TASK-4641- Implement an API key to control the number of queries

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

@@ -18,6 +18,7 @@
 
 import com.beust.jcommander.*;
 import org.opencb.cellbase.app.cli.CliOptionsParser;
+import org.opencb.cellbase.core.api.key.ApiKeyQuota;
 
 import java.util.HashMap;
 import java.util.List;
@@ -34,7 +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;
@@ -51,7 +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();
@@ -63,7 +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);
@@ -152,20 +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 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)
+        @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 = {"--organization"}, description = "Organization (to be used with the --create-token parameter)", arity = 1)
+        @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-api-key to specify the"
+                + " organization", arity = 1)
         public String organization;
 
-        @Parameter(names = {"--view-token"}, description = "Token to view", arity = 1)
-        public String tokenToView;
+        @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 = ApiKeyQuota.DEFAULT_MAX_NUM_QUERIES;
+
+        @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")
@@ -233,8 +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)
@@ -341,8 +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;
@@ -393,9 +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/ApiKeyCommandExecutor.java

@@ -0,0 +1,129 @@
+/*
+ * Copyright 2015-2020 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.opencb.cellbase.app.cli.admin.executors;
+
+import io.jsonwebtoken.SignatureAlgorithm;
+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.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;
+import java.security.Key;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Base64;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+
+public class ApiKeyCommandExecutor extends CommandExecutor {
+
+    private AdminCliOptionsParser.ApiKeyCommandOptions apiKeyCommandOptions;
+
+    private DateFormat dateFormatter = new SimpleDateFormat("dd/MM/yyyy");
+
+
+    public ApiKeyCommandExecutor(AdminCliOptionsParser.ApiKeyCommandOptions apiKeyCommandOptions) {
+        super(apiKeyCommandOptions.commonOptions.logLevel, apiKeyCommandOptions.commonOptions.conf);
+
+        this.apiKeyCommandOptions = apiKeyCommandOptions;
+    }
+
+
+    /**
+     * Execute one of the selected actions according to the input parameters.
+     */
+    public void execute() {
+        checkParameters();
+
+        Key key = new SecretKeySpec(Base64.getEncoder().encode(configuration.getSecretKey().getBytes(StandardCharsets.UTF_8)),
+                SignatureAlgorithm.HS256.getJcaName());
+        ApiKeyManager apiKeyManager = new ApiKeyManager(SignatureAlgorithm.HS256.getValue(), key);
+
+        try {
+            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 (apiKeyCommandOptions.expiration != null) {
+                    payload.setExpiration(parseDate(apiKeyCommandOptions.expiration));
+                }
+                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();
+        }
+
+    }
+
+    private void checkParameters() {
+        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(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(apiKeyCommandOptions.createWithDataSources)) {
+            if (StringUtils.isEmpty(apiKeyCommandOptions.organization)) {
+                throw new IllegalArgumentException("Missing organization");
+            }
+        }
+
+        if (StringUtils.isEmpty(configuration.getSecretKey())) {
+            throw new IllegalArgumentException("Missing secret key in the CellBase configuration file.");
+        }
+    }
+
+    private Map<String, Date> parseSources(String sources) throws ParseException {
+        Map<String, Date> sourcesMap = new HashMap<>();
+        if (StringUtils.isNotEmpty(sources)) {
+            String[] split = sources.split(",");
+            for (String source : split) {
+                String[] splits = source.split(":");
+                if (splits.length == 1) {
+                    sourcesMap.put(splits[0], parseDate("31/12/999999"));
+                } else {
+                    sourcesMap.put(splits[0], parseDate(splits[1]));
+                }
+            }
+        }
+        return sourcesMap;
+    }
+
+    private Date parseDate(String date) throws ParseException {
+        return dateFormatter.parse(date);
+    }
+}

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

@@ -59,7 +59,7 @@ 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;
@@ -72,7 +72,7 @@ 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);
 
@@ -429,7 +429,7 @@ 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-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;