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Merge remote-tracking branch 'origin/feature/web-extjs' into develop
Conflicts: eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/FilesWSServer.java eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/GeneWSServer.java eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/RegionWSServer.java eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/StudyWSServer.java eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/VariantWSServer.java eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/ga4gh/GA4GHVariantCallSetWSServer.java eva-web/src/js/eva-variant-widget-panel.js eva-web/src/js/variant-widget/eva-variant-widget.js
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2 changes: 1 addition & 1 deletion
2
...ion/eva/server/ws/CORSResponseFilter.java → ...iation/eva/server/CORSResponseFilter.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| package uk.ac.ebi.variation.eva.server.ws; | ||
| package uk.ac.ebi.variation.eva.server; | ||
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| import java.io.IOException; | ||
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4 changes: 2 additions & 2 deletions
4
eva-server/src/main/java/uk/ac/ebi/variation/eva/server/EvaWSRegistry.java
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9 changes: 9 additions & 0 deletions
9
eva-server/src/main/java/uk/ac/ebi/variation/eva/server/exception/SpeciesException.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,9 @@ | ||
| package uk.ac.ebi.variation.eva.server.exception; | ||
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| @SuppressWarnings("serial") | ||
| public class SpeciesException extends Exception { | ||
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| public SpeciesException(String msg) { | ||
| super(msg); | ||
| } | ||
| } |
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eva-server/src/main/java/uk/ac/ebi/variation/eva/server/exception/VersionException.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| package uk.ac.ebi.variation.eva.server.exception; | ||
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| @SuppressWarnings("serial") | ||
| public class VersionException extends Exception { | ||
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| public VersionException(String msg) { | ||
| super(msg); | ||
| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
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@@ -5,56 +5,66 @@ | |
| import java.util.Arrays; | ||
| import javax.naming.NamingException; | ||
| import javax.servlet.http.HttpServletRequest; | ||
| import javax.ws.rs.DefaultValue; | ||
| import javax.ws.rs.GET; | ||
| import javax.ws.rs.Path; | ||
| import javax.ws.rs.PathParam; | ||
| import javax.ws.rs.Produces; | ||
| import javax.ws.rs.QueryParam; | ||
| import javax.ws.rs.*; | ||
| import javax.ws.rs.core.Context; | ||
| import javax.ws.rs.core.MediaType; | ||
| import javax.ws.rs.core.Response; | ||
| import javax.ws.rs.core.UriInfo; | ||
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| import com.wordnik.swagger.annotations.Api; | ||
| import com.wordnik.swagger.annotations.ApiOperation; | ||
| import java.util.logging.Level; | ||
| import java.util.logging.Logger; | ||
| import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException; | ||
| import org.opencb.opencga.storage.core.variant.adaptors.VariantSourceDBAdaptor; | ||
| import uk.ac.ebi.variation.eva.lib.datastore.DBAdaptorConnector; | ||
| import uk.ac.ebi.variation.eva.lib.storage.metadata.VariantSourceEvaproDBAdaptor; | ||
| import uk.ac.ebi.variation.eva.server.exception.SpeciesException; | ||
| import uk.ac.ebi.variation.eva.server.exception.VersionException; | ||
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| /** | ||
| * | ||
| * @author Cristina Yenyxe Gonzalez Garcia <[email protected]> | ||
| */ | ||
| @Path("/{version}/files") | ||
| @Produces(MediaType.APPLICATION_JSON) | ||
| @Produces("application/json") | ||
| @Api(value = "Files", description = "Files RESTful Web Services API") | ||
| public class FilesWSServer extends EvaWSServer { | ||
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| private VariantSourceDBAdaptor variantSourceEvaproDbAdaptor; | ||
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| public FilesWSServer() throws IllegalOpenCGACredentialsException { | ||
| super(); | ||
| } | ||
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| public FilesWSServer(@DefaultValue("") @PathParam("version") String version, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) | ||
| throws NamingException { | ||
| public FilesWSServer(@DefaultValue("") @PathParam("version") String version, | ||
| @Context UriInfo uriInfo, @Context HttpServletRequest hsr) throws NamingException { | ||
| super(version, uriInfo, hsr); | ||
| variantSourceEvaproDbAdaptor = new VariantSourceEvaproDBAdaptor(); | ||
| } | ||
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| @GET | ||
| @Path("/all") | ||
| @ApiOperation(httpMethod = "GET", value = "Gets the files of a species") | ||
| public Response getFiles(@QueryParam("species") String species) | ||
| throws UnknownHostException, IllegalOpenCGACredentialsException, IOException { | ||
| if (species != null && !species.isEmpty()) { | ||
| queryOptions.put("species", species); | ||
| try { | ||
| checkParams(); | ||
| } catch (VersionException | SpeciesException ex) { | ||
| return createErrorResponse(ex.toString()); | ||
| } | ||
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| VariantSourceDBAdaptor variantSourceMongoDbAdaptor = DBAdaptorConnector.getVariantSourceDBAdaptor(species); | ||
| return createOkResponse(variantSourceMongoDbAdaptor.getAllSources(queryOptions)); | ||
| } | ||
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| @GET | ||
| @Path("/{files}/url") | ||
| @ApiOperation(httpMethod = "GET", value = "Gets the URL of a file") | ||
| public Response getFileUrl(@PathParam("files") String filenames) { | ||
| try { | ||
| checkParams(); | ||
| } catch (VersionException | SpeciesException ex) { | ||
| return createErrorResponse(ex.toString()); | ||
| } | ||
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| return createOkResponse(variantSourceEvaproDbAdaptor.getSourceDownloadUrlByName(Arrays.asList(filenames.split(",")))); | ||
| } | ||
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| } | ||
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