globalbioticinteractions -

Features

n/a

Improvements

• update to newwer PBDB taxon url schema while keeping backward compati… …bility; related to https://github.com/globalbioticinteractions/nomer/issues/201
• support newer NBN url scheme https://species.nbnatlas.org/species/NHM… …SYS0021060385 in addition to https://data.nbn.org.uk/Taxa/NHMSYS0000080189; related to https://github.com/globalbioticinteractions/nomer/issues/202

Bugs

n/a

- Java
Published by jhpoelen 8 months ago

globalbioticinteractions -

Features

Improvements

• better align arctos guid urls for integration (http/https); related to https://github.com/globalbioticinteractions/msb-para/issues/12
• capture AMNH-style association records; https://github.com/globalbioticinteractions/AMNH-hymenoptera/issues/2

Bugs

- Java
Published by jhpoelen 9 months ago

globalbioticinteractions -

Features

Improvements

• introduce core and neo4j modules; only test java 21 with core modules
• implement workaround for old mdd permanent link https://github.com/mammaldiversity/mammaldiversity-org/issues/29 https://github.com/mammaldiversity/mammaldiversity-org/issues/29
• reduce transaction batch size
• inverse of hasParasite is parasiteOf; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1070
• add external mapping for [:root parasite of]
• add external mapping for [:hemi parasite of]

Bugs

• parse [on flower: xyz] as { "interactionTypeName": "on flower", "targ… …etTaxonName": "xyz" } https://github.com/globalbioticinteractions/ucsb-izc/issues/7

- Java
Published by jhpoelen 9 months ago

globalbioticinteractions -

Features

Improvements

• re-interpret dwc:associatedSequences as documented in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1063
• add some more Arctos associatedOccurrences patterns; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1062

Bugs

n/a

- Java
Published by jhpoelen 11 months ago

globalbioticinteractions -

Features

Improvements

• ignore missing tables for dwc-dp indexing support https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1049 @tucotuco

Bugs

n/a

- Java
Published by jhpoelen 12 months ago

globalbioticinteractions -

Features

• initial pass at dwc-dp indexing support https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1049 @tucotuco

Improvements

n/a

Bugs

n/a

- Java
Published by jhpoelen 12 months ago

globalbioticinteractions -

Features

n/a

Improvements

• update supported Relations Ontology Mappings; big thanks to @mdrishti @ddooley @cmungall @nataled @bpeters42 @anitacaron for helping to introduce the hasAllelopath, inverse of allelopathOf via oborel/obo-relations#809

Bugs

• do not merge table schemas on config override; instead, replace them … …if present

- Java
Published by jhpoelen 12 months ago

globalbioticinteractions -

Features

n/a

Improvements

• make hash calculation for cached content configurable (related to https://github.com/globalbioticinteractions/elton/issues/69)

Bugs

n/a

- Java
Published by jhpoelen 12 months ago

globalbioticinteractions -

Features

n/a

Improvements

• upgrade to globi taxon graph v0.5.4
• disable geonames lookup for now
• add some more default interaction types as inspired by https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1045 fyi @qgroom
• avoid primary key name conflict with target/source mappings
• support resolving relative resources in directory-based archive related to https://github.com/globalbioticinteractions/elton/issues/68

Bugs

n/a

- Java
Published by jhpoelen 12 months ago

globalbioticinteractions -

Features

n/a

Improvements

• improved body part mappings as provided by @mdrishti (thank you!) https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1031 .
  • towards supporting discoverlife in rendering GloBI search results; re… …lated to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1038
  • make default interaction type mappings visible in provenance graphs: make interaction type mappings explicit by shipping them along with the dependency manifest (related to https://github.com/globalbioticinteractions/elton/issues/61)

example

bash elton update --prov-mode globalbioticinteractions/template-dataset | grep csv | grep hasVersion

results in:

<classpath:/org/globalbioticinteractions/interaction_types_ignored.csv> <http://purl.org/pav/hasVersion> <hash://sha256/f49f665c540214e7d00466e359821de1bc03206f8373d4974220d608ed7b98f3> <urn:uuid:1d66567d-ea58-4b05-b167-42cbf054f5bb> . <classpath:/org/globalbioticinteractions/interaction_types_mapping.csv> <http://purl.org/pav/hasVersion> <hash://sha256/ef045408607c6fb19d6bdf8145e7ce16a0e16bc8be45acbe31da33e1db0c9ea7> <urn:uuid:1d66567d-ea58-4b05-b167-42cbf054f5bb> . <classpath:/org/globalbioticinteractions/interaction_types_ro_unmapped.csv> <http://purl.org/pav/hasVersion> <hash://sha256/43aba7b90c686a4890aebd4a90a02d6f82259664524bdad1b22102a29fe9fa07> <urn:uuid:1d66567d-ea58-4b05-b167-42cbf054f5bb> . <classpath:/org/globalbioticinteractions/interaction_types_ro.csv> <http://purl.org/pav/hasVersion> <hash://sha256/7dc2797003a95ac7b97be06fda48b4dc25e7a555a2839a19ad7dc7a148427e43> <urn:uuid:1d66567d-ea58-4b05-b167-42cbf054f5bb> .

where hash://sha256/ef045408607c6fb19d6bdf8145e7ce16a0e16bc8be45acbe31da33e1db0c9ea7 is the content id/hash of one of the default mappings shipped with Elton -

with

preston cat --remote https://linker.bio hash://sha256/ef045408607c6fb19d6bdf8145e7ce16a0e16bc8be45acbe31da33e1db0c9ea7\ | head\ | mlr --icsv --omd cat\ | head

resulting in:

| providedinteractiontypelabel | providedinteractiontypeid | mappedtointeractiontypelabel | mappedtointeractiontypeid | | --- | --- | --- | --- | | associated with | | interactsWith | http://purl.obolibrary.org/obo/RO0002437 | | plant associations | | interactsWith | http://purl.obolibrary.org/obo/RO0002437 | | | | interactsWith | http://purl.obolibrary.org/obo/RO0002437 | | ex | | hasHost | http://purl.obolibrary.org/obo/RO0002454 | | ex. | | hasHost | http://purl.obolibrary.org/obo/RO0002454 | | reared ex | | hasHost | http://purl.obolibrary.org/obo/RO0002454 | | reared ex. | | hasHost | http://purl.obolibrary.org/obo/RO0002454 | | host to | | hostOf | http://purl.obolibrary.org/obo/RO0002453 | | host | | hasHost | http://purl.obolibrary.org/obo/RO_0002454 |

Bugs

- Java
Published by jhpoelen about 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• support configuring of specific versions of dataset resources to help work towards behavior described in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1030 https://github.com/globalbioticinteractions/elton/issues/52 https://github.com/globalbioticinteractions/elton/issues/62

previously, json ... "resources": { "https://example.org/old": "https://example.org/new" }

now,

json ... "resources": { "https://example.org/old": "https://example.org/new" }, "versions": { "https://example.org/new": "hash://sha256/1234..." }

which would peg the resource to a specific version (e.g, hash://sha256/1234...)

• upgrade jetty to address https://github.com/advisories/GHSA-j26w-f9rq-mr2q Moderate severity
• migrate registry module to elton

Bugs

• create tmpdir if none exists

- Java
Published by jhpoelen about 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• CacheUtil improvements to help work towards integration with Preston https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1030 https://github.com/globalbioticinteractions/elton/issues/52

Bugs

n/a

- Java
Published by jhpoelen about 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• cleanup tmp files on closing of inputstream #999 .

Bugs

n/a

- Java
Published by jhpoelen about 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• (again) towards separating provenance (i.e. access.tsv) and content (i.e. sha256) paths to facilitate preston-elton interoperability

Bugs

n/a

- Java
Published by jhpoelen about 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• towards separating provenance (i.e. access.tsv) and content (i.e. sha256) paths

Bugs

n/a

- Java
Published by jhpoelen over 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• append more aliases for wikipedia; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1011
• add mapping for allelopathOf for external use
• towards separating provenance (i.e. access.tsv) and content (i.e. sha256) paths

Bug fixes

n/a

- Java
Published by jhpoelen over 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• default workdir to "."
• use workdir when tmp files are created https://github.com/globalbioticinteractions/globalbioticinteractions/issues/999
  
• add custom service unavailable strategy as used in https://github.com/bio-guoda/preston/issues/301

Bug fixes

• make sure to include all dataset versions known to Zenodo; reproduces and fixes https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1017
• configure assembly plugin to allow for larger data products; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1016

- Java
Published by jhpoelen over 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• working towards using explicit cache dir to allow for better management of no longer used tmp files https://github.com/globalbioticinteractions/globalbioticinteractions/issues/999

Bug fixes

n/a

- Java
Published by jhpoelen over 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• add support for rootparasite_of http://purl.obolibrary.org/obo/RO_000… …2236; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/993#issuecomment-2254590484
• towards making workdir configurable; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/999

Bug fixes

n/a

- Java
Published by jhpoelen over 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• improve separated values in table cell values; https://github.com/globalbioticinteractions/globalbioticinteractions/issues/982
• skip BOM when reading csv/tsv files; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/992
• remove substitution of source doi/urls on reference level to prevent … …sticky study citation seen in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/992
• add support for http://purl.obolibrary.org/obo/RO_0002555 (allelopath… … of) related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/993#issuecomment-2209219735
• upgrade to Poelen, J. H. (2024). Global Biotic Interactions: Taxon Gr… …aph hash://sha256/5f5213f691969481aa349f0726a19bf5466dcdfd5a6223c71488ff2d48e01683 hash://md5/daee82c37dc0503a87d78ecdb80608d1 (0.5.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12724138
• disable uri normalization in httpclient; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/997
• allow for RO_ prefix in addition to RO: prefixes

Bug fixes

n/a

- Java
Published by jhpoelen over 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• update globi taxon graph 0.4.5-> 0.4.6
• add support for separated values in CSV meta table definition. For example see https://github.com/globalbioticinteractions/globalbioticinteractions/blob/b5259582794568ca78077412cf694b9ba51ed3a9/eol-globi-data-sources/src/test/resources/org/eol/globi/data/test-meta-globi-separator.json

Example below, with special focus on separator field in the Sequences column.

```json { "@context": [ "http://www.w3.org/ns/csvw", { "@language": "en" } ], "rdfs:comment": [ "inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/" ], "tables": [ { "@context": [ "http://www.w3.org/ns/csvw", { "@language": "en" } ], "rdfs:comment": [ "inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/" ], "url": "https://figshare.com/ndownloader/files/2196534", "dcterms:bibliographicCitation": "Wardeh, M., Risley, C., McIntyre, M. et al. Database of host-pathogen and related species interactions, and their global distribution. Sci Data 2, 150049 (2015). https://doi.org/10.1038/sdata.2015.49", "delimiter": ",", "headerRowCount": 1, "interactionTypeName": "hasHost", "interactionTypeId": "http://purl.obolibrary.org/obo/RO_0002454", "null": [ "" ], "tableSchema": { "columns": [ { "name": "sourceTaxonName", "titles": "Cargo", "datatype": "string" }, { "name": "Cargo classification", "titles": "Cargo classification", "datatype": "string" }, { "name": "targetTaxonName", "titles": "Carrier", "datatype": "string" }, { "name": "Carrier classification", "titles": "Carrier classification", "datatype": "string" }, { "name": "Sequences count", "titles": "Sequences count", "datatype": "string" }, { "name": "Publications count", "titles": "Publications count", "datatype": "string" }, { "name": "referenceUrl", "titles": "Sequences", "separator": ";", "datatype": { "base": "string", "valueUrl": "https://www.ncbi.nlm.nih.gov/nuccore/{referenceUrl}" } }, { "name": "Publications", "titles": "Publications", "datatype": "string" } ] } } ] }

```

Bug fixes

n/a

- Java
Published by jhpoelen over 1 year ago

globalbioticinteractions -

Features

• allow for linking of tables via primary/foreign keys in a globi.json schema definition. Inspired by https://github.com/globalbioticinteractions/globalbioticinteractions/issues/982 as well as many other datasets that split their interaction data across different tables (e.g., links, taxonomy, references) instead of providing a wide table that contains all information in a single row.

In the example below, a json configuration (note the primaryKey and foreignKeys parts) is shown that links resource/consumer (taxa) and reference id in a three column metaweb table to their associated data in taxonomy and reference tables.

json { "@context": [ "http://www.w3.org/ns/csvw", { "@language": "en" } ], "rdfs:comment": [ "inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/" ], "resources": { "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Reference": "references.tsv", "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Metaweb": "metaweb.tsv", "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Node%20Taxonomy": "taxonomy.tsv" }, "tables": [ { "dcterms:bibliographicCitation": "Adhurya, Sagar; Lee, Da-Yeong; Park, Young-Seuk (2024). KF-metaweb: A trophic metaweb of freshwater ecosystems of South Korea (Version 1.0) [Dataset]. Dryad. https://doi.org/10.5061/dryad.cz8w9gjbc", "url": "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Reference", "headerRowCount": 1, "delimiter": "\t", "null": [ "NULL", "" ], "tableSchema": { "columns": [ { "name": "referenceId", "titles": "Reference number", "datatype": "string" }, { "name": "referenceCitation", "titles": "Reference", "datatype": "string" } ], "primaryKey": "referenceId" } }, { "dcterms:bibliographicCitation": "Adhurya, Sagar; Lee, Da-Yeong; Park, Young-Seuk (2024). KF-metaweb: A trophic metaweb of freshwater ecosystems of South Korea (Version 1.0) [Dataset]. Dryad. https://doi.org/10.5061/dryad.cz8w9gjbc", "url": "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Metaweb", "headerRowCount": 1, "delimiter": "\t", "interactionTypeName": "eats", "interactionTypeId": "http://purl.obolibrary.org/obo/RO_0002470", "null": [ "NULL", "" ], "tableSchema": { "columns": [ { "name": "targetTaxonId", "titles": "resource", "datatype": "string" }, { "name": "sourceTaxonId", "titles": "consumer", "datatype": "string" }, { "name": "referenceId", "titles": "Reference", "datatype": "string", "separator": "," } ], "foreignKeys": [ { "columnReference": "targetTaxonId", "reference": { "columnReference": "taxonId" } }, { "columnReference": "sourceTaxonId", "reference": { "columnReference": "taxonId" } }, { "columnReference": "referenceId", "reference": { "columnReference": "referenceId" } } ] } }, { "dcterms:bibliographicCitation": "Adhurya, Sagar; Lee, Da-Yeong; Park, Young-Seuk (2024). KF-metaweb: A trophic metaweb of freshwater ecosystems of South Korea (Version 1.0) [Dataset]. Dryad. https://doi.org/10.5061/dryad.cz8w9gjbc", "url": "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Node%20Taxonomy", "headerRowCount": 1, "delimiter": "\t", "null": [ "NULL", "" ], "tableSchema": { "columns": [ { "name": "taxonId", "titles": "Node", "datatype": "string" }, { "name": "taxonGenusName", "titles": "Genus", "datatype": "string" }, { "name": "taxonFamilyName", "titles": "Family", "datatype": "string" }, { "name": "taxonOrderName", "titles": "Order", "datatype": "string" }, { "name": "taxonClassName", "titles": "Class", "datatype": "string" }, { "name": "taxonPhylumName", "titles": "Phylum", "datatype": "string" }, { "name": "taxonKingdomName", "titles": "Kingdom", "datatype": "string" }, { "name": "Category", "titles": "Category", "datatype": "string" } ], "primaryKey": "taxonId" } } ] }

Improvements

• add support for http://purl.obolibrary.org/obo/RO_0008509 [[has roost] , a term introduced by @diatomsRcool

Bug fixes

n/a

- Java
Published by jhpoelen over 1 year ago

globalbioticinteractions -

Features

n/a

Improvements

• do not truncate Candidate names when attempting to resolve to higher taxa #968 @kbseah
• remove triple constraints after expanding GloBI capacity related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/963

Bug fixes

n/a

- Java
Published by jhpoelen almost 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• include higher taxa authorities as taxon path shortcut in Taxon Domain object in GloBI core libraries. Related to https://github.com/globalbioticinteractions/name-alignment-template/issues/18 inspired by @whitfarnum

Bug fixes

n/a

- Java
Published by jhpoelen almost 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• support occurrenceRemarks with pattern "Collected from ..." see #956
• remove non-breaking whitespaces when parsing lat/lng pairs see #962
• add specific logging for suspicious DwC records https://github.com/BioKIC/Symbiota/issues/758

Bug fixes

n/a

- Java
Published by jhpoelen almost 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• reduce memory use when indexing DwC-A; #949
• elton4n - towards clean shutdown of database between running commands to avoid state pollution

Bug fixes

• close DwC-A stream after processing; related to https://github.com/globalbioticinteractions/elton/issues/58

- Java
Published by jhpoelen about 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

n/a

Bug fixes

• use tabular info from eml.xml only if a table definition is available in eml https://github.com/globalbioticinteractions/elton/issues/57

- Java
Published by jhpoelen about 2 years ago

globalbioticinteractions -

Features

• towards support for EML to index interaction data table; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/942#issuecomment-1830436945 @zedomel @filipi-soares

Improvements

• add support for TROPHICALLYINTERACTSWITH related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/923
• support for parsing MSB:Bird-style stomach content dynamic properties [stomach cont… …ents=...]; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/63

Bug fixes

n/a

- Java
Published by jhpoelen about 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add Accept: */* header to make grlc happy #923 fyi @tkuhn
• enable table specific index configuration

Bug fixes

n/a

- Java
Published by jhpoelen over 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• upgrade to globi taxon graph v0.4.5 related to https://github.com/globalbioticinteractions/globalwebdb/issues/1
• allow for multiple identifiers in wikidata taxon id resolving https://github.com/CatalogueOfLife/general/issues/100

Bug fixes

• allow for aligning occurrence-taxa resource relations in DwC-A https://github.com/globalbioticinteractions/inaturalist/issues/8
• make Zenodo metadata parser more lenient https://github.com/globalbioticinteractions/globalbioticinteractions/issues/488#issuecomment-1787448458 to avoid unexpected crashing on indexing. Related (unresolved) external data integration issue https://github.com/zenodo/zenodo/issues/2503 .

- Java
Published by jhpoelen over 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• Bump org.eclipse.jetty:jetty-servlets from 9.4.41.v20210516 to 9.4.52.v20230823.
• allow for enrichment of source/target taxon id from DwC-A dependencies; https://github.com/globalbioticinteractions/globalbioticinteractions/issues/427
• allow for disabling individual genbank/inaturalist occurrence id enrichment

Bug fixes

n/a

- Java
Published by jhpoelen over 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add support for "tsn:" and "TSN:" as a more intuitive ITIS taxonomic … …serial number prefix. related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/915
  • make interaction type interpretation more lenient by trimming whitesp… …aces from candidate IRIs.
• reduce logging verbosity

Bug fixes

n/a

- Java
Published by jhpoelen over 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• upgrade to GloBI taxon graph v0.4.1
• only process non blank eventDates
• add association patterns re: [visiting] and [caught after visiting], …
• add integration test for supporting Symbiota/NEON style associatedOcc…
  …urrences; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/903 @mandrewj
  • add "on tree trunk of" pattern; associated with 200f6783-1ec5-4170-8a…
  • add tribe/subtribe; https://github.com/globalbioticinteractions/nomer/issues/159 @whitfarnum
  • add support for importing jsonlines to parse results from preston tw-… …stream; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/373

Bug fixes

n/a

- Java
Published by jhpoelen over 2 years ago

globalbioticinteractions -

Features

n/a

Improvements

• make room for Paleobiology Database name relation (https://github.com/globalbioticinteractions/name-alignment-template/issues/9)

Bug fixes

n/a

- Java
Published by jhpoelen about 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add support for "OCCURS_IN" name relation (https://github.com/globalbioticinteractions/nomer/issues/133)

Bug fixes

n/a

- Java
Published by jhpoelen about 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• towards supporting neo4j schema indexes (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/860)
• add entry for Mammal Diversity Database as taxonomy provider https://github.com/globalbioticinteractions/nomer/issues/141

Bug fixes

n/a

- Java
Published by jhpoelen about 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• when no taxonMap/Cache is provided in elton4n, empty maps are used https://github.com/globalbioticinteractions/globalbioticinteractions/issues/859
• add man page installation / generation to elton4n / deb packaging

Bug fixes

n/a

- Java
Published by jhpoelen about 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

n/a

Bug fixes

• ~~gracefully handle indexed values that do not fit into neo4j index~~ do not index values that are too large to fit into neo4j index #857

- Java
Published by jhpoelen about 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• let elton4n use https://picocli.org just like elton, nomer, and preston. So, for instance, now the help is little more consistent, e.g., $ elton4n help Usage: elton4n [-hV] [COMMAND] compile, interpret, index, and repackage existing species interaction datasets using Neo4J -h, --help Show this help message and exit. -V, --version Print version information and exit. Commands: compile, import compile and import datasets into Neo4J link links compiled interaction datasets package package interaction datasets into data products help Displays help information about the specified command

• attempt to align elton4n default values with elton so that using tools side by side is facilitated: elton update globalbioticinteractions/ucsb-izc elton4n compile elton4n link -taxonCache file://$PWD/taxonCache.tsv.gz -taxonMap file://$PWD/taxonMap.tsv.gz elton4n package -exportDir /some/path/export

Bug fixes

• gracefully handle indexed values that do not fit into neo4j index #857

- Java
Published by jhpoelen about 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• facilitate install/remove elton4n via apt-get (Debian package manager) https://github.com/globalbioticinteractions/globalbioticinteractions/issues/855

Bug fixes

n/a

- Java
Published by jhpoelen about 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• request datacite metadata prefix instead of datacite3; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/845 @slint

Bug fixes

n/a

- Java
Published by jhpoelen over 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• more improvement to reduce time to discover locally indexed datasets (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/834)
• add support for Catalogue of Life integration via wikidata https://github.com/globalbioticinteractions/nomer/issues/102 https://github.com/CatalogueOfLife/general/issues/94 @Daniel-Mietchen
• add support for World of Flora Online integration via Wikidata https://github.com/globalbioticinteractions/globalbioticinteractions/commit/fb1d338374313cfd4b08cd871fa71f422ab4e154 @Daniel-Mietchen
• make templates for wikidata sparql queries https://github.com/globalbioticinteractions/globalbioticinteractions/issues/835 suggested by @Daniel-Mietchen
  
• add support for exporting interactions.tsv/csv without taxonomic name interpretation as verbatim-interactions.tsv/csv and refuted-verbatim-interactions.tsv/csv https://github.com/globalbioticinteractions/globalbioticinteractions/issues/826 @BarbaraMeulenbelt @seltmann

Bug fixes

• allow for taxonCache/taxonMap to be resolved via non-local resource services (https://github.com/globalbioticinteractions/nomer/issues/125)
• reduce disable mapdb "hack" that accessed non-public accessors programmatically https://github.com/globalbioticinteractions/globalbioticinteractions/commit/c4721ef7fb0875439fed69231f5c3c989d1e766e

- Java
Published by jhpoelen over 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• reduce time to discover locally indexed datasets (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/834)

Bug fixes

n/a

- Java
Published by jhpoelen over 3 years ago

globalbioticinteractions -

Features

• add support for exporting all GloBI namespaces as separate data product in preparation for addressing https://github.com/globalbioticinteractions/globalbioticinteractions/issues/826 by @BarbaraMeulenbelt

Improvements

• add support to use GloBI tools behind a http proxy wall https://github.com/globalbioticinteractions/nomer/issues/121 @zedomel

Bug fixes

n/a

- Java
Published by jhpoelen over 3 years ago

globalbioticinteractions -

Features

• add support for Terrestrial Parasite Tracker prefix TPT: to support https://github.com/njdowdy/tpt-taxonomy @njdowdy @EMTuckerLab @Jegelewicz @vijaybarve https://github.com/globalbioticinteractions/globalbioticinteractions/issues/694

Improvements

• add support for hemiparasite interactions http://purl.obolibrary.org/obo/RO_0002237 https://github.com/globalbioticinteractions/globalbioticinteractions/pull/823 @zedomel n/a
• various library upgrades (mockito, jsoup, springframework)

Bug fixes

• reduce warnings by refactoring mapdb use https://github.com/globalbioticinteractions/nomer/issues/44

- Java
Published by jhpoelen over 3 years ago

globalbioticinteractions -

Features

• add support for World of Flora Online prefix WFO: and schemes https://github.com/globalbioticinteractions/nomer/issues/96

Improvements

n/a

Bug fixes

n/a

- Java
Published by jhpoelen over 3 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add documentation for exposed fields in API https://github.com/globalbioticinteractions/globalbioticinteractions/commit/4de8b97f96ec516ec889d68a71391555824d3337
• escape column headers in csv/tsv when needed https://github.com/globalbioticinteractions/globalbioticinteractions/commit/1aa420872299197a356d8e5437bc9cb2ff0c8d2b
• add support for Catalogue of Life (#286)
• extend default interaction type mappings https://github.com/globalbioticinteractions/globalbioticinteractions/commit/123ec0c66763b2984d82e3bf4de2868582d8be6a @seltmann
• migrate code used by nomer only
  

Bug fixes

n/a

- Java
Published by jhpoelen over 3 years ago

globalbioticinteractions -

Features

• initial support for graph streaming protocol (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/769)

Improvements

• refactoring of resource handling to prepare for https://github.com/globalbioticinteractions/elton/issues/52
  • upgrade to taxon-graph v0.3.36; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/757
  • make attack claim parser (e.g., cat attack) a little more specific; r…
  • move Open Tree of Life support to Nomer (https://github.com/globalbioticinteractions/nomer/issues/30)
  • move orcid resolver to nomer

Bug fixes

n/a

- Java
Published by jhpoelen almost 4 years ago

globalbioticinteractions -

Features

n/a

Improvements

• reduce pageSize for iNaturalist api scraping as suggested by @kueda; …
• add explicitly unmapped wikidata taxon providers
• add support for parsing isolation source data; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/755
• add catalogue of life taxonomy provider; see https://github.com/globalbioticinteractions/nomer/issues/47

https://github.com/globalbioticinteractions/nomer/issues/47

Bug fixes

• removing overly greedy term [dor] to detect [dead on road] remarks; r… …elated to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/733

- Java
Published by jhpoelen about 4 years ago

globalbioticinteractions - v0.23.3

Features

• introduce iNaturalist occurrence id enricher to populate taxonomic/geospatial if missing (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/455 https://github.com/globalbioticinteractions/jeught2021/issues/1) thanks to @qgroom
• introduce GenBank (occurrence) id enricher to infer host relations if present (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/755 https://github.com/ArctosDB/arctos/issues/3172 )

Improvements

• add mapping for nutrients interactions; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/754 suggested by @ZekeMarshall
• first attempt at parsing of occurrence remarks re: dog/cat/road/vehicle kills and euthanasia (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/733) thanks to @ewommack @acdoll @Jegelewicz @dustymc
• implement custom specimen citation formats for UCSB-IZ @seltmann https://github.com/globalbioticinteractions/ucsb-izc/issues/4 and USNM @birdje https://github.com/globalbioticinteractions/usnm/issues/3
• add columns subgenus name/id for source/target taxa; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/732
  • upgrade commons-io v2.7 -> v2.10.0; related to https://github.com/globalbioticinteractions/nomer/issues/66
  • update to globi taxon v0.3.35
  • work towards introducing iso8601 datetime for interactions; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/699
  • add Wikidata Index Fungorum/BOLD/ Open Tree of Life Mappinsg; related to https://github.com/globalbioticinteractions/nomer/issues/71
  • add some minor backwards compatibility for unix epoch https://github.com/globalbioticinteractions/globalbioticinteractions/issues/699#issuecomment-1013456658 thanks to @Grace89 , @lee-michellej and @seltmann

Bug fixes

• fix taxon rank parsing issue reported by @KatjaSchulz via https://github.com/globalbioticinteractions/globalbioticinteractions/issues/757

- Java
Published by jhpoelen about 4 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add epiphiteOf/hasEpiphite to externally supported interaction types
• upgrade jena from v1.0.2 -> v3.17.0
• upgrade commons-lang3 to 3.12.0

Bug fixes

• detect/resolve java11 related bugs by adding java11 as github action test target (related to https://github.com/globalbioticinteractions/elton/issues/49)

- Java
Published by jhpoelen over 4 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add indexing support for Siyu Zhou, Bo Liu, Yelin Han, Yuyang Wang, Lihong Chen, Zhiqiang Wu, Jian Yang, ZOVER: the database of zoonotic and vector-borne viruses, Nucleic Acids Research, 2021;, gkab862, https://doi.org/10.1093/nar/gkab862 (see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/715) as suggested by @kephelps
• update maven-dependency-plugin from v2.8 to v3.1.0

Bug fixes

n/a

- Java
Published by jhpoelen over 4 years ago

globalbioticinteractions -

Features

n/a

Improvements

• upgrade fuseki v2.4.0 -> v3.17.0 https://github.com/globalbioticinteractions/globalbioticinteractions/commit/8c9283283e5579f2e80d57c87e2f9a281c6f15e1
• introduce name type "HOMONYM_OF" as suggested by @seltmann (https://github.com/globalbioticinteractions/nomer/issues/53)
• make term match listener order arguments more intuitive subj verb object https://github.com/globalbioticinteractions/globalbioticinteractions/commit/3dff277d1b06d2457a413116883ee511d3718724
• reduce neo4j index transaction log volume
• maintenance of maven build configuration

Bug fixes

n/a

- Java
Published by jhpoelen over 4 years ago

globalbioticinteractions -

Features

n/a

Improvements

• upgrade globi taxon graph v0.3.34
• include adjacentTo in list of external interaction types via api
• upgrade various library dependencies (e.g., jackson, commons-collections4, commons-lang3)
• update neo4j v3.4.18 -> v3.5.29
• add support for linking to new BatBase citation schema and interaction record landing pages; related to #706
• add authorship and accepted name type for taxa
• update IRMNG url prefixes, retain the legacy ones; related to #711
• improved taxon data parsing https://github.com/globalbioticinteractions/globi-taxon-names/issues/9
• include both [FMNH] as [F] as institution codes for Field Museum to help construct direct links globalbioticinteractions/fmnh#2
• ## Bug fixes
• index references by externalId, doi, or title; related to #710
• prevent overwriting of taxon properties; related to #712

- Java
Published by jhpoelen over 4 years ago

globalbioticinteractions -

Features

• first version of elton4n, a command-line tool for per-dataset neo4j-based interaction data transformation.

Improvements

• index DwC habitat values (see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/684)
• add error handling for unexpected NOAA REEM responses; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/687
• upgrade neo4j v2.3.12 -> v3.4.18 and associated dependencies (e.g., lucene v3.6.2 -> v5.5.5)
• improve import performance by reduce number of neo4j transactions
• add support for WoRMS taxon id prefix urn:lsid:marinespecies.org:taxname: used by @ekrimmel in ekrimmel/paleo-interactions-test@ec37fd3
• add field museum occurrence id enricher; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/702 @magpiedin @rondlg

Bug fixes

• fix invalid csv exports by handling value arrays in cypher json; https://github.com/globalbioticinteractions/globalbioticinteractions/issues/698
• handle case sensitive identifiers when mapping interaction types; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/704

- Java
Published by jhpoelen over 4 years ago

globalbioticinteractions -

Features

n/a

Improvements

• update globi taxon graph to v0.3.33 (#672)
• add some handling for likely virus names (#672)

Bug fixes

• Smithsonian-style USNM occurrenceRemarks host records no longer indexed (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/680)

- Java
Published by jhpoelen over 4 years ago

globalbioticinteractions -

Features

n/a

Improvements

• first pass at adding support for mapping dynamic properties for Manter Parasite collection ( https://github.com/globalbioticinteractions/unl-nsm/issues/4)
• add hasHabitat/createsHabitatFor to exposed interaction types in api
• map Arctos [(host of)] -> RO hasParasite http://purl.obolibrary.org/obo/RO0002445 to align with https://arctos.database.museum/info/ctDocumentation.cfm?table=ctidreferences#host_of

Bug fixes

n/a

- Java
Published by jhpoelen over 4 years ago

globalbioticinteractions -

Features

• introduce reference/dataset index (see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/544)
• add resourceTypes as property to interaction records to document the type of resources interactions were extracted from. For now, only DwC-A related rowTypes (e.g., http://rs.tdwg.org/dwc/terms/dynamicProperties, http://rs.tdwg.org/dwc/terms/Occurrence ). The value of resourceTypes is a pipe delimited list of resource types. Example: http://rs.tdwg.org/dwc/terms/dynamicProperties | http://rs.tdwg.org/dwc/terms/Occurrence or http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence. (see https://github.com/bio-guoda/preston/issues/115 and https://github.com/globalbioticinteractions/elton/issues/47) .

Improvements

• improve record linking by introducing mapping for custom US Parasite Collection catalogNumber -> occurrenceId mapping; related to globalbioticinteractions/msb-para#4
• improve record linking by applying patches for malformed json chunks in USNM Extant Specimen Records (see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/505)

Bug fixes

• introduce specific iNaturalist accordingTo redirect for backward compatibility after introducing reference/dataset index (see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/668)

- Java
Published by jhpoelen over 4 years ago

globalbioticinteractions -

Features

• first pass at dataset dependency declarations via RSS categories: xml <?xml version="1.0"?> <rss version="2.0" ... <channel> <title>MSB Parasite Collection and Dependencies RSS</title> ... <item> <title>MSB Parasite Collection (Arctos)</title> ... <!-- this is the main dataset to be indexed --> <ipt:dwca>http://ipt.vertnet.org:8080/ipt/archive.do?r=msb_para</ipt:dwca> </item> <item> <title>MSB Host Collection (Arctos)</title> ... <!-- this is a dataset that msb para depends on (e.g., references one or more of their occurrence records) --> <ipt:dwca>http://ipt.vertnet.org:8080/ipt/archive.do?r=msb_host</ipt:dwca> ... <!-- category used to indicate that an item is a dependency and should used to resolve linked content, and not as a source of interaction data --> <category domain="http://www.w3.org/ns/prov">http://www.w3.org/ns/prov#wasUsedBy</category> </item> ...

Improvements

• upgrade to GloBI taxon graph v0.3.32
• re-introduce some public convenience methods
• explicitly set version number to 0.21.1

Bug fixes

n/a

- Java
Published by jhpoelen almost 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• improved support for MCZ associatedOccurrences notation (https://github.com/globalbioticinteractions/mcz/issues/1)
• improved cross/intra-dataset record linking; related to #616 #659

Bug fixes

n/a

- Java
Published by jhpoelen almost 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• initial support for MCZ associatedOccurrences notation (https://github.com/globalbioticinteractions/mcz/issues/1)
• only consider dwc description extensions of type "ecology", "disease", "associations" and "dispersal" when looking for interaction/association data (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/660)
• various minor api information access improvements (https://github.com/globalbioticinteractions/globalbioticinteractions/commit/75d0b63f7016717bc2aa43bf95c018707b7f66be https://github.com/globalbioticinteractions/globalbioticinteractions/commit/ab9de92904ba5ed3c0068a9554b1df99188713ac and https://github.com/globalbioticinteractions/globalbioticinteractions/commit/6ad81b93262e323fb481d1f39db2cfb2cc2c1ca1)

Bug fixes

n/a

- Java
Published by jhpoelen almost 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add support for co-roosting / acquires nutrients from / has habitat terms (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/583)
  • add refuted-interactions.tsv/csv as data products (related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/638)
  • upgrade to GloBI taxon graph 0.3.31
  • support more flexible taxon related column name mappings (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/653)
• use taxon common names when no other taxonomic information is available (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/643)

Bug fixes

n/a

- Java
Published by jhpoelen almost 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add support for BOLD BIN and Taxa
• add API support for retrieving source/target collectionCode/institutionCode ( https://github.com/globalbioticinteractions/globalbioticinteractions/issues/606)
• upgrade to GloBI Taxon Graph v0.3.30
• exclude refutation records in interactions.tsv/csv.gz export to avoid confusion
• initial support for linking common names
• support parsing of species interactions from resource relation remarks used by field museum collections ( https://github.com/globalbioticinteractions/globalbioticinteractions/issues/609 )

Bug fixes

n/a

- Java
Published by jhpoelen almost 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add shutdown hooks for deleting tmp dwc archives (#577)
• improved handling of homonyms (#595)
• library upgrades (jetty 9.4.35.v20201120, hibernate-validator v6.2.0, spring v3.2.18.RELEASE)
• enhanced support for taxon id linking (#597)
• upgrade to GloBI Taxon Graph v0.3.29 (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/569#issuecomment-764692642) ## Bug fixes
• avoid write lock when building indexes in parallel (https://github.com/globalbioticinteractions/nomer/issues/31#issuecomment-774031917)

- Java
Published by jhpoelen about 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• support new BatBase taxonomic rank schema (#576)
• generalize interaction translation/mapping scheme to support most formats (#573)
  
• upgrade to use GloBI's doi4j v0.1.0 via maven central
• upgrade to use GloBI's maven-s3-wagon v0.0.3 via maven central
• add config for automated testing via GitHub actions

Bug fixes

• set server url for automated publication workflow (https://github.com/globalbioticinteractions/globalbioticinteractions/commit/04466f611e80c84d55c2a53476303c5a8df7e485)

- Java
Published by jhpoelen about 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• test logs cleanup
• more reliable release publication configuration

Bug fixes

n/a

- Java
Published by jhpoelen about 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• incorporate citations/references via DwC-References extension (see #553)
• towards supporting basic iso8601 format 20110101 in addition to 2011-01-01 and (see #542)
• add support for basic year-month notation like 201603 (march 2016) (see #542)
• allow for deploying to non-aws endpoints that support s3-apis like https://min.io (see #568)
• switch from commons-logging to slf4j (see #571)

Bug fixes

n/a

- Java
Published by jhpoelen about 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add support for indexing DwC-A Description Extension (see #553)
• add support for deprecating datasets (see #372)
• introduce Citable interface (see #544)
• add OpenBioDiv prefixes (https://github.com/globalbioticinteractions/globalbioticinteractions/commit/becc1c3bb2f3c6e3259c327cc8b5a56a8c21b9bb)
• added interaction types aggressorOf and hasAggressor ; related to #540 .

Bug fixes

n/a

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• move openbiodiv taxon lookup to nomer (https://github.com/globalbioticinteractions/nomer/issues/24)
• use Pensoft DOIs instead of OpenBiodiv URIs for reference linking
• refactor sparql client functionality
• remove deprecated methods

Bug fixes

n/a

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

• add taxon mappings for Mammal Species of the World (MSW)
• support explicit searches for refuting and supporting records (https://github.com/globalbioticinteractions/refuted-biotic-interactions-by-eol/issues/2)
• support to resolving Plazi taxon concepts, taxonomic treatments and related literature DOIs (https://github.com/globalbioticinteractions/nomer/issues/23 )

Improvements

• improved handling of unresponsive web resources by reducing timeout (https://github.com/globalbioticinteractions/elton/issues/40)
• removed verbose "sourceCitation" (dataset citation) property on reference objects, using the primary dataset node citation instead
• improved logging (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/532)
• removed under-used ecoregion search index (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/473)
  • add catalogNumber, collectionCode and institution code mappings for DwC-ish exports (#529)
  • upgrade to GloBI taxon graph v0.3.26 (https://github.com/globalbioticinteractions/nomer/issues/23)
  • improved indexing of Pensoft tables via https://github.com/pensoft/pensoft-interaction-tables and OpenBiodiv (https://github.com/pensoft/pensoft-interaction-tables/issues/11#issuecomment-707591310 https://github.com/globalbioticinteractions/globalbioticinteractions/issues/481 https://github.com/globalbioticinteractions/globalbioticinteractions/issues/526 https://github.com/globalbioticinteractions/globalbioticinteractions/issues/524)

Bug fixes

• improve DwC ISO8601 datetime range handling (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/535)

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• enhanced support for common taxon id prefixes NCBI, ITIS (https://github.com/globalbioticinteractions/nomer/issues/21)
• enhanced wikidata integration (https://github.com/globalbioticinteractions/nomer/issues/22)
• add journal name and spaces between author names; related to #488
• add support for Mammal Species of the World taxon ids; related to #446
• upgrade GloBI Taxon Graph to v0.3.25 (https://github.com/globalbioticinteractions/nomer/issues/20)

Bug fixes

n/a

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

• add support for indexing Pensoft annotated biotic interaction tables; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/481 .
  
• add support for indexing Zenodo biotic association metadata; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/488 .
  

Improvements

n/a

Bug fixes

n/a

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• allow custom type mapping on missing interactiontypeignore.csv (https://github.com/globalbioticinteractions/globalbioticinteractions/issues/521)
• enable "blank" type mapping to define default interaction type (https://github.com/globalbioticinteractions/inhs-insects/issues/1, https://github.com/globalbioticinteractions/globalbioticinteractions/issues/520)
• remove quotes and backslashes in DwC associatedTaxa values like "eats": "Homo sapiens" and \"eats\": \"Homo sapiens\" (https://github.com/globalbioticinteractions/uwsp-para/issues/1)
• remove additional dependencies on term master (see https://datatracker.ietf.org/doc/draft-knodel-terminology/)

Bug fixes

• enable custom type mapping on missing interaction_types_ignored.csv (#521)

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• resource access/caching: deprecate exposing local URI; favor location agnostic streams instead.
• web api: list exact match in fuzzy search first (see https://github.com/globalbioticinteractions/globalbioticinteractions.github.io/issues/58)
• remove dependency on term "master" in GitHub Utils (see https://datatracker.ietf.org/doc/draft-knodel-terminology/)

Bug fixes

n/a

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• use occurrenceId as citation when available.
• add fieldNumber / catalogNumber mapping for USNM host structures #504
• account for use of ~ tilde to annotate date range #507
• reproduce and fix event date mapping #506
• make batbase id prefixes and base url configurable #497

Bug fixes

n/a

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• support specimen sex fields in web API; related to #503
• add support for parsing USNM National Parasite Collection occurrenceRemarks json snippets with host info; see #504
• add support for parsing owl pellet notation used in Royal Saskatchewan Museum - Owl Pellet Collection - see #500

Bug fixes

n/a

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

n/a

Improvements

• upgrade to GloBI taxon graph v0.3.23
• add schema mapping for (two-part) species names using targetTaxonSpecies and sourceTaxonSpecies in addition to existing genus and specificEpithet mappings.
  • use wikidata to lookup images/common names associated with wikidata supported taxonomic ids (e.g., ncbi, itis) in addition to the existing functinality of lookup by taxon with explicit link to wikidata entitiy.

Bug fixes

n/a

- Java
Published by jhpoelen over 5 years ago

globalbioticinteractions -

Features

• support batplant taxon ids (see #340 )

Improvements

• toward normalizing dataset citations

Bug fixes

• commit index transactions to avoid issues on multiple processes using single cache (see https://github.com/globalbioticinteractions/nomer/issues/19)
  

- Java
Published by jhpoelen almost 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

n/a

Bug fixes

• account for ISO88591 encoding of dbatvir ecma3 json to avoid json parsing exceptions

- Java
Published by jhpoelen almost 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• remove dependencies on opengeo (see #460 #470)
• make paging batchsize for dbatvir configurable

Bug fixes

n/a

- Java
Published by jhpoelen almost 6 years ago

globalbioticinteractions -

Features

• add support for indexing http://batplant.org (see #340 )
• add support for indexing Database of Bat associated Viruses (DBatVir) (see #476 )

Improvements

• add taxon path id and taxon rank mappings
• add check for date range. Inspired by https://github.com/qgroom/batinterations/issues/3

Bug fixes

n/a

- Java
Published by jhpoelen almost 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• remove unused code and other maintenance
• upgrade to GloBI Taxon Graph v0.3.22
• update default interaction types mapping (see https://github.com/ParasiteTracker/tpt-reporting/issues/15 and
• ignore dwc:dynamicProperties without interaction data (related to https://github.com/globalbioticinteractions/elton/issues/34)
  
• performance improvements on generating reports
• add logging for reporting slow API queries
• avoid logging unnecessary information in provenance log (https://github.com/globalbioticinteractions/globalbioticinteractions/commit/e16f723c53bdadd5f7176885913c46c2d46f1c31)

Bug fixes

n/a

- Java
Published by jhpoelen almost 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• make NHM London Interactions Bank parser more lenient
• disable ecoregion indexing (see #473)
• do not add already cached resources to provenance logs

Bug fixes

• only list cached namespaces when they have valid provenance (related to https://github.com/globalbioticinteractions/elton/issues/31)
  

- Java
Published by jhpoelen almost 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• upgrade to taxon graph v0.3.21
• exclude slow inherited maven repository (see #470)
• improved handling of paged api queries (see #471)
• improved error logging

Bug fixes

• add taxonomic links using original taxon (see #448)
• detect taxon id prefixes to prevent unexpected queries (see #464)

- Java
Published by jhpoelen almost 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• upgrade to taxon graph v0.3.21
• exclude slow inherited maven repository (see #470)
• improved handling of paged api queries (see #471)
• improved error logging

Bug fixes

• add taxonomic links using original taxon (see #448)
• detect taxon id prefixes to prevent unexpected queries (see #464)

- Java
Published by jhpoelen almost 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

n/a

Bug fixes

• fix to ensure that Arctos occurrence records are linked as expected (see #461)
• ensure that read-only cache does not create directories

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

• introduce ContentStore and ContentRegistry consistent with discussion in https://github.com/cboettig/contenturi/issues/2#issuecomment-586047126 with @cboettig
• allow for GloBI datasets to provide interaction type mappings (#442)
• provide default interaction type mappings and supported GloBI interaction terms in csv files interactiontypesmappings.csv and interactiontypesro.csv respectively.

Improvements

• allow for non-Arctos collection to be mined from IPT RSS feeds (e.g., fmnh globi.json )
• allow for including and excluding datasets from RSS feeds based on regular expressions (see e.g., vertnet globi.json
• add information logging to show what dwca archives were indexed, how many records were scanned and how many interaction records were detected (see https://github.com/globalbioticinteractions/elton/issues/28 and https://github.com/ParasiteTracker/tpt-reporting/issues/8#issuecomment-586487251)
• add location from which a DwC archive was accessed in the source citation (e.g., Field Museum of Natural History (Zoology) Insect, Arachnid and Myriapod Collection - Version 12.21. Accessed at <https: //fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_insects> on 21 Feb 2020.)

Bug fixes

• fix to ensure access to provenance log

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

n/a

Bug fixes

• fix to ensure access to provenance log

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

n/a

Bug fixes

• use https endpoint for maven repository endpoints

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• code maintenance - package migration, apply more intuitive names
• use https for maven repository endpoints

Bug fixes

n/a

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

n/a

Bug fixes

• prevent non-match via Zenodo GloBI discovery from crashing elton update

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• reduce usage of GitHub API to avoid quota constraints
• use "smart" https git transport to retrieve most recent git commit hash for remote repository
• improved support for stream activity logging
• optimize usage of Zenodo API calls

Bug fixes

n/a

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• re-introduced log information on non-interaction records
• improved progress reporting, avoiding silence when processing large amounts records with no interactions in it.
• enhanced use of EML information for citing data.

Bug fixes

n/a

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• add collectionID mapping for DwC-A records.
• add interaction type mappings as suggested by @seltmann
• make interaction type mapping case insensitive

Bug fixes

• preserve interaction type name casing ( see https://github.com/globalbioticinteractions/ucsb-izc/issues/3 )

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• do not use GitHub API authentication when no credentials are available

Bug fixes

n/a

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• update review notes messages in response to suggestions by @seltmann
• use http basic authentication for GitHub API access ( see https://developer.github.com/changes/2019-11-05-deprecated-passwords-and-authorizations-api/#authenticating-using-query-parameters )
  • use Archive URL in source citation when no absolute resource is available.

Bug fixes

n/a

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

n/a

Improvements

• extend support for importing provided taxon hierarchies to DwC-A indexer
• additional integration tests

Bug fixes

n/a

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

Improvements

• bump taxon graph to v0.3.20 ; related to #441 and #438
• improved support for importing provided taxon hierarchies
• add terms "sex", "catalogNumber", "collectionCode", "institutionCode"
• introduce generic property interface for specimen records (set/getProperty)
• mapping maintenance for Arctos associations (see https://github.com/globalbioticinteractions/globalbioticinteractions/commit/7f6a75ff6881defc6ae8f688211171114f2cea23)

Bug fixes

• ignore empty genus value when picking most granular taxon name, allowing higher order taxa to be selected when an explicitly empty genus (e.g., ""`) name is present.

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

Improvements

• upgrade dwca-io to 2.6
• gracefully handle IllegalStateException thrown by dwca-io library to avoid crash due to https://github.com/gbif/dwca-io/issues/48
• attempt to compensate for common name duplicates from wikidata; see #434
• various DwC related improvements: consolidating interaction type mapping, expose institutionCode, catalogNumber, collection information in source/target specimen.
• report on Arctos restricted event dates. Related to https://github.com/ArctosDB/arctos/issues/2426
• more structured import logging to work towards supporting https://github.com/globalbioticinteractions/elton/issues/11

Bug fixes

• fix greedy matching against target taxon names. https://github.com/globalbioticinteractions/globalbioticinteractions/issues/433
• fix download issue due to duplicates in return fields https://github.com/globalbioticinteractions/globalbioticinteractions/commit/a6a9e58ed0fa3b8c28d16fbdd72431b84860e3da

- Java
Published by jhpoelen about 6 years ago

globalbioticinteractions -

Features

• mine common names from wikidata https://github.com/globalbioticinteractions/globalbioticinteractions/commit/686e86f0797d8233508129f2d9ebb4e6aeee01f5

Improvements

• upgrade cypher queries to Cypher v2.3
• refactor resource handling to allow for tracking resource processing

Bug fixes

• fix greedy matching for taxon names. related to #414

- Java
Published by jhpoelen about 6 years ago