core: rename token to apiKey, #TASK-4791, #TASK-4641

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java

@@ -18,7 +18,7 @@
 
 import com.beust.jcommander.*;
 import org.opencb.cellbase.app.cli.CliOptionsParser;
-import org.opencb.cellbase.core.token.TokenQuota;
+import org.opencb.cellbase.core.api.key.ApiKeyQuota;
 
 import java.util.HashMap;
 import java.util.List;
@@ -35,7 +35,7 @@ public class AdminCliOptionsParser extends CliOptionsParser {
     private DownloadCommandOptions downloadCommandOptions;
     private BuildCommandOptions buildCommandOptions;
     private DataReleaseCommandOptions dataReleaseCommandOptions;
-    private DataTokenCommandOptions dataTokenCommandOptions;
+    private ApiKeyCommandOptions apiKeyCommandOptions;
     private LoadCommandOptions loadCommandOptions;
     private ExportCommandOptions exportCommandOptions;
     private CustomiseCommandOptions customiseCommandOptions;
@@ -52,7 +52,7 @@ public AdminCliOptionsParser() {
         downloadCommandOptions = new DownloadCommandOptions();
         buildCommandOptions = new BuildCommandOptions();
         dataReleaseCommandOptions = new DataReleaseCommandOptions();
-        dataTokenCommandOptions = new DataTokenCommandOptions();
+        apiKeyCommandOptions = new ApiKeyCommandOptions();
         loadCommandOptions = new LoadCommandOptions();
         exportCommandOptions = new ExportCommandOptions();
         customiseCommandOptions = new CustomiseCommandOptions();
@@ -64,7 +64,7 @@ public AdminCliOptionsParser() {
         jCommander.addCommand("download", downloadCommandOptions);
         jCommander.addCommand("build", buildCommandOptions);
         jCommander.addCommand("data-release", dataReleaseCommandOptions);
-        jCommander.addCommand("data-token", dataTokenCommandOptions);
+        jCommander.addCommand("api-key", apiKeyCommandOptions);
         jCommander.addCommand("load", loadCommandOptions);
         jCommander.addCommand("export", exportCommandOptions);
         jCommander.addCommand("customise", customiseCommandOptions);
@@ -153,31 +153,31 @@ public class DataReleaseCommandOptions {
         public String versions;
     }
 
-    @Parameters(commandNames = {"data-token"}, commandDescription = "Manage data access tokens in order to access to restricted/licensed data sources")
-    public class DataTokenCommandOptions {
+    @Parameters(commandNames = {"api-key"}, commandDescription = "Manage API keys in order to access to restricted/licensed data sources and set quota")
+    public class ApiKeyCommandOptions {
 
         @ParametersDelegate
         public CommonCommandOptions commonOptions = commonCommandOptions;
 
-        @Parameter(names = {"--create-token"}, description = "Create a data access token with the data sources indicated separated by"
+        @Parameter(names = {"--create-api-key"}, description = "Create an API key with the licensed data sources indicated separated by"
                 + " commas and optionally the expiration date: source[:dd/mm/yyyy]. e.g.: cosmic:31/01/2025,hgmd. In addition the"
                 + " 'organization' has to be specified", arity = 1)
         public String createWithDataSources;
 
-        @Parameter(names = {"--expiration"}, description = "Use this parameter in conjunction with --create-token to specify the"
+        @Parameter(names = {"--expiration"}, description = "Use this parameter in conjunction with --create-api-key to specify the"
                 + " expiration date in format dd/mm/yyyy, e.g.: 03/09/2030", arity = 1)
         public String expiration;
 
-        @Parameter(names = {"--organization"}, description = "Use this parameter in conjunction with --create-token to specify the"
+        @Parameter(names = {"--organization"}, description = "Use this parameter in conjunction with --create-api-key to specify the"
                 + " organization", arity = 1)
         public String organization;
 
-        @Parameter(names = {"--max-num-queries"}, description = "Use this parameter in conjunction with --create-token to specify the"
+        @Parameter(names = {"--max-num-queries"}, description = "Use this parameter in conjunction with --create-api-key to specify the"
                 + " maximum number of queries per month", arity = 1)
-        public long maxNumQueries = TokenQuota.DEFAULT_MAX_NUM_QUERIES;
+        public long maxNumQueries = ApiKeyQuota.DEFAULT_MAX_NUM_QUERIES;
 
-        @Parameter(names = {"--view-token"}, description = "Token to view", arity = 1)
-        public String tokenToView;
+        @Parameter(names = {"--view-api-key"}, description = "API key to view", arity = 1)
+        public String apiKeyToView;
     }
 
     @Parameters(commandNames = {"load"}, commandDescription = "Load the built data models into the database")
@@ -245,8 +245,8 @@ public class ExportCommandOptions {
         @Parameter(names = {"--data-release"}, description = "Data release for exporting data.", required = true, arity = 1)
         public int dataRelease;
 
-        @Parameter(names = {"--token"}, description = "Data token to export licensed data.", arity = 1)
-        public String token;
+        @Parameter(names = {"--api-key"}, description = "API key to export licensed data.", arity = 1)
+        public String apiKey;
 
         @Parameter(names = {"--gene"}, description = "List of genes (separated by commas). Exported data will be related to these genes"
                 + " (gene coordinates will be taken into account).", required = true, arity = 1)
@@ -353,8 +353,8 @@ public class ValidationCommandOptions {
         @Parameter(names = {"--data-release"}, description = "Data release. To use the default data release, 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 = {"-i", "--input-file"}, description = "Full path to VCF", required = true, arity = 1)
         public String inputFile;
@@ -405,9 +405,7 @@ public DataReleaseCommandOptions getDataReleaseCommandOptions() {
         return dataReleaseCommandOptions;
     }
 
-    public DataTokenCommandOptions getDataTokenCommandOptions() {
-        return dataTokenCommandOptions;
-    }
+    public ApiKeyCommandOptions getApiKeyCommandOptions() {return apiKeyCommandOptions; }
 
     public LoadCommandOptions getLoadCommandOptions() { return loadCommandOptions; }
 

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminMain.java

@@ -66,8 +66,8 @@ public static void main(String[] args) {
                     case "data-release":
                         commandExecutor = new DataReleaseCommandExecutor(cliOptionsParser.getDataReleaseCommandOptions());
                         break;
-                    case "data-token":
-                        commandExecutor = new DataTokenCommandExecutor(cliOptionsParser.getDataTokenCommandOptions());
+                    case "api-key":
+                        commandExecutor = new ApiKeyCommandExecutor(cliOptionsParser.getApiKeyCommandOptions());
                         break;
                     case "load":
                         commandExecutor = new LoadCommandExecutor(cliOptionsParser.getLoadCommandOptions());

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/DataTokenCommandExecutor.java → cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/ApiKeyCommandExecutor.java

@@ -20,9 +20,9 @@
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.cellbase.app.cli.CommandExecutor;
 import org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser;
-import org.opencb.cellbase.core.token.DataAccessTokenManager;
-import org.opencb.cellbase.core.token.TokenJwtPayload;
-import org.opencb.cellbase.core.token.TokenQuota;
+import org.opencb.cellbase.core.api.key.ApiKeyJwtPayload;
+import org.opencb.cellbase.core.api.key.ApiKeyManager;
+import org.opencb.cellbase.core.api.key.ApiKeyQuota;
 
 import javax.crypto.spec.SecretKeySpec;
 import java.nio.charset.StandardCharsets;
@@ -35,17 +35,17 @@
 import java.util.HashMap;
 import java.util.Map;
 
-public class DataTokenCommandExecutor extends CommandExecutor {
+public class ApiKeyCommandExecutor extends CommandExecutor {
 
-    private AdminCliOptionsParser.DataTokenCommandOptions dataTokenCommandOptions;
+    private AdminCliOptionsParser.ApiKeyCommandOptions apiKeyCommandOptions;
 
     private DateFormat dateFormatter = new SimpleDateFormat("dd/MM/yyyy");
 
 
-    public DataTokenCommandExecutor(AdminCliOptionsParser.DataTokenCommandOptions dataTokenCommandOptions) {
-        super(dataTokenCommandOptions.commonOptions.logLevel, dataTokenCommandOptions.commonOptions.conf);
+    public ApiKeyCommandExecutor(AdminCliOptionsParser.ApiKeyCommandOptions apiKeyCommandOptions) {
+        super(apiKeyCommandOptions.commonOptions.logLevel, apiKeyCommandOptions.commonOptions.conf);
 
-        this.dataTokenCommandOptions = dataTokenCommandOptions;
+        this.apiKeyCommandOptions = apiKeyCommandOptions;
     }
 
 
@@ -57,27 +57,27 @@ public void execute() {
 
         Key key = new SecretKeySpec(Base64.getEncoder().encode(configuration.getSecretKey().getBytes(StandardCharsets.UTF_8)),
                 SignatureAlgorithm.HS256.getJcaName());
-        DataAccessTokenManager datManager = new DataAccessTokenManager(SignatureAlgorithm.HS256.getValue(), key);
+        ApiKeyManager apiKeyManager = new ApiKeyManager(SignatureAlgorithm.HS256.getValue(), key);
 
         try {
-            if (StringUtils.isNotEmpty(dataTokenCommandOptions.createWithDataSources)) {
-                // Create the token payload
-                TokenJwtPayload payload = new TokenJwtPayload();
-                payload.setSubject(dataTokenCommandOptions.organization);
-                payload.setVersion(TokenJwtPayload.CURRENT_VERSION);
+            if (StringUtils.isNotEmpty(apiKeyCommandOptions.createWithDataSources)) {
+                // Create the API key JWT payload
+                ApiKeyJwtPayload payload = new ApiKeyJwtPayload();
+                payload.setSubject(apiKeyCommandOptions.organization);
+                payload.setVersion(ApiKeyJwtPayload.CURRENT_VERSION);
                 payload.setIssuedAt(new Date());
-                if (dataTokenCommandOptions.expiration != null) {
-                    payload.setExpiration(parseDate(dataTokenCommandOptions.expiration));
+                if (apiKeyCommandOptions.expiration != null) {
+                    payload.setExpiration(parseDate(apiKeyCommandOptions.expiration));
                 }
-                payload.setSources(parseSources(dataTokenCommandOptions.createWithDataSources));
-                payload.setQuota(new TokenQuota(dataTokenCommandOptions.maxNumQueries));
-
-                // Create token
-                String token = datManager.encode(payload);
-                System.out.println("Data access token generated:\n" + token);
-            } else if (StringUtils.isNotEmpty(dataTokenCommandOptions.tokenToView)) {
-                // View data token
-                datManager.display(dataTokenCommandOptions.tokenToView);
+                payload.setSources(parseSources(apiKeyCommandOptions.createWithDataSources));
+                payload.setQuota(new ApiKeyQuota(apiKeyCommandOptions.maxNumQueries));
+
+                // Create API key
+                String apiKey = apiKeyManager.encode(payload);
+                System.out.println("API key generated:\n" + apiKey);
+            } else if (StringUtils.isNotEmpty(apiKeyCommandOptions.apiKeyToView)) {
+                // View API key
+                apiKeyManager.display(apiKeyCommandOptions.apiKeyToView);
             }
         } catch (ParseException e) {
             e.printStackTrace();
@@ -86,18 +86,18 @@ public void execute() {
     }
 
     private void checkParameters() {
-        if (StringUtils.isNotEmpty(dataTokenCommandOptions.createWithDataSources)
-                && StringUtils.isNotEmpty(dataTokenCommandOptions.tokenToView)) {
+        if (StringUtils.isNotEmpty(apiKeyCommandOptions.createWithDataSources)
+                && StringUtils.isNotEmpty(apiKeyCommandOptions.apiKeyToView)) {
             throw new IllegalArgumentException("Please, select only one of these input parameters: create or view");
         }
-        if (StringUtils.isEmpty(dataTokenCommandOptions.createWithDataSources)
-                && StringUtils.isEmpty(dataTokenCommandOptions.tokenToView)) {
+        if (StringUtils.isEmpty(apiKeyCommandOptions.createWithDataSources)
+                && StringUtils.isEmpty(apiKeyCommandOptions.apiKeyToView)) {
             throw new IllegalArgumentException("Please, it is mandatory to select one of these input parameters: create or view");
         }
 
         // Check create parameters
-        if (StringUtils.isNotEmpty(dataTokenCommandOptions.createWithDataSources)) {
-            if (StringUtils.isEmpty(dataTokenCommandOptions.organization)) {
+        if (StringUtils.isNotEmpty(apiKeyCommandOptions.createWithDataSources)) {
+            if (StringUtils.isEmpty(apiKeyCommandOptions.organization)) {
                 throw new IllegalArgumentException("Missing organization");
             }
         }

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

@@ -58,7 +58,7 @@ public class ExportCommandExecutor extends CommandExecutor {
     private Path output;
     private String[] dataToExport;
     private int dataRelease;
-    private String token;
+    private String apiKey;
 
     private String database;
     private CellBaseManagerFactory managerFactory;
@@ -71,7 +71,7 @@ public ExportCommandExecutor(AdminCliOptionsParser.ExportCommandOptions exportCo
         this.exportCommandOptions = exportCommandOptions;
 
         this.dataRelease = exportCommandOptions.dataRelease;
-        this.token = exportCommandOptions.token;
+        this.apiKey = exportCommandOptions.apiKey;
 
         this.output = Paths.get(exportCommandOptions.output);
 
@@ -324,7 +324,7 @@ private int exportClinicalVariantData(List<Region> regions) throws CellBaseExcep
         ClinicalManager clinicalManager = managerFactory.getClinicalManager(species, assembly);
         ClinicalVariantQuery query = new ClinicalVariantQuery();
         query.setDataRelease(dataRelease);
-        query.setToken(token);
+        query.setApiKey(apiKey);
         int counter = 0;
         for (Region region : regions) {
             query.setRegions(Collections.singletonList(region));

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

@@ -72,7 +72,7 @@ public void execute() {
         VariantAnnotationCalculator variantAnnotationCalculator = null;
         try {
             variantAnnotationCalculator = new VariantAnnotationCalculator(validationCommandOptions.species,
-                    validationCommandOptions.assembly, validationCommandOptions.dataRelease, validationCommandOptions.token,
+                    validationCommandOptions.assembly, validationCommandOptions.dataRelease, validationCommandOptions.apiKey,
                     cellBaseManagerFactory);
         } catch (CellBaseException e) {
             e.printStackTrace();

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

@@ -31,6 +31,8 @@ public class CellBaseClient {
     private final String species;
     private final String assembly;
     private final String dataRelease;
+    private final String apiKey;
+    @Deprecated
     private final String token;
     private ClientConfiguration clientConfiguration;
 
@@ -53,14 +55,15 @@ public CellBaseClient(String species, String assembly, String dataRelease, Clien
         this(species, assembly, dataRelease, null, clientConfiguration);
     }
 
-    public CellBaseClient(String species, String assembly, String dataRelease, String token, ClientConfiguration clientConfiguration) {
+    public CellBaseClient(String species, String assembly, String dataRelease, String apiKey, ClientConfiguration clientConfiguration) {
         if (StringUtils.isBlank(species)) {
             throw new IllegalArgumentException("Species parameter cannot be empty when building a CellBaseClient");
         }
         this.species = species;
         this.assembly = StringUtils.isEmpty(assembly) ? null : assembly;
         this.dataRelease = StringUtils.isEmpty(dataRelease) ? null : dataRelease;
-        this.token = token;
+        this.token = apiKey;
+        this.apiKey = apiKey;
         if (clientConfiguration != null && clientConfiguration.getRest() != null
                 && clientConfiguration.getRest().getHosts() != null
                 && !clientConfiguration.getRest().getHosts().isEmpty()
@@ -75,39 +78,39 @@ public CellBaseClient(String species, String assembly, String dataRelease, Strin
     }
 
     public GeneClient getGeneClient() {
-        return getClient("GENE", () -> new GeneClient(species, assembly, dataRelease, token, clientConfiguration));
+        return getClient("GENE", () -> new GeneClient(species, assembly, dataRelease, apiKey, clientConfiguration));
     }
 
     public TranscriptClient getTranscriptClient() {
-        return getClient("TRANSCRIPT", () -> new TranscriptClient(species, assembly, dataRelease, token, clientConfiguration));
+        return getClient("TRANSCRIPT", () -> new TranscriptClient(species, assembly, dataRelease, apiKey, clientConfiguration));
     }
 
 //    public VariationClient getVariationClient() {
 //        return getClient("VARIATION", () -> new VariationClient(species, assembly, clientConfiguration));
 //    }
 
     public VariantClient getVariantClient() {
-        return getClient("VARIANT", () -> new VariantClient(species, assembly, dataRelease, token, clientConfiguration));
+        return getClient("VARIANT", () -> new VariantClient(species, assembly, dataRelease, apiKey, clientConfiguration));
     }
 
     public ProteinClient getProteinClient() {
-        return getClient("PROTEIN", () -> new ProteinClient(species, assembly, dataRelease, token, clientConfiguration));
+        return getClient("PROTEIN", () -> new ProteinClient(species, assembly, dataRelease, apiKey, clientConfiguration));
     }
 
     public GenomicRegionClient getGenomicRegionClient() {
-        return getClient("GENOME_REGION", () -> new GenomicRegionClient(species, assembly, dataRelease, token, clientConfiguration));
+        return getClient("GENOME_REGION", () -> new GenomicRegionClient(species, assembly, dataRelease, apiKey, clientConfiguration));
     }
 
     public MetaClient getMetaClient() {
-        return getClient("META", () -> new MetaClient(species, assembly, dataRelease, token, clientConfiguration));
+        return getClient("META", () -> new MetaClient(species, assembly, dataRelease, apiKey, clientConfiguration));
     }
 
     public ClinicalVariantClient getClinicalClient() {
-        return getClient("CLINICAL", () -> new ClinicalVariantClient(species, assembly, dataRelease, token, clientConfiguration));
+        return getClient("CLINICAL", () -> new ClinicalVariantClient(species, assembly, dataRelease, apiKey, clientConfiguration));
     }
 
     public GenericClient getGenericClient() {
-        return getClient("GENERIC", () -> new GenericClient(species, assembly, dataRelease, token, clientConfiguration));
+        return getClient("GENERIC", () -> new GenericClient(species, assembly, dataRelease, apiKey, clientConfiguration));
     }
 
     @SuppressWarnings("unchecked")
@@ -144,8 +147,13 @@ public String getDataRelease() {
         return dataRelease;
     }
 
+    public String getApiKey() {
+        return apiKey;
+    }
+
+    @Deprecated
     public String getToken() {
-        return token;
+        return apiKey;
     }
 
     public ClientConfiguration getClientConfiguration() {

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

@@ -30,8 +30,8 @@
  */
 public class ClinicalVariantClient extends ParentRestClient<Variant> {
 
-    ClinicalVariantClient(String species, String assembly, String dataRelease, String token, ClientConfiguration configuration) {
-        super(species, assembly, dataRelease, token, configuration);
+    ClinicalVariantClient(String species, String assembly, String dataRelease, String apiKey, ClientConfiguration configuration) {
+        super(species, assembly, dataRelease, apiKey, configuration);
 
         this.clazz = Variant.class;