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104 update mongodb#821

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giraygi wants to merge 201 commits intoEBISPOT:devEBISPOT/ols4:devfrom TIBHannover:104-update-mongodbTIBHannover/ols4:104-update-mongodbCopy head branch name to clipboard

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Commits on Feb 15, 2024

• enabled all rest controllers

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• added imports

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• added skos tree generation controllers

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• enabled hastopconcept option by making conceptSchema a term

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• implemented graph definition call for visualization

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• removed yet to be introduced caching for now and moved graph method below

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Commits on Feb 16, 2024

• renamed call signatures with respect to EBI conventions in EBISPOT#625

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Commits on Feb 19, 2024

• handled null relations for some ontologies in EBISPOT#625 and #1

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Commits on Feb 20, 2024

• changed skos variable name in the config file

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• added skos tree configuration parameters for frontend in EBISPOT#625 and #1

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Commits on Feb 21, 2024

• added ontology filter methods based on ontology metadata

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• enabled collection and subject variables in config

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• added composite classification variable for filtering

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• enabled filtering from composite type

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• filtering for filterby, search, select, suggest methods

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• added classifications as a composite variable to the config

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• implemented call for listing available schema keys

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• implemented schema values method

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• paginated the schemakeys and schemavalues methods

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• enabled all rest controllers

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• added imports

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• added config file for testing in #3

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• moved sample labeled config to configs directory in #3

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Commits on Feb 22, 2024

• renamed test config file and corrected variable name inside it for #3

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• refactored and added repo_url config variable

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Commits on Feb 29, 2024

• added composite license variable in config for #3

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Commits on Mar 4, 2024

• refactored and handled null cases

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Commits on Mar 7, 2024

• implemented statistics method enhanced with filtering for #3

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Commits on Mar 8, 2024

• refactored statistics methods

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Commits on Mar 11, 2024

• implemented call that retrieves all statistics with respect to schema

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• handled null case and added swagger documentation

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Commits on Mar 27, 2024

• implemented filtering for v2 ontology controller

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Commits on Mar 28, 2024

• changed the underlying ontology repository class to v2 for ontology statistics

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Commits on Apr 3, 2024

• implemented skos v2 api for EBISPOT#625 and #1

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Commits on Apr 10, 2024

• refactored with enum for skos relations

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Commits on Apr 11, 2024

• refactored the whole skos functionaliuty of v1 and v2 for EBISPOT#625 and #1

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• reverted the get first method of olssolrclient

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• Merge pull request #6 from TIBHannover/1-skos-api-support

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Commits on Apr 15, 2024

• added composite classification based filtering as well as string and collection based filtering options for #3

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Commits on Apr 16, 2024

• added filter option for licenses in #3

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• Merge branch 'EBISPOT:dev' into dev

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• added composite and license type filtering options to v1 api for #3

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Commits on Apr 17, 2024

• documented the filteroption parameter in all endpoints. Removed unnecessary parameters from allstatsbyschema endpoint.

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• Merge branch 'dev' into 3-ontology-filtering

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• Merge pull request #4 from TIBHannover/3-ontology-filtering

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Commits on Apr 22, 2024

• updated some docker files and scripts for #8

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Commits on Apr 25, 2024

• updated pom file and neo4j command script for #8

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Commits on May 24, 2024

• initialized a neo4j import module for #8

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Commits on May 27, 2024

• added a split function to extract json in csv and a routine for generating and executing relationship importer queries in #8

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Commits on May 28, 2024

• added ontology remove, ingest and authentication menu options to CSV Importer in #8

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• added commons cli dependency

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• changed condition for input files in #8

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• Merge pull request #12 from TIBHannover/8-neo4j-5

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Commits on May 29, 2024

• Added null check while parsing anootators

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Commits on Jun 3, 2024

• Merge pull request #15 from TIBHannover/11-several-ontologies-of-tib-fail-in-ingestion

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• handled exceptions and made transaction safe mode optional

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Commits on Jun 7, 2024

• narrowed down relationship creation query for #14

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Commits on Jun 12, 2024

• added logic to convert ontologies to RDF/XML format before parsing

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Commits on Jun 14, 2024

• handled several buggy cases in query creation for #14

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Commits on Jun 18, 2024

• added logic to convert ontologies to rdf format. Added "convertToRDF" as

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• owl & ttl files required for the conversion

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• added filter to the relation creation query for #14

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Commits on Jun 24, 2024

• Merge remote-tracking branch 'origin/dev' into

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Commits on Jul 18, 2024

• reimplemented csv2neo with commons-csv and opencsv parsers for #14

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Commits on Jul 24, 2024

• Merge pull request #18 from TIBHannover/11-several-ontologies-of-tib-fail-in-ingestion

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• trimmed leading and trailing blanks in parser and corrected missing blank in relation query for #14

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• made indexes conditional for #14

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• updated dataload documentation for #14

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• updated numbering on dataload documentation for #14

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• refactored query execution for #14

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Commits on Jul 25, 2024

• handled specific json syntax exception for #14

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• handled specific uncoercible value exception for #14

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• Merge pull request #16 from TIBHannover/14-improve-ingestion-performance

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• Merge branch 'dev' into 17-facet-data-is-missing-from-the-search-call-response-v1

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• Merge pull request #20 from TIBHannover/17-facet-data-is-missing-from-the-search-call-response-v1

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• added missing import

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Commits on Aug 6, 2024

• implemented alternative query generation approach with external query parameters on a template query for #22

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• refactored for #22

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• Merge pull request #23 from TIBHannover/22-special-character-problem-in-neo4j-queries

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Commits on Aug 7, 2024

• batch based solution is implemented for query based data creation in #25

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Commits on Aug 8, 2024

• multithreading is implemented for query based data creation in #25

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• Merge pull request #26 from TIBHannover/25-huge-ontologies-are-ingested-slowly

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Commits on Aug 9, 2024

• resolved conflicts for #27

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Commits on Aug 13, 2024

• implemented routine for array type query along with string type queries for #30#

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• Merge pull request #34 from TIBHannover/30-test

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• Merge pull request #35 from TIBHannover/sync2

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• added count queries for #29

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Commits on Aug 14, 2024

• revised command line modes and added metadata summary option to be used in consistency checks for #29

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Commits on Aug 15, 2024

• implemented configurable multiple attempts for each transaction in #29

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• Merge pull request #36 from TIBHannover/29-fault-tolerance

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Commits on Aug 22, 2024

• converted the rest statistics functionality from ols3 to ols4 for #10

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• removed the experimentall call that lists all rest calls for #10

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• removed unnecessary import

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• Merge pull request #40 from TIBHannover/10-rest-call-statistics-fix

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Commits on Aug 26, 2024

• formatted code as it is in EBI

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• resolved conflicts

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• Merge branch 'EBISPOT-dev' into formattingIssues

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• Merge pull request #42 from TIBHannover/formattingIssues

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Commits on Sep 1, 2024

• Merge branch 'EBISPOT:dev' into dev

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Commits on Sep 4, 2024

• Merge branch 'EBISPOT:dev' into dev

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Commits on Sep 5, 2024

• set convertToRDF option not to have argument for #46

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• assigned purl as the iri to ontologies with no iri for #48

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Commits on Sep 9, 2024

• Merge pull request #49 from TIBHannover/48-null-iri-in-rdf2json-output

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Commits on Sep 10, 2024

• made rdf2json idependent from execution directory and default input ontologies for #46

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Commits on Sep 11, 2024

• handled the rdf conversion exception when the ontology isn't available as a raw file but IRI for #46

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• Merge pull request #52 from TIBHannover/46-problems-in-robot-based-conversion-to-rdf

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• prevented double ontology assignment for #46

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• Merge pull request #53 from TIBHannover/46-problems-in-robot-based-conversion-to-rdf

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Commits on Sep 12, 2024

• used approved url protocol for ontology without a raw file for #46

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• Merge pull request #54 from TIBHannover/46-problems-in-robot-based-conversion-to-rdf

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Commits on Sep 13, 2024

• added an obo to owl conversion routine to rdf2json for #47

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• ensured structure of rdf ontologies and refactored for #47

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• implemented save functionality of original and refactored ontologies and refactored for #47

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• ensured always the converted rdf to be parsed and refactored the exceptions for #47

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• Merge pull request #55 from TIBHannover/47-ontology-parsing-errors-of-jena-libraries-in-rdf2json

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Commits on Sep 16, 2024

• refactored ontology conversion to detect source ontology type and do the conversion to rdf accordingly for #56

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• implemented automatic conversion to RDF option upon ontology parsing error for #56

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Commits on Sep 23, 2024

• stored converted imports in different files and handled exceptions for #56

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• Merge pull request #57 from TIBHannover/56-automatic-conversion-to-rdf

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• resolved conflicts

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• Merge branch 'EBISPOT-dev' into dev

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Commits on Sep 24, 2024

• made correction in displaycsv numbers for #44

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Commits on Sep 25, 2024

• provided more accurate data and put latccountdown to the final reachable place in runners for #44

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• displayed differences between planned and ingested for #44

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• fixed UnsupportedOperationException for #44

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Commits on Sep 27, 2024

• fixed plan and result calculation for #44

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• implemented multiple removal options for #44

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• Merge pull request #62 from TIBHannover/44-csv2neo-does-not-finalize-ocassionally

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Commits on Sep 28, 2024

• detected self importing IRIs that cause a loop for #63

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• simplified loop detection for #63

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• ensured importUrls list size in loop detection for #63

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• contains check instead of equality check in loop detection for #63

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Commits on Sep 29, 2024

• ensured RDFXML format in convertToRDF option for #63

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Commits on Sep 30, 2024

• generalized detection of import loops for #63

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• avoided null property value for #63

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Commits on Oct 1, 2024

• Merge pull request #64 from TIBHannover/63-more-parsing-errors-in-rdf2json

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Commits on Oct 2, 2024

• debug the cause of relation loop

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Commits on Oct 8, 2024

• splitted output files based on ontology for #60

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• closed all PrintWriters by the end of execution for #60

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Commits on Oct 9, 2024

• updated load into solr script based on the json2solr module outputs for #60

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Commits on Oct 11, 2024

• Merge pull request #66 from TIBHannover/60-split-json2solr-output-into-batches

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• ensure output csv directory is present

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• Merge pull request #67 from TIBHannover/60-split-json2solr-output-into-batches

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Commits on Oct 14, 2024

• Merge remote-tracking branch 'origin/dev' into 65-annotation-error-related-to-oneof-propertyvalues-1

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• added condition to remove self reference in relatedFrom property

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Commits on Oct 21, 2024

• merged with Dev

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• merged import from Dev

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Commits on Oct 22, 2024

• added null check for JSONElement in solr response

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Commits on Oct 23, 2024

• updated dockerized dataload based on csv2neo for #76

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Commits on Oct 24, 2024

• Merge pull request #79 from TIBHannover/77-search-filtering-based-on-type-individual-returns-500

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• added fix for "expanded" in search result. Fixes #78

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• added old neo4j load script as backup and disabled duplicate start of neo4j for #76

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• Merge pull request #81 from TIBHannover/78-search-field-expanded-is-missing-from-the-search-reult-for-ols4-v1-1

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• added JsonNull check in objectToString. Fixes #83

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• Merge pull request #84 from TIBHannover/83-ontology-list-returns-500-for-page-size-1000

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• initialized null jsonelements with default jsonobject and generalized exception for #85

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• Merge pull request #86 from TIBHannover/85-graph-endpont-returns-500

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• added logic for unconfigured preferredprefixes on #73

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• corrected logic for #73

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• corrected logic for #73

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• Merge pull request #87 from TIBHannover/73-ontology_prefix-is-sometimes-missing-from-the-select-result

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• added convertToRDF parameter to rdf2json in dockerized installation for #76

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• removed duplicate neo4j index step for #76

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• reverted changes in unused create neo4j indexes script for #76

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• made dockerized csv2neo configurable for #76

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• updated uri writing to json.

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• Merge pull request #82 from TIBHannover/76-dockerized-use-of-csv2neo-and-splitted-json2solr

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• configured max row size in filter queries for #72

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• Merge pull request #88 from TIBHannover/72-search-filter-based-on-collection-returns-nothing

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• Merge pull request #75 from TIBHannover/65-annotation-error-related-to-oneof-propertyvalues-1

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• updated neo4j and solr and made their download optional for #59

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• placed copy and build commands in order for #59

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• added code to retrieve FullJSTree with viewMode and siblings. Fixes #74

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• Merge pull request #89 from TIBHannover/59-update-solr-and-neo4j

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• ontology filters are converted to default COMPOSITE in v2 statistics for #91

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• computed last loaded time for subset of ontologies in #91

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• handled null and empty cases in composite filter for #91

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• added logic to handle property fullTree. Fixes #74

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• removed unnecessary parameter from allstatsbyschema endpoint for #91

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• Merge pull request #92 from TIBHannover/91-stats-endpoints

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• readded schema parameter on allstatsbyschema endpoint for #91

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• Merge pull request #94 from TIBHannover/91-stats-endpoints

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• used annotation extractor class for mapping in #96

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• Merge pull request #97 from TIBHannover/96-annotations-field-is-null-for-ontologies

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• added relatedfrom and equivalentclasses endpoint for #98

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• updated logic to get label for relationship. Fixes #99

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• Merge pull request #95 from TIBHannover/74-viewmode=all-does-not-work-in-ols4-v1

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• added a paginated term instances endpoint and made related from and equivalent class endpoints paginated for #98

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• added json endpoint for v1 term in #98

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• added superclasses endpoint for #98

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• removed unnecessary parameters from json endpoint for #98

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• Merge pull request #100 from TIBHannover/99-graph-endpoint-only-returns-subclassof-relations

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• Merge pull request #101 from TIBHannover/98-equivalent-class-and-related-from-endpoints

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• resolved conflicts

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• Merge branch 'EBISPOT-dev' into sync4 with unresolved contribution for RelatedAnnotator.java in commit EBISPOT@270b92b

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• merged with EBI latest changes and included fix for fibo

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• updated null check for fillerNode

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• Merge pull request #103 from TIBHannover/resolve-relatedAnnotator-conflicts-fiboIngestion

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• Merge pull request #102 from TIBHannover/sync4

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• updated mongo and neo4j versions for #104

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• updated mongo to latest for #104

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