check if column names match
maps.py: Added cols_combinable() and use it in combinable(). Added join_combinable() and associates helper functions. Added documentation labels to each section.
xml_parse.py: ConsecXmlInputStream: Removed read() because that's now defined in streams.FilterStream
xml_parse.py: parse_next(): Strip control characters from input stream because they mess up the parser
streams.py: FilterStream: Forward all reads to readline()
strings.py: Added is_ctrl() and strip_ctrl()
xml_parse.py: parse_next(): On parser error, advance to next XML document since the rest of the current document is corrupted
streams.py: Added consume(). Added documentation labels to each section.
bin/map: For XML inputs, wrap sys.stdin in a LineCountStream and use new xml_parse.docs_iter() on_error() to add input line # to XML parsing exceptions
xml_parse.py: Added on_error() handler to parse_next() (passed through by docs_iter()), so that the caller can add useful info like the input line # to the exception message, and decide not to suppress rather than re-raising the exception
VegX-VegBIEN.organisms.csv: Renamed individualOrganismObservation user-defined field identificationLabel2 to identificationLabel. Distinguish what are now two identificationLabel fields of the same name by tagging each one with [@id=2] or [@id=1]. inputs/SALVIAS-CSV/maps/VegX.organisms.csv: Merge tag1/stem_tag1 and tag2/stem_tag2 using _alt, since they are never set to different values when both are not NULL (although sometimes just one or just the other is not NULL).
VegX-VegBIEN.organisms.csv: Renamed individualOrganismObservation user-defined field tag2 to identificationLabel2 to reflect that it will become a second instance of identificationLabel
VegX-VegBIEN.organisms.csv: Re-mapped individualOrganismObservation user-defined field lineCover to already existing volumeCanopy
VegX-VegBIEN.organisms.csv: Re-mapped individualOrganismObservation user-defined field cover to already existing attribute.coverPercent
VegX-VegBIEN.organisms.csv: Re-mapped individualOrganismObservation user-defined field count to already existing aggregateOrganismObservation.aggregateValue
vegbien.ERD.mwb: Fixed lines
README.TXT: Documented that `make reinstall_db` will delete your VegBIEN DB
README.TXT: Documented that `make empty_db` will delete your VegBIEN DB
root Makefile: empty_db: Confirm deletion just like for rm_db. rm_db: put $(confirmRmDb) on a separate line and move the $(error) call to the main $(confirm) macro since you always want to abort make if the user cancels (not just not run that command).
root Makefile: rm_db: If user cancels, abort in case target was reinstall_db to prevent installing
root Makefile: core, rm_core: Fixed bug where no longer existing prerequisites postgres_user, rm_postgres_user were not removed
root Makefile: rm_db: Confirm deletion with user. Merged postgres_user, rm_postgres_user into db, rm_db so that deletion confirmation applies to user deletion as well (which would indirectly cause the DB to be deleted).
README.TXT: Testing: Updated to add missing mappings
root Makefile: test-all: Added missing_mappings
Moved maps validation targets from main Makefile to input.Makefile. main Makefile: maps validation: Summarize the output of the inputs' maps validations.
Makefile: Also find missing input mappings, in addition to missing join mappings
join: Also produce warnings for no input mapping (if no comment explaining why no input mapping), in addition to no join mapping
inputs/NY/maps/DwC.specimens.csv: Documented why there is no input mapping for key
VegX-VegBIEN.organisms.csv: Renamed individualOrganismObservation user-defined fields stem* to remove the stem* prefix to be consistent with VegBIEN
VegX-VegBIEN.organisms.csv: Renamed individualOrganismObservation/plotObservation user-defined fields sourceaccessioncode to sourceAccessionCode to be consistent with VegX case sensitivity
VegX-VegBIEN.organisms.csv: Renamed individualOrganismObservation user-defined field interceptCm to lineCover to be consistent with VegBIEN
VegX-VegBIEN.organisms.csv: Renamed individualOrganismObservation user-defined field individualCode to authorPlantCode to be consistent with VegBIEN
VegX-VegBIEN.organisms.csv: Renamed individualOrganismObservation user-defined field htFirstBranchM to heightFirstBranch to be consistent with VegBIEN
