server: remove token from WS servers, #TASK-4791, #TASK-4641

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/CellBaseCliOptionsParser.java

@@ -74,8 +74,8 @@ public class VariantAnnotationCommandOptions {
         @Parameter(names = {"--data-release"}, description = "Data release. To use the default data relese, please, set this parameter to 0", required = false, arity = 1)
         public int dataRelease = 0;
 
-        @Parameter(names = {"--token"}, description = "Data token to get access to licensed/restricted data sources such as COSMIC or HGMD", required = false, arity = 1)
-        public String token;
+        @Parameter(names = {"--api-key"}, description = "API key to get access to licensed/restricted data sources such as COSMIC or HGMD", required = false, arity = 1)
+        public String apiKey;
 
         @Parameter(names = {"-l", "--local"}, description = "Database credentials for local annotation are read from configuration.json file", required = false, arity = 0)
         public boolean local;

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java

@@ -204,7 +204,7 @@ private boolean runAnnotation() throws Exception {
                     CellBaseManagerFactory cellBaseManagerFactory = new CellBaseManagerFactory(configuration);
                     VariantAnnotationCalculator variantAnnotationCalculator =
                             new VariantAnnotationCalculator(this.species, this.assembly, variantAnnotationCommandOptions.dataRelease,
-                                    variantAnnotationCommandOptions.token, cellBaseManagerFactory);
+                                    variantAnnotationCommandOptions.apiKey, cellBaseManagerFactory);
                     List<CellBaseDataResult<VariantAnnotation>> annotationByVariantList =
                             variantAnnotationCalculator.getAnnotationByVariantList(variants, serverQueryOptions);
 
@@ -480,7 +480,7 @@ private VariantAnnotator createCellBaseAnnotator() throws CellBaseException {
             // equals the number of returned annotations
             CellBaseManagerFactory cellBaseManagerFactory = new CellBaseManagerFactory(configuration);
             return new CellBaseLocalVariantAnnotator(new VariantAnnotationCalculator(species, assembly,
-                    variantAnnotationCommandOptions.dataRelease, variantAnnotationCommandOptions.token, cellBaseManagerFactory),
+                    variantAnnotationCommandOptions.dataRelease, variantAnnotationCommandOptions.apiKey, cellBaseManagerFactory),
                     serverQueryOptions);
         } else {
             try {

cellbase-client/src/main/java/org/opencb/cellbase/client/rest/CellBaseClient.java

@@ -32,8 +32,6 @@ public class CellBaseClient {
     private final String assembly;
     private final String dataRelease;
     private final String apiKey;
-    @Deprecated
-    private final String token;
     private ClientConfiguration clientConfiguration;
 
     private final Map<String, ParentRestClient> clients;
@@ -62,7 +60,6 @@ public CellBaseClient(String species, String assembly, String dataRelease, Strin
         this.species = species;
         this.assembly = StringUtils.isEmpty(assembly) ? null : assembly;
         this.dataRelease = StringUtils.isEmpty(dataRelease) ? null : dataRelease;
-        this.token = apiKey;
         this.apiKey = apiKey;
         if (clientConfiguration != null && clientConfiguration.getRest() != null
                 && clientConfiguration.getRest().getHosts() != null
@@ -151,11 +148,6 @@ public String getApiKey() {
         return apiKey;
     }
 
-    @Deprecated
-    public String getToken() {
-        return apiKey;
-    }
-
     public ClientConfiguration getClientConfiguration() {
         return clientConfiguration;
     }

cellbase-client/src/main/java/org/opencb/cellbase/client/rest/ParentRestClient.java

@@ -449,7 +449,7 @@ private <U> CellBaseDataResponse<U> restCall(List<String> hosts, String version,
         String apiKeyParam = null;
         if (VersionUtils.isMinVersion("v5.7", configuration.getVersion())) {
             apiKeyParam = API_KEY_PARAM;
-        } else if (VersionUtils.isMinVersion("v5.3", configuration.getVersion())) {
+        } else if (VersionUtils.isMinVersion("v5.4", configuration.getVersion())) {
             apiKeyParam = TOKEN_PARAM;
         }
 

cellbase-core/src/main/java/org/opencb/cellbase/core/ParamConstants.java

@@ -119,7 +119,7 @@ public Type type() {
     public static final String API_KEY_PARAM = "apiKey";
     public static final String API_KEY_DESCRIPTION = "API key to allow access to licensed/restricted data sources such as"
             + " Cosmic or HGMD";
-    // For backward-compatibility, but it should be deprecated
+    // For backward-compatibility, from v5.7 "token" is not used anymore
     public static final String TOKEN_PARAM = "token";
 
 

cellbase-core/src/main/java/org/opencb/cellbase/core/api/query/CellBaseQueryOptions.java

@@ -46,7 +46,7 @@ public enum Order {
     public CellBaseQueryOptions() {
     }
 
-    public CellBaseQueryOptions(Integer limit, Integer skip, Boolean count, String sort, Order order, String facet, String token) {
+    public CellBaseQueryOptions(Integer limit, Integer skip, Boolean count, String sort, Order order, String facet) {
         this.limit = limit;
         this.skip = skip;
         this.count = count;
@@ -55,7 +55,7 @@ public CellBaseQueryOptions(Integer limit, Integer skip, Boolean count, String s
         this.facet = facet;
     }
 
-    public CellBaseQueryOptions(Integer limit, Integer skip, Boolean count, String sort, Order order, String facet, String token,
+    public CellBaseQueryOptions(Integer limit, Integer skip, Boolean count, String sort, Order order, String facet,
                                 List<String> includes, List<String> excludes) {
         super(includes, excludes);
 

cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/CellBaseCoreDBAdaptor.java

@@ -97,6 +97,6 @@ default CellBaseDataResult<Long> count(Q query) throws CellBaseException {
 
     CellBaseDataResult<String> distinct(Q query) throws CellBaseException;
 
-    List<CellBaseDataResult<T>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String token)
+    List<CellBaseDataResult<T>> info(List<String> ids, ProjectionQueryOptions queryOptions, int dataRelease, String apiKey)
             throws CellBaseException;
 }

cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/ClinicalManager.java

@@ -70,7 +70,7 @@ public CellBaseDataResult<Variant> search(ClinicalVariantQuery query) throws Que
 
         Set<String> validSources = apiKeyManager.getValidSources(query.getApiKey(), ApiKeyLicensedDataUtils.UNLICENSED_CLINICAL_DATA);
 
-        // Check if is necessary to use the token licensed variant iterator
+        // Check if is necessary to use the API key licensed variant iterator
         if (ApiKeyLicensedDataUtils.needFiltering(validSources, ApiKeyLicensedDataUtils.LICENSED_CLINICAL_DATA)) {
             return ApiKeyLicensedDataUtils.filterDataSources(results, validSources);
         } else {
@@ -89,13 +89,13 @@ public List<CellBaseDataResult<Variant>> search(List<ClinicalVariantQuery> queri
     }
 
     @Override
-    public List<CellBaseDataResult<Variant>> info(List<String> ids, CellBaseQueryOptions queryOptions, int dataRelease, String token)
+    public List<CellBaseDataResult<Variant>> info(List<String> ids, CellBaseQueryOptions queryOptions, int dataRelease, String apiKey)
             throws CellBaseException {
-        List<CellBaseDataResult<Variant>> results = getDBAdaptor().info(ids, queryOptions, dataRelease, token);
+        List<CellBaseDataResult<Variant>> results = getDBAdaptor().info(ids, queryOptions, dataRelease, apiKey);
 
-        Set<String> validSources = apiKeyManager.getValidSources(token, ApiKeyLicensedDataUtils.UNLICENSED_CLINICAL_DATA);
+        Set<String> validSources = apiKeyManager.getValidSources(apiKey, ApiKeyLicensedDataUtils.UNLICENSED_CLINICAL_DATA);
 
-        // Check if is necessary to use the token licensed variant iterator
+        // Check if is necessary to use the API key licensed variant iterator
         if (ApiKeyLicensedDataUtils.needFiltering(validSources, ApiKeyLicensedDataUtils.LICENSED_CLINICAL_DATA)) {
             return ApiKeyLicensedDataUtils.filterDataSources(results, validSources);
         } else {
@@ -107,7 +107,7 @@ public List<CellBaseDataResult<Variant>> info(List<String> ids, CellBaseQueryOpt
     public CellBaseIterator<Variant> iterator(ClinicalVariantQuery query) throws CellBaseException {
         Set<String> validSources = apiKeyManager.getValidSources(query.getApiKey(), ApiKeyLicensedDataUtils.UNLICENSED_CLINICAL_DATA);
 
-        // Check if is necessary to use the token licensed variant iterator
+        // Check if is necessary to use the API key licensed variant iterator
         if (ApiKeyLicensedDataUtils.needFiltering(validSources, ApiKeyLicensedDataUtils.LICENSED_CLINICAL_DATA)) {
             return new ApiKeyFilteredVariantIterator(getDBAdaptor().iterator(query), validSources);
         } else {
@@ -129,7 +129,7 @@ public CellBaseDataResult<Variant> search(Query query, QueryOptions queryOptions
             includes = Arrays.asList(queryOptions.getString(EXCLUDE).split(","));
         }
 
-        // Check if is necessary to use the token licensed variant iterator
+        // Check if is necessary to use the API key licensed variant iterator
         if (ApiKeyLicensedDataUtils.needFiltering(validSources, ApiKeyLicensedDataUtils.LICENSED_CLINICAL_DATA)) {
             return ApiKeyLicensedDataUtils.filterDataSources(result, validSources);
         } else {

cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/GeneManager.java

@@ -59,8 +59,8 @@ public CellBaseCoreDBAdaptor<GeneQuery, Gene> getDBAdaptor() {
     }
 
     public List<CellBaseDataResult<Gene>> info(List<String> ids, ProjectionQueryOptions query, String source, int dataRelease,
-                                               String token) throws CellBaseException {
-        return geneDBAdaptor.info(ids, query, source, dataRelease, token);
+                                               String apiKey) throws CellBaseException {
+        return geneDBAdaptor.info(ids, query, source, dataRelease, apiKey);
     }
 
     public CellBaseDataResult<GenomeSequenceFeature> getSequence(GeneQuery query) throws CellBaseException {

cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/PharmacogenomicsManager.java

@@ -51,7 +51,7 @@ public CellBaseCoreDBAdaptor<PharmaChemicalQuery, PharmaChemical> getDBAdaptor()
     }
 
     public List<CellBaseDataResult<PharmaChemical>> info(List<String> ids, ProjectionQueryOptions query, int dataRelease,
-                                               String token) throws CellBaseException {
-        return pharmacogenomicsDBAdaptor.info(ids, query, dataRelease, token);
+                                               String apiKey) throws CellBaseException {
+        return pharmacogenomicsDBAdaptor.info(ids, query, dataRelease, apiKey);
     }
 }

cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/TranscriptManager.java

@@ -55,8 +55,8 @@ public CellBaseCoreDBAdaptor<TranscriptQuery, Transcript> getDBAdaptor() {
     }
 
     public List<CellBaseDataResult<Transcript>> info(List<String> ids, ProjectionQueryOptions query, String source, int dataRelease,
-                                                     String token) throws CellBaseException {
-        return transcriptDBAdaptor.info(ids, query, source, dataRelease, token);
+                                                     String apiKey) throws CellBaseException {
+        return transcriptDBAdaptor.info(ids, query, source, dataRelease, apiKey);
     }
 
 

cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/VariantManager.java

@@ -151,7 +151,7 @@ public List<CellBaseDataResult<VariantAnnotation>> getAnnotationByVariant(QueryO
                                                                               Boolean checkAminoAcidChange,
                                                                               String consequenceTypeSource,
                                                                               int dataRelease,
-                                                                              String token)
+                                                                              String apiKey)
             throws ExecutionException, InterruptedException, CellBaseException, QueryException, IllegalAccessException {
         List<Variant> variantList = parseVariants(variants);
         logger.debug("queryOptions: " + queryOptions);
@@ -194,7 +194,7 @@ public List<CellBaseDataResult<VariantAnnotation>> getAnnotationByVariant(QueryO
         }
 
         VariantAnnotationCalculator variantAnnotationCalculator = new VariantAnnotationCalculator(species, assembly,
-                dataRelease, token, cellbaseManagerFactory);
+                dataRelease, apiKey, cellbaseManagerFactory);
         List<CellBaseDataResult<VariantAnnotation>> queryResults = variantAnnotationCalculator.getAnnotationByVariantList(variantList,
                 queryOptions);
         return queryResults;
@@ -310,8 +310,8 @@ public List<CellBaseDataResult<Variant>> getPopulationFrequencyByVariant(List<Va
         return variantDBAdaptor.getPopulationFrequencyByVariant(variants, queryOptions, dataRelease);
     }
 
-    public CellBaseDataResult<SpliceScore> getSpliceScoreVariant(Variant variant, String token, int dataRelease) throws CellBaseException {
-        Set<String> validSources = apiKeyManager.getValidSources(token, ApiKeyLicensedDataUtils.UNLICENSED_SPLICE_SCORES_DATA);
+    public CellBaseDataResult<SpliceScore> getSpliceScoreVariant(Variant variant, String apiKey, int dataRelease) throws CellBaseException {
+        Set<String> validSources = apiKeyManager.getValidSources(apiKey, ApiKeyLicensedDataUtils.UNLICENSED_SPLICE_SCORES_DATA);
 
         CellBaseDataResult<SpliceScore> result = spliceDBAdaptor.getScores(variant.getChromosome(), variant.getStart(),
                 variant.getReference(), variant.getAlternate(), dataRelease);
@@ -323,9 +323,9 @@ public CellBaseDataResult<SpliceScore> getSpliceScoreVariant(Variant variant, St
         }
     }
 
-    public List<CellBaseDataResult<SpliceScore>> getSpliceScoreVariant(List<Variant> variants, String token, int dataRelease)
+    public List<CellBaseDataResult<SpliceScore>> getSpliceScoreVariant(List<Variant> variants, String apiKey, int dataRelease)
             throws CellBaseException {
-        Set<String> validSources = apiKeyManager.getValidSources(token, ApiKeyLicensedDataUtils.UNLICENSED_SPLICE_SCORES_DATA);
+        Set<String> validSources = apiKeyManager.getValidSources(apiKey, ApiKeyLicensedDataUtils.UNLICENSED_SPLICE_SCORES_DATA);
 
         List<CellBaseDataResult<SpliceScore>> cellBaseDataResults = new ArrayList<>(variants.size());
         if (ApiKeyLicensedDataUtils.needFiltering(validSources, ApiKeyLicensedDataUtils.LICENSED_SPLICE_SCORES_DATA)) {

cellbase-lib/src/test/java/org/opencb/cellbase/lib/GenericMongoDBAdaptorTest.java

@@ -51,7 +51,7 @@ public class GenericMongoDBAdaptorTest {
 
     private DataReleaseManager dataReleaseManager;
     protected int dataRelease;
-    protected String token;
+    protected String apiKey;
 
     protected String cellBaseName;
 
@@ -68,6 +68,7 @@ public class GenericMongoDBAdaptorTest {
     protected CellBaseConfiguration cellBaseConfiguration;
     protected CellBaseManagerFactory cellBaseManagerFactory;
 
+    // API keys for testing
     protected String UNIVERSAL_ACCES_API_KEY = "eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwNywiaGdtZCI6OTIyMzM3MjAzNjg1NDc3NTgwNywic3BsaWNlYWkiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJtYXhOdW1RdWVyaWVzIjoxMDAwMDAwMCwidmVyc2lvbiI6IjEuMCIsInN1YiI6IlRFU1QiLCJpYXQiOjE2ODk4MzczODZ9.ALdEFGmVuatoUEj-K3HAHt2KlqeNm2Fv7m-DODhz0LU";
     protected String HGMD_ACCESS_API_KEY = "eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImhnbWQiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJtYXhOdW1RdWVyaWVzIjoxMDAwMDAwMCwidmVyc2lvbiI6IjEuMCIsInN1YiI6IlRFU1QiLCJpYXQiOjE2ODk4Mzc0MjZ9.zqEU-WhIzhbpbmwGWnAjgmgfOtBbP5nXq2uqX5wV5uY";
     protected String COSMIC_ACCESS_API_KEY = "eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwN30sIm1heE51bVF1ZXJpZXMiOjEwMDAwMDAwLCJ2ZXJzaW9uIjoiMS4wIiwic3ViIjoiVEVTVCIsImlhdCI6MTY4OTgzNzQ2MX0.K6SEGvScpJ2a99SLPaUi4KRJ8FJ_LNPduoHW_LSSNGU";
@@ -77,8 +78,6 @@ public class GenericMongoDBAdaptorTest {
     protected String COSMIC_SPLICEAI_ACCESS_API_KEY = "eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwNywic3BsaWNlYWkiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJtYXhOdW1RdWVyaWVzIjoxMDAwMDAwMCwidmVyc2lvbiI6IjEuMCIsInN1YiI6IlRFU1QiLCJpYXQiOjE2ODk4Mzc1MzZ9.CkXvpNg0NWAXL3N06R2gCqe0kF4ptBk0MPvaAdDSEpQ";
 
     protected LoadRunner loadRunner = null;
-//    protected MongoDBAdaptorFactory dbAdaptorFactory;
-
 
     protected Logger logger = LoggerFactory.getLogger(this.getClass());
 
@@ -87,11 +86,6 @@ public GenericMongoDBAdaptorTest() {
             cellBaseConfiguration = CellBaseConfiguration.load(
                     GenericMongoDBAdaptorTest.class.getClassLoader().getResourceAsStream("configuration.test.yaml"),
                     CellBaseConfiguration.ConfigurationFileFormat.YAML);
-//            cellBaseConfiguration.getDatabases().getMongodb().setHost("localhost:27037");
-//            cellBaseConfiguration.getDatabases().getMongodb().setUser("cellbase");
-//            cellBaseConfiguration.getDatabases().getMongodb().setPassword("cellbase");
-//            cellBaseConfiguration.getDatabases().getMongodb().getOptions().put("authenticationDatabase", "admin");
-//            cellBaseConfiguration.getDatabases().getMongodb().getOptions().put("authenticationMechanism", "SCRAM-SHA-256");
 
             String[] versionSplit = GitRepositoryState.get().getBuildVersion().split("\\.");
             cellBaseConfiguration.setVersion("v" + versionSplit[0] + "." + versionSplit[1]);