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lib: rename params, #TASK-4791, #TASK-4641
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@jtarraga
jtarraga committed Aug 28, 2023
1 parent 39d17e7 commit be9c607
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Showing 23 changed files with 93 additions and 98 deletions.
6 changes: 3 additions & 3 deletions cellbase-client/src/main/java/org/opencb/cellbase/client/rest/ParentRestClient.java
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Expand Up @@ -447,8 +447,8 @@ private <U> CellBaseDataResponse<U> restCall(List<String> hosts, String version,
if (assembly != null && StringUtils.isEmpty(queryOptions.getString("assembly"))) {
callUrl = callUrl.queryParam("assembly", assembly);
}
if (dataRelease != null && StringUtils.isEmpty(queryOptions.getString(AbstractQuery.DATA_RELEASE))) {
callUrl = callUrl.queryParam(AbstractQuery.DATA_RELEASE, dataRelease);
if (dataRelease != null && StringUtils.isEmpty(queryOptions.getString(AbstractQuery.DATA_RELEASE_PARAM))) {
callUrl = callUrl.queryParam(AbstractQuery.DATA_RELEASE_PARAM, dataRelease);
}
if (apiKey != null && StringUtils.isEmpty(queryOptions.getString(AbstractQuery.API_KEY_PARAM))) {
callUrl = callUrl.queryParam(AbstractQuery.API_KEY_PARAM, apiKey);
Expand All @@ -458,7 +458,7 @@ private <U> CellBaseDataResponse<U> restCall(List<String> hosts, String version,
callUrl = callUrl.queryParam("assembly", assembly);
}
if (dataRelease != null) {
callUrl = callUrl.queryParam(AbstractQuery.DATA_RELEASE, dataRelease);
callUrl = callUrl.queryParam(AbstractQuery.DATA_RELEASE_PARAM, dataRelease);
}
if (apiKey != null) {
callUrl = callUrl.queryParam(AbstractQuery.API_KEY_PARAM, apiKey);
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4 changes: 4 additions & 0 deletions cellbase-core/src/main/java/org/opencb/cellbase/core/api/key/ApiKeyManager.java
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Expand Up @@ -64,6 +64,10 @@ public ApiKeyManager(String algorithm, Key secretKey) {
defaultApiKey = encode(payload);
}

public ApiKeyManager() {
jwtParser = Jwts.parserBuilder().build();
}

public String encode(ApiKeyJwtPayload payload) {
JwtBuilder jwtBuilder = Jwts.builder();

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19 changes: 4 additions & 15 deletions cellbase-core/src/main/java/org/opencb/cellbase/core/api/query/AbstractQuery.java
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Original file line number Diff line number Diff line change
Expand Up @@ -45,10 +45,10 @@ public abstract class AbstractQuery extends CellBaseQueryOptions {
// public static final int DEFAULT_LIMIT = 50;
public static final int DEFAULT_SKIP = 0;

public static final String DATA_RELEASE = "dataRelease";
public static final String DATA_RELEASE_PARAM = "dataRelease";
public static final String API_KEY_PARAM = "apiKey";
@Deprecated
public static final String TOKEN_PARAM = "token";
// @Deprecated
// public static final String TOKEN_PARAM = "token";

// list of fields in this class
private Map<String, Field> classFields;
Expand All @@ -59,7 +59,7 @@ public abstract class AbstractQuery extends CellBaseQueryOptions {
// key = camelCase name (transcriptsBiotype) to annotations
private Map<String, QueryParameter> annotations;

@QueryParameter(id = DATA_RELEASE)
@QueryParameter(id = DATA_RELEASE_PARAM)
private Integer dataRelease;

@QueryParameter(id = API_KEY_PARAM)
Expand Down Expand Up @@ -469,15 +469,4 @@ public AbstractQuery setApiKey(String apiKey) {
this.apiKey = apiKey;
return this;
}

@Deprecated
public String getToken() {
return apiKey;
}

@Deprecated
public AbstractQuery setToken(String token) {
this.apiKey = token;
return this;
}
}
17 changes: 9 additions & 8 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ClinicalMongoDBAdaptor.java
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Expand Up @@ -103,15 +103,15 @@ public CellBaseDataResult<Long> count(Query query) throws CellBaseException {
Bson bson = parseQuery(query);

MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE, 0));
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
return new CellBaseDataResult<>(mongoDBCollection.count(bson));
}

public CellBaseDataResult distinct(Query query, String field) throws CellBaseException {
Bson bson = parseQuery(query);

MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE, 0));
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
return new CellBaseDataResult<>(mongoDBCollection.distinct(field, bson));
}

Expand All @@ -128,7 +128,7 @@ public CellBaseDataResult<Variant> get(Query query, QueryOptions options) throws
logger.debug("queryOptions: {}", options.toJson());

MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE, 0));
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
return new CellBaseDataResult<>(mongoDBCollection.find(bson, null, Variant.class, parsedOptions));
}

Expand All @@ -140,7 +140,7 @@ public CellBaseDataResult nativeGet(Query query, QueryOptions options) throws Ce
logger.debug("queryOptions: {}", options.toJson());

MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE, 0));
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
return new CellBaseDataResult<>(mongoDBCollection.find(bson, parsedOptions));
}

Expand All @@ -152,7 +152,7 @@ public Iterator nativeIterator(Query query, QueryOptions options) throws CellBas
Bson bson = parseQuery(query);

MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease,
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE, 0));
(Integer) query.getOrDefault(AbstractQuery.DATA_RELEASE_PARAM, 0));
return mongoDBCollection.nativeQuery().find(bson, options);
}

Expand Down Expand Up @@ -223,6 +223,7 @@ public Bson parseQuery(ClinicalVariantQuery query) {
Object value = entry.getValue();
switch (dotNotationName) {
case "token":
case "apiKey":
case "dataRelease":
// Do nothing
break;
Expand Down Expand Up @@ -416,8 +417,8 @@ private CellBaseDataResult<Variant> getClinicalVariant(Variant variant, GenomeMa
}

// Add data release to query
if (!query.containsKey(AbstractQuery.DATA_RELEASE)) {
query.put(AbstractQuery.DATA_RELEASE, dataRelease);
if (!query.containsKey(AbstractQuery.DATA_RELEASE_PARAM)) {
query.put(AbstractQuery.DATA_RELEASE_PARAM, dataRelease);
}
}

Expand Down Expand Up @@ -471,7 +472,7 @@ public CellBaseIterator iterator(ClinicalVariantQuery query) throws CellBaseExce

@Override
public List<CellBaseDataResult<ClinicalVariant>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease,
String token) {
String apiKey) {
return null;
}

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9 changes: 5 additions & 4 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptor.java
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Expand Up @@ -82,13 +82,13 @@ public CellBaseDataResult<Gene> aggregationStats(GeneQuery query) {
}

@Override
public List<CellBaseDataResult<Gene>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String token)
public List<CellBaseDataResult<Gene>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String apiKey)
throws CellBaseException {
return info(ids, queryOptions, null, dataRelease, token);
return info(ids, queryOptions, null, dataRelease, apiKey);
}

public List<CellBaseDataResult<Gene>> info(List<String> ids, ProjectionQueryOptions queryOptions, String source, int dataRelease,
String token) throws CellBaseException {
String apiKey) throws CellBaseException {
List<CellBaseDataResult<Gene>> results = new ArrayList<>();
Bson projection = getProjection(queryOptions);
for (String id : ids) {
Expand Down Expand Up @@ -205,9 +205,10 @@ public Bson parseQuery(GeneQuery geneQuery) {
case "mirna":
createMirnaQuery(value, andBsonList);
break;
case "token":
case "apiKey":
case "source":
case "dataRelease":
case "token":
// do nothing
break;
default:
Expand Down
5 changes: 3 additions & 2 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GenomeMongoDBAdaptor.java
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Expand Up @@ -523,7 +523,7 @@ public CellBaseDataResult<String> distinct(GenomeQuery query) throws CellBaseExc
}

@Override
public List<CellBaseDataResult<Chromosome>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String token)
public List<CellBaseDataResult<Chromosome>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String apiKey)
throws CellBaseException {
List<CellBaseDataResult<Chromosome>> results = new ArrayList<>();
MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease, dataRelease);
Expand All @@ -548,8 +548,9 @@ public Bson parseQuery(GenomeQuery query) {
case "name":
createAndOrQuery(value, "chromosomes.name", QueryParam.Type.STRING, andBsonList);
break;
case "dataRelease":
case "token":
case "apiKey":
case "dataRelease":
// Do nothing
break;
default:
Expand Down
4 changes: 2 additions & 2 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/OntologyMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,8 +69,8 @@ public CellBaseIterator<OntologyTerm> iterator(OntologyQuery query) throws CellB
}

@Override
public List<CellBaseDataResult<OntologyTerm>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String token)
throws CellBaseException {
public List<CellBaseDataResult<OntologyTerm>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease,
String apiKey) throws CellBaseException {
List<CellBaseDataResult<OntologyTerm>> results = new ArrayList<>();
Bson projection = getProjection(queryOptions);
MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease, dataRelease);
Expand Down
5 changes: 3 additions & 2 deletions ...e-lib/src/main/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptor.java
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Expand Up @@ -69,7 +69,7 @@ public CellBaseDataResult<PharmaChemical> aggregationStats(PharmaChemicalQuery q

@Override
public List<CellBaseDataResult<PharmaChemical>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease,
String token) throws CellBaseException {
String apiKey) throws CellBaseException {
List<CellBaseDataResult<PharmaChemical>> results = new ArrayList<>();
Bson projection = getProjection(queryOptions);
for (String id : ids) {
Expand Down Expand Up @@ -114,8 +114,9 @@ public Bson parseQuery(PharmaChemicalQuery pharmaQuery) {
String dotNotationName = entry.getKey();
Object value = entry.getValue();
switch (dotNotationName) {
case "dataRelease":
case "token":
case "apiKey":
case "dataRelease":
// do nothing
break;
default:
Expand Down
5 changes: 3 additions & 2 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ProteinMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -300,7 +300,7 @@ public CellBaseIterator<Entry> iterator(ProteinQuery query) throws CellBaseExcep
}

@Override
public List<CellBaseDataResult<Entry>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String token)
public List<CellBaseDataResult<Entry>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String apiKey)
throws CellBaseException {
List<CellBaseDataResult<Entry>> results = new ArrayList<>();
MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease, dataRelease);
Expand Down Expand Up @@ -364,8 +364,9 @@ public Bson parseQuery(ProteinQuery proteinQuery) {
case "keyword":
createAndOrQuery(value, "keyword.value", QueryParam.Type.STRING, andBsonList);
break;
case "dataRelease":
case "token":
case "apiKey":
case "dataRelease":
// Do nothing
break;
default:
Expand Down
2 changes: 1 addition & 1 deletion cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/PublicationMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ public CellBaseIterator<PubmedArticle> iterator(PublicationQuery query) throws C

@Override
public List<CellBaseDataResult<PubmedArticle>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease,
String token) throws CellBaseException {
String apiKey) throws CellBaseException {
List<CellBaseDataResult<PubmedArticle>> results = new ArrayList<>();
Bson projection = getProjection(queryOptions);
MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease, dataRelease);
Expand Down
5 changes: 3 additions & 2 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/RegulationMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,9 @@ public Bson parseQuery(RegulationQuery query) {
case "region":
createRegionQuery(query, value, MongoDBCollectionConfiguration.REGULATORY_REGION_CHUNK_SIZE, andBsonList);
break;
case "dataRelease":
case "token":
case "apiKey":
case "dataRelease":
// Do nothing
break;
default:
Expand Down Expand Up @@ -104,7 +105,7 @@ public CellBaseIterator<RegulatoryFeature> iterator(RegulationQuery query) throw

@Override
public List<CellBaseDataResult<RegulatoryFeature>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease,
String token) {
String apiKey) {
return null;
}

Expand Down
2 changes: 1 addition & 1 deletion cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ReleaseMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -152,7 +152,7 @@ public CellBaseDataResult<String> distinct(AbstractQuery query) {
}

@Override
public List<CellBaseDataResult> info(List ids, ProjectionQueryOptions queryOptions, int dataRelease, String token) {
public List<CellBaseDataResult> info(List ids, ProjectionQueryOptions queryOptions, int dataRelease, String apiKey) {
return null;
}

Expand Down
5 changes: 3 additions & 2 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/RepeatsMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -67,8 +67,9 @@ public Bson parseQuery(RepeatsQuery query) {
case "region":
createRegionQuery(query, value, MongoDBCollectionConfiguration.REPEATS_CHUNK_SIZE, andBsonList);
break;
case "dataRelease":
case "token":
case "apiKey":
case "dataRelease":
// Do nothing
break;
default:
Expand Down Expand Up @@ -100,7 +101,7 @@ public CellBaseIterator iterator(RepeatsQuery query) throws CellBaseException {
}

@Override
public List<CellBaseDataResult<Repeat>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String token) {
public List<CellBaseDataResult<Repeat>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String apiKey) {
return null;
}

Expand Down
9 changes: 5 additions & 4 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/TranscriptMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -84,12 +84,12 @@ public CellBaseIterator<Transcript> iterator(TranscriptQuery query) throws CellB

@Override
public List<CellBaseDataResult<Transcript>> info(List<String> ids, ProjectionQueryOptions projectionQueryOptions, int dataRelease,
String token) throws CellBaseException {
return info(ids, projectionQueryOptions, null, dataRelease, token);
String apiKey) throws CellBaseException {
return info(ids, projectionQueryOptions, null, dataRelease, apiKey);
}

public List<CellBaseDataResult<Transcript>> info(List<String> ids, ProjectionQueryOptions projectionQueryOptions, String source,
int dataRelease, String token) throws CellBaseException {
int dataRelease, String apiKey) throws CellBaseException {
List<CellBaseDataResult<Transcript>> results = new ArrayList<>();
QueryOptions queryOptions = getInfoQueryOptions(projectionQueryOptions);
for (String id : ids) {
Expand Down Expand Up @@ -221,9 +221,10 @@ public Bson parseQuery(TranscriptQuery query) {
case "transcripts.supportLevel":
andBsonList.add(Filters.regex("transcripts.supportLevel", "^" + value));
break;
case "token":
case "source":
case "apiKey":
case "dataRelease":
case "token":
// Do nothing
break;
default:
Expand Down
4 changes: 2 additions & 2 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -252,7 +252,7 @@ public Bson parseQuery(VariantQuery query) {
case "region":
createRegionQuery(query, query.getRegions(), MongoDBCollectionConfiguration.VARIATION_CHUNK_SIZE, andBsonList);
break;
case VariantQuery.DATA_RELEASE:
case VariantQuery.DATA_RELEASE_PARAM:
case "svType":
// don't do anything, this is parsed later
break;
Expand Down Expand Up @@ -740,7 +740,7 @@ public CellBaseDataResult<String> distinct(VariantQuery query) {
}

@Override
public List<CellBaseDataResult<Variant>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String token)
public List<CellBaseDataResult<Variant>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String apiKey)
throws CellBaseException {
List<CellBaseDataResult<Variant>> results = new ArrayList<>();
MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease, dataRelease);
Expand Down
5 changes: 3 additions & 2 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/XRefMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ public CellBaseIterator<Xref> iterator(XrefQuery query) throws CellBaseException
}

@Override
public List<CellBaseDataResult<Xref>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String token)
public List<CellBaseDataResult<Xref>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String apiKey)
throws CellBaseException {
List<CellBaseDataResult<Xref>> results = new ArrayList<>();
for (String id : ids) {
Expand Down Expand Up @@ -153,8 +153,9 @@ public Bson parseQuery(XrefQuery query) {
case "dbname":
createAndOrQuery(value, "transcripts.xrefs.dbName", QueryParam.Type.STRING, andBsonList);
break;
case "dataRelease":
case "token":
case "apiKey":
case "dataRelease":
// Do nothing
break;
default:
Expand Down
6 changes: 1 addition & 5 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/AbstractManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,6 @@
import java.util.List;

import static org.opencb.cellbase.core.api.query.AbstractQuery.API_KEY_PARAM;
import static org.opencb.cellbase.core.api.query.AbstractQuery.TOKEN_PARAM;

public class AbstractManager implements AutoCloseable {

Expand Down Expand Up @@ -84,10 +83,7 @@ public AbstractManager(String species, String assembly, CellBaseConfiguration co
}

protected String getApiKey(QueryOptions queryOptions) {
if (queryOptions.containsKey(API_KEY_PARAM)) {
return queryOptions.getString(API_KEY_PARAM);
}
return queryOptions.getString(TOKEN_PARAM);
return queryOptions.getString(API_KEY_PARAM);
}

@Deprecated
Expand Down
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