diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java index ada8cd6e3..10cb89a2a 100644 --- a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java +++ b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java @@ -81,6 +81,8 @@ public void search( @RequestParam(value = "lang", defaultValue = "en") String lang, HttpServletResponse response ) throws IOException, SolrServerException { + System.out.println("fieldList 1 = " + fieldList); + System.out.println("type = " + types); final SolrQuery solrQuery = new SolrQuery(); // 1 @@ -206,15 +208,15 @@ public void search( * Fix: End */ solrQuery.add("wt", format); + System.out.println("fieldList 2 = " + fieldList); - - System.out.println(solrQuery.jsonStr()); + System.out.println("solrQuery=" + solrQuery.jsonStr()); QueryResponse qr = solrClient.dispatchSearch(solrQuery, "ols4_entities"); List docs = new ArrayList<>(); for(SolrDocument res : qr.getResults()) { - + System.out.println("res = " + res.toString()); String _json = (String)res.get("_json"); if(_json == null) { throw new RuntimeException("_json was null"); @@ -256,7 +258,9 @@ public void search( if (fieldList.contains("obo_id")) outDoc.put("obo_id", JsonHelper.getString(json, "curie")); if (fieldList.contains("is_defining_ontology")) outDoc.put("is_defining_ontology", JsonHelper.getString(json, "isDefiningOntology") != null && JsonHelper.getString(json, "isDefiningOntology").equals("true")); - if (fieldList.contains("type")) outDoc.put("type", "class"); + if (fieldList.contains("type")) { + outDoc.put("type", JsonHelper.getType(json, "type")); + } if (fieldList.contains("synonym")) outDoc.put("synonym", JsonHelper.getStrings(json, "synonym")); if (fieldList.contains("ontology_prefix")) outDoc.put("ontology_prefix", JsonHelper.getString(json, "ontologyPreferredPrefix")); if (fieldList.contains("subset")) outDoc.put("subset", JsonHelper.getStrings(json, "http://www.geneontology.org/formats/oboInOwl#inSubset")); diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java index 208629ac9..38a4a34e7 100644 --- a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java +++ b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java @@ -161,7 +161,9 @@ public void select( if (fieldList.contains("obo_id")) outDoc.put("obo_id", JsonHelper.getString(json, "curie")); if (fieldList.contains("is_defining_ontology")) outDoc.put("is_defining_ontology", JsonHelper.getString(json, "isDefiningOntology") != null && JsonHelper.getString(json, "isDefiningOntology").equals("true")); - if (fieldList.contains("type")) outDoc.put("type", "class"); + if (fieldList.contains("type")) { + outDoc.put("type", JsonHelper.getType(json, "type")); + } if (fieldList.contains("synonym")) outDoc.put("synonym", JsonHelper.getStrings(json, "synonym")); if (fieldList.contains("ontology_prefix")) outDoc.put("ontology_prefix", JsonHelper.getString(json, "ontologyPreferredPrefix")); diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/JsonHelper.java b/backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/JsonHelper.java index 3ee0d50af..3d729eafd 100644 --- a/backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/JsonHelper.java +++ b/backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/JsonHelper.java @@ -64,6 +64,18 @@ public static List getStrings(JsonObject json, String predicate) { return getValues(json, predicate).stream().map(JsonHelper::objectToString).collect(Collectors.toList()); } + /** + * This methi + * @param json + * @param predicate + * @return + */ + public static String getType(JsonObject json, String predicate){ + List types = getValues(json, predicate).stream().map(JsonHelper::objectToString).collect(Collectors.toList()); + types.remove("entity"); + return types.get(0); + } + public static List getObjects(JsonObject json, String predicate) { return getValues(json, predicate).stream().map(v -> v.getAsJsonObject()).collect(Collectors.toList()); } diff --git a/dataload/configs/gaz.json b/dataload/configs/gaz.json new file mode 100644 index 000000000..e53f6abc4 --- /dev/null +++ b/dataload/configs/gaz.json @@ -0,0 +1,59 @@ +{ + "ontologies": [ + { + "activity_status": "inactive", + "build": { + "method": "archive", + "path": "archive", + "source_url": "http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/*zip*/archive.zip" + }, + "contact": { + "email": "lschriml@som.umaryland.edu", + "github": "lschriml", + "label": "Lynn Schriml", + "orcid": "0000-0001-8910-9851" + }, + "description": "A gazetteer constructed on ontological principles", + "homepage": "http://environmentontology.github.io/gaz/", + "id": "gaz", + "preferredPrefix": "GAZ", + "layout": "ontology_detail", + "license": { + "label": "CC0 1.0", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png", + "url": "https://creativecommons.org/publicdomain/zero/1.0/" + }, + "mailing_list": "https://groups.google.com/forum/#!forum/obo-gazetteer", + "ontology_purl": "http://purl.obolibrary.org/obo/gaz.owl", + "products": [ + { + "id": "gaz.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/gaz.owl" + }, + { + "id": "gaz.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/gaz.obo" + } + ], + "repository": "https://github.com/EnvironmentOntology/gaz", + "title": "Gazetteer", + "tracker": "https://github.com/EnvironmentOntology/gaz/issues", + "hierarchical_property":[ + "http://purl.obolibrary.org/obo/BFO_0000050", + "http://purl.obolibrary.org/obo/RO_0001025", + "http://purl.obolibrary.org/obo/RO_0002151", + "http://purl.obolibrary.org/obo/RO_0002376", + "http://purl.obolibrary.org/obo/RO_0002377", + "http://purl.obolibrary.org/obo/UBREL_0000001", + "http://purl.obolibrary.org/obo/RO_0002219", + "http://purl.obolibrary.org/obo/RO_0002379", + "http://purl.obolibrary.org/obo/RO_0002378", + "http://purl.obolibrary.org/obo/RO_0002090", + "http://purl.obolibrary.org/obo/TEMP#proper_partof", + "http://purl.obolibrary.org/obo/TEMP#overlapped_by", + "http://purl.obolibrary.org/obo/RO_0002131", + "http://purl.obolibrary.org/obo/RO_0002220" + ] + } + ] +}