-
Notifications
You must be signed in to change notification settings - Fork 21
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Fix curie issue oio tests api (#736)
* - Add logic for curies format in linker * - Add preferredPrefix in rdf2json - Change curie logic linker pass 1 * - Add preferredPrefix in rdf2json - Change curie logic linker pass 1 * - Fix isDefinedBy curie object * - Fix isDefinedBy curie object array * - Fix isDefinedBy value object * - Fix defining entity * - Update testcases * - Update testcases * - Update TestCases
- Loading branch information
1 parent
b95620e
commit 8078aad
Showing
2,853 changed files
with
39,305 additions
and
27,785 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| #!/usr/bin/env bash | ||
| diff -r -q -a -B -w --strip-trailing-cr --exclude=.gitkeep testcases_output/testcases testcases_expected_output/ > testcases_compare_result.log |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| { | ||
| "ontologies": [ | ||
| { | ||
| "id": "idocovid19", | ||
| "preferredPrefix": "IDO-COVID-19", | ||
| "title": "The COVID-19 Infectious Disease Ontology", | ||
| "uri": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19", | ||
| "description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.", | ||
| "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", | ||
| "mailing_list": "[email protected]", | ||
| "definition_property": [ | ||
| "http://purl.obolibrary.org/obo/IAO_0000115" | ||
| ], | ||
| "synonym_property": [ | ||
| "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" | ||
| ], | ||
| "hierarchical_property": [ | ||
| "http://purl.obolibrary.org/obo/BFO_0000050" | ||
| ], | ||
| "base_uri": [ | ||
| "http://purl.obolibrary.org/obo/IDO-COVID-19" | ||
| ], | ||
| "oboSlims": false, | ||
| "reasoner": "OWL2", | ||
| "ontology_purl": "https://gist.githubusercontent.com/haideriqbal/9b5245af626bd7687831c19c2c8076e8/raw/2c75495f31df0a379062bf12d3fab323eedbb7a9/idocovid19.owl" | ||
| }, | ||
| { | ||
| "id": "oio", | ||
| "ontology_purl": "https://gist.githubusercontent.com/haideriqbal/4a2b1a9aa81d9fa26cae81e0b0b7730b/raw/527665128b9be9d7d6133f9a796379600151c737/oboInOwl.owl", | ||
| "base_uri": ["http://www.geneontology.org/formats/oboInOwl#"] | ||
| } | ||
| ] | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| #!/usr/bin/env bash | ||
|
|
||
| if [ $# == 0 ]; then | ||
| echo "Usage: $0 <rel_json_config_url> <rel_output_dir>" | ||
| echo "If <rel_json_config_url> is a file it will read and load this single configuration." | ||
| echo "If <rel_json_config_url> as a directory, it will read and load all json configuration in the directory and | ||
| subdirectories." | ||
| exit 1 | ||
| fi | ||
|
|
||
| config_url=$1 | ||
| out_dir=$2 | ||
|
|
||
| # Create or clean output directory | ||
| if [ -d "$out_dir" ]; then | ||
| echo "$out_dir already exists and will now be cleaned." | ||
| rm -Rf $out_dir/* | ||
| else | ||
| echo "$out_dir does not exist and will now be created." | ||
| mkdir "$out_dir" | ||
| fi | ||
|
|
||
| function process_config { | ||
| echo "process_config param1="$1 | ||
| echo "process_config param2="$2 | ||
|
|
||
| local config_url=$1 | ||
| local out_dir=$2 | ||
|
|
||
|
|
||
| if [ -d "$config_url" ]; then | ||
| echo "$config_url is a directory. Processing config files in $config_url" | ||
| local basename=$(basename $config_url) | ||
| echo "basename for config_url="$basename | ||
| local out_dir_basename=$out_dir/$basename | ||
| mkdir $out_dir_basename | ||
| for filename in $config_url/*.json; do | ||
| echo "filename="$filename | ||
| process_config $filename $out_dir_basename | ||
| done | ||
| for dir in $config_url/*/; do | ||
| process_config $dir $out_dir_basename | ||
| done | ||
| elif [ -f "$config_url" ]; then | ||
| echo "$config_url is a file. Processing single config file." | ||
| local basename=$(basename $config_url .json) | ||
|
|
||
| local relative_out_dir=$out_dir/$basename | ||
| mkdir $relative_out_dir | ||
|
|
||
| local absolute_out_dir=$(realpath -q $relative_out_dir) | ||
| echo "absolute_out_dir="$absolute_out_dir | ||
|
|
||
| $OLS4_HOME/dataload/create_datafiles.sh $config_url $absolute_out_dir --noDates | ||
|
|
||
| $OLS4_HOME/dev-testing/load_test_into_solr.sh $absolute_out_dir | ||
| else | ||
| echo "$config_url does not exist." | ||
| fi | ||
| } | ||
|
|
||
| $OLS4_HOME/dev-testing/clean-neo4j.sh | ||
| $OLS4_HOME/dev-testing/clean-solr.sh | ||
| $OLS4_HOME/dev-testing/start-solr.sh | ||
|
|
||
| process_config $config_url $out_dir | ||
|
|
||
| $OLS4_HOME/dev-testing/load_test_into_neo4j.sh $out_dir | ||
| $OLS4_HOME/dev-testing/start-neo4j.sh |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.