lib: refactor code by changing the DownloadProperties.URLProperties, …

…#TASK-5775, #TASK-5564

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

@@ -349,7 +349,7 @@ private CellBaseBuilder buildConservation() {
     }
 
     private CellBaseBuilder buildClinicalVariants() throws CellBaseException {
-        Path clinicalVariantFolder = downloadFolder.resolve(EtlCommons.CLINICAL_VARIANTS_FOLDER);
+        Path clinicalVariantFolder = downloadFolder.resolve(EtlCommons.CLINICAL_VARIANTS_FOLDER_NAME);
 
         List<Path> versionFiles = new ArrayList<>();
         List<String> versionFilenames = Arrays.asList(CLINVAR_VERSION_FILENAME, COSMIC_VERSION_FILENAME, GWAS_VERSION_FILENAME,

cellbase-core/src/main/java/org/opencb/cellbase/core/config/DownloadProperties.java

@@ -16,7 +16,7 @@
 
 package org.opencb.cellbase.core.config;
 
-import java.util.List;
+import java.util.Map;
 
 /**
  * Created by imedina on 19/08/16.
@@ -614,7 +614,7 @@ public static class URLProperties {
 
         private String host;
         private String version;
-        private List<String> files;
+        private Map<String, String> files;
 
         public String getHost() {
             return host;
@@ -633,11 +633,11 @@ public URLProperties setVersion(String version) {
             return this;
         }
 
-        public List<String> getFiles() {
+        public Map<String, String> getFiles() {
             return files;
         }
 
-        public URLProperties setFiles(List<String> files) {
+        public URLProperties setFiles(Map<String, String> files) {
             this.files = files;
             return this;
         }

cellbase-core/src/main/java/org/opencb/cellbase/core/models/DataRelease.java

@@ -21,14 +21,9 @@
 public class DataRelease {
     private int release;
     private String date;
-    /**
-     * @deprecated it is maintained to back-compatibility with previous CellBase versions to v5.5
-     */
-    @Deprecated
-    private boolean active;
     private List<String> activeByDefaultIn;
     private Map<String, String> collections;
-    private List<DataReleaseSource> sources;
+    private List<DataSource> sources;
 
     public DataRelease() {
         this.activeByDefaultIn = Collections.emptyList();
@@ -37,7 +32,7 @@ public DataRelease() {
     }
 
     public DataRelease(int release, String date, List<String> activeByDefaultIn, Map<String, String> collections,
-                       List<DataReleaseSource> sources) {
+                       List<DataSource> sources) {
         this.release = release;
         this.date = date;
         this.activeByDefaultIn = activeByDefaultIn;
@@ -75,15 +70,6 @@ public DataRelease setDate(String date) {
         return this;
     }
 
-    public boolean isActive() {
-        return active;
-    }
-
-    public DataRelease setActive(boolean active) {
-        this.active = active;
-        return this;
-    }
-
     public List<String> getActiveByDefaultIn() {
         return activeByDefaultIn;
     }
@@ -102,11 +88,11 @@ public DataRelease setCollections(Map<String, String> collections) {
         return this;
     }
 
-    public List<DataReleaseSource> getSources() {
+    public List<DataSource> getSources() {
         return sources;
     }
 
-    public DataRelease setSources(List<DataReleaseSource> sources) {
+    public DataRelease setSources(List<DataSource> sources) {
         this.sources = sources;
         return this;
     }

cellbase-core/src/main/java/org/opencb/cellbase/core/models/DataSource.java

@@ -0,0 +1,98 @@
+/*
+ * 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.core.models;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class DataSource {
+
+    private String name;
+    private String category;
+    private String version;
+    private String downloadDate;
+    private List<String> urls;
+
+    public DataSource() {
+        this.urls = new ArrayList<>();
+    }
+
+    public DataSource(String name, String category, String version, String downloadDate, List<String> urls) {
+        this.name = name;
+        this.category = category;
+        this.version = version;
+        this.downloadDate = downloadDate;
+        this.urls = urls;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("DataSourceDescr{");
+        sb.append("name='").append(name).append('\'');
+        sb.append(", category='").append(category).append('\'');
+        sb.append(", version='").append(version).append('\'');
+        sb.append(", downloadDate='").append(downloadDate).append('\'');
+        sb.append(", urls=").append(urls);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public DataSource setName(String name) {
+        this.name = name;
+        return this;
+    }
+
+    public String getCategory() {
+        return category;
+    }
+
+    public DataSource setCategory(String category) {
+        this.category = category;
+        return this;
+    }
+
+    public String getVersion() {
+        return version;
+    }
+
+    public DataSource setVersion(String version) {
+        this.version = version;
+        return this;
+    }
+
+    public String getDownloadDate() {
+        return downloadDate;
+    }
+
+    public DataSource setDownloadDate(String downloadedDate) {
+        this.downloadDate = downloadedDate;
+        return this;
+    }
+
+    public List<String> getUrls() {
+        return urls;
+    }
+
+    public DataSource setUrls(List<String> urls) {
+        this.urls = urls;
+        return this;
+    }
+}