Replaced Provider classes with CompositeProvider that is configured by a json file

pom.xml

@@ -96,6 +96,11 @@
             <artifactId>commons-io</artifactId>
             <version>2.4</version>
         </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.6.2</version>
+        </dependency>
     </dependencies>
     
     <build>

src/main/java/de/cebitec/common/dbxref/api/GenericResource.java

@@ -77,4 +77,8 @@ public class GenericResource implements Resource {
         }
     }
 
+    @Override
+    public String toString() {
+        return "GenericResource{" + "type=" + type + ", dbxref=" + dbxref + ", uri=" + uri + '}';
+    }
 }

src/main/java/de/cebitec/common/dbxref/providers/CompositeProvider.java

+/*
+ * Copyright (C) 2016 Lukas Jelonek - Lukas.Jelonek at computational.bio.uni-giessen.de
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package de.cebitec.common.dbxref.providers;
+
+import com.google.common.collect.Iterables;
+import com.google.gson.Gson;
+import de.cebitec.common.dbxref.api.DbXRef;
+import de.cebitec.common.dbxref.api.Resource;
+import de.cebitec.common.dbxref.spi.DbXRefResolver;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import org.kohsuke.MetaInfServices;
+
+/**
+ *
+ */
+@MetaInfServices(DbXRefResolver.class)
+public class CompositeProvider implements DbXRefResolver {
+
+    private final List<DbXRefResolver> providers = new ArrayList<>();
+
+    public CompositeProvider() {
+        Gson gson = new Gson();
+        InputStream is = this.getClass().getResourceAsStream("providers.json");
+        InputStreamReader isr = new InputStreamReader(is);
+        List<Map<String, List<String>>> fromJson = gson.fromJson(isr, List.class);
+        for (Map<String, List<String>> entry : fromJson) {
+            GenericDbXRefProvider.ResolverData data = new GenericDbXRefProvider.ResolverData();
+            for (String prefix : entry.get("prefixes")) {
+                data.addPrefix(prefix);
+            }
+            if (entry.containsKey("html")) {
+                for (String template : entry.get("html")) {
+                    data.addResourceTemplate(Resource.Type.Html, template);
+                }
+            }
+            if (entry.containsKey("xml")) {
+                for (String template : entry.get("xml")) {
+                    data.addResourceTemplate(Resource.Type.Xml, template);
+                }
+            }
+            if (entry.containsKey("text")) {
+                for (String template : entry.get("text")) {
+                    data.addResourceTemplate(Resource.Type.Text, template);
+                }
+            }
+
+            GenericDbXRefProvider provider = new GenericDbXRefProvider(data);
+            providers.add(provider);
+        }
+    }
+
+    @Override
+    public Iterable<String> getDatabasePrefixes() {
+        List<String> prefixes = new ArrayList<>();
+        for (DbXRefResolver provider : providers) {
+            Iterables.addAll(prefixes, provider.getDatabasePrefixes());
+        }
+        return prefixes;
+    }
+
+    @Override
+    public boolean canHandle(DbXRef ref) {
+        for (DbXRefResolver provider : providers) {
+            if (provider.canHandle(ref)) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+    @Override
+    public Collection<? extends Resource> resolve(DbXRef ref) {
+        for (DbXRefResolver provider : providers) {
+            if (provider.canHandle(ref)) {
+                return provider.resolve(ref);
+            }
+        }
+        return Collections.<Resource>emptyList();
+    }
+
+}

src/main/java/de/cebitec/common/dbxref/providers/ECProvider.java

-/*
- * Copyright (C) 2014 Lukas Jelonek <ljelonek at cebitec.uni-bielefeld.de>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author Lukas Jelonek {@literal <ljelonek at cebitec.uni-bielefeld.de>}
- */
-@MetaInfServices(DbXRefResolver.class)
-public class ECProvider extends GenericDbXRefProvider {
-
-    public ECProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("EC", "Enzyme");
-        resolverData.addResourceTemplate(Type.Html, "http://enzyme.expasy.org/EC/%i");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/GIProvider.java

-/*
- * Copyright (C) 2012 cb
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author cb
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class GIProvider extends GenericDbXRefProvider {
-
-    public GIProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("GI");
-        resolverData.addResourceTemplate(Type.Html, "http://www.ncbi.nlm.nih.gov/protein/GI:%i");
-        resolverData.addResourceTemplate(Type.Xml, "http://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&db=protein&dopt=xml&sort=&val=%i&retmode=file");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/GOProvider.java

-/*
- * Copyright (C) 2012 cb
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author cb
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class GOProvider extends GenericDbXRefProvider {
-
-    public GOProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("GO");
-        resolverData.addResourceTemplate(Type.Html, "http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:%i");
-        resolverData.addResourceTemplate(Type.Xml, "http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:%i&format=oboxml");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/GeneIDProvider.java

-/*
- * Copyright (C) 2012 cb
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author cb
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class GeneIDProvider extends GenericDbXRefProvider {
-
-    public GeneIDProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("GeneID");
-        resolverData.addResourceTemplate(Type.Html, "http://www.ncbi.nlm.nih.gov/gene/%i");
-        resolverData.addResourceTemplate(Type.Xml, "http://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&db=gene&dopt=xml&sort=&val=%i&retmode=file");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/PDBProvider.java

-/*
- * Copyright (C) 2012 cb
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author cb
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class PDBProvider extends GenericDbXRefProvider {
-
-    public PDBProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("PDB");
-        resolverData.addResourceTemplate(Type.Html, "http://www.rcsb.org/pdb/explore/explore.do?structureId=%i");
-        resolverData.addResourceTemplate(Type.Xml, "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=xml&compression=NO&structureId=%i");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/PFamProvider.java

-/*
- * Copyright (C) 2012 cb
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author cb
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class PFamProvider extends GenericDbXRefProvider {
-
-    public PFamProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("PFAM");
-        resolverData.addResourceTemplate(Type.Html, "http://pfam.xfam.org/family/%i");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/PubMedProvider.java

-/*
- * Copyright (C) 2013 amaier
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author amaier
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class PubMedProvider extends GenericDbXRefProvider {
-
-    public PubMedProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("pubmed", "Pubmed");
-        resolverData.addResourceTemplate(Type.Html, "http://www.ncbi.nlm.nih.gov/pubmed/%i");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/RFamProvider.java

-/*
- * Copyright (C) 2012 cb
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author cb
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class RFamProvider extends GenericDbXRefProvider {
-
-    public RFamProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("RFAM");
-        resolverData.addResourceTemplate(Type.Html, "http://rfam.sanger.ac.uk/family/%i");
-        resolverData.addResourceTemplate(Type.Xml, "http://rfam.sanger.ac.uk/family/%i?content-type=text%2Fxml");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/SOProvider.java

-/*
- * Copyright (C) 2014 Lukas Jelonek <ljelonek at cebitec.uni-bielefeld.de>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author Lukas Jelonek {@literal <ljelonek at cebitec.uni-bielefeld.de>}
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class SOProvider extends GenericDbXRefProvider {
-
-    public SOProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("SO");
-        resolverData.addResourceTemplate(Type.Html, "http://www.sequenceontology.org/browser/current_svn/term/SO:%i");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/TaxonomyProvider.java

-/*
- * Copyright (C) 2012 cb
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author cb
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class TaxonomyProvider extends GenericDbXRefProvider {
-
-    public TaxonomyProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("Taxon", "taxon", "taxid");
-        resolverData.addResourceTemplate(Type.Html, "http://www.uniprot.org/taxonomy/%i");
-        resolverData.addResourceTemplate(Type.Xml, "http://www.uniprot.org/taxonomy/%i.rdf");
-        return resolverData;
-    }
-}

src/main/java/de/cebitec/common/dbxref/providers/UniProtProvider.java

-/*
- * Copyright (C) 2012 cb
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-package de.cebitec.common.dbxref.providers;
-
-import de.cebitec.common.dbxref.api.Resource.Type;
-import de.cebitec.common.dbxref.spi.DbXRefResolver;
-import org.kohsuke.MetaInfServices;
-
-/**
- *
- * @author cb
- */
-@MetaInfServices(DbXRefResolver.class) 
-public class UniProtProvider extends GenericDbXRefProvider {
-
-    public UniProtProvider() {
-        super(createResolverData());
-    }
-
-    public static ResolverData createResolverData() {
-        ResolverData resolverData = new ResolverData("UniProtKB/TrEMBL", "UniProtKB/Swiss-Prot");
-        resolverData.addResourceTemplate(Type.Html, "http://www.uniprot.org/uniprot/%i");
-        resolverData.addResourceTemplate(Type.Xml, "http://www.uniprot.org/uniprot/%i.xml");
-        return resolverData;
-    }
-}
\ No newline at end of file

src/main/resources/de/cebitec/common/dbxref/providers/providers.json

+[
+    {
+        "prefixes": ["EC", "Enzyme"],
+        "html": ["http://enzyme.expasy.org/EC/%i"]
+    },
+    {
+        "prefixes": ["GI"],
+        "html": ["http://www.ncbi.nlm.nih.gov/protein/GI:%i"],
+        "xml": ["http://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&db=protein&dopt=xml&sort=&val=%i&retmode=file"]
+    },
+    {
+        "prefixes": ["UniProtKB/TrEMBL", "UniProtKB/Swiss-Prot"],