diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java index f58b44b4b..63f096308 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java @@ -66,7 +66,7 @@ public Response getJbrowseFeatures(@PathParam("refseq_name") String refseqName, @Path("dnaseq/{organismAbbrev}") @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseDNASeqTracks(@PathParam("organismAbbrev") String organismAbbrev, - @DefaultValue("1") @QueryParam("appVersion") String appVersion) throws IOException { + @DefaultValue("1") @QueryParam("appType") String appType) throws IOException { String gusHome = getWdkModel().getGusHome(); String projectId = getWdkModel().getProjectId(); @@ -79,7 +79,7 @@ public Response getJbrowseDNASeqTracks(@PathParam("organismAbbrev") String organ command.add(projectId); command.add(buildNumber); command.add(webservicesDir); - command.add(appVersion); + command.add(appType); return responseFromCommand(command); } @@ -89,7 +89,7 @@ public Response getJbrowseDNASeqTracks(@PathParam("organismAbbrev") String organ @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseRNASeqJunctionTracks(@PathParam("organismAbbrev") String organismAbbrev, @DefaultValue("0") @QueryParam("isApollo") String isApollo, - @DefaultValue("1") @QueryParam("appVersion") String appVersion + @DefaultValue("1") @QueryParam("appType") String appType ) throws IOException { String gusHome = getWdkModel().getGusHome(); @@ -100,7 +100,7 @@ public Response getJbrowseRNASeqJunctionTracks(@PathParam("organismAbbrev") Stri command.add(organismAbbrev); command.add(projectId); command.add(isApollo); - command.add(appVersion); + command.add(appType); return responseFromCommand(command); } @@ -110,7 +110,7 @@ public Response getJbrowseRNASeqJunctionTracks(@PathParam("organismAbbrev") Stri @Path("{tracks}/{publicOrganismAbbrev}/aa/trackList.json") @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseAaTracks(@PathParam("publicOrganismAbbrev") String publicOrganismAbbrev, - @DefaultValue("1") @QueryParam("appVersion") String appVersion, + @DefaultValue("1") @QueryParam("appType") String appType, @PathParam("tracks") String tracks) throws IOException { //NOTE: this service call is public facing so we use the publicOrganismAbbrev here @@ -125,7 +125,7 @@ public Response getJbrowseAaTracks(@PathParam("publicOrganismAbbrev") String pub command.add(projectId); command.add(String.valueOf(isPbrowse)); command.add(tracks); - command.add(appVersion); + command.add(appType); return responseFromCommand(command); } @@ -134,7 +134,7 @@ public Response getJbrowseAaTracks(@PathParam("publicOrganismAbbrev") String pub @Path("{tracks}/{publicOrganismAbbrev}/trackList.json") @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseTracks(@PathParam("publicOrganismAbbrev") String publicOrganismAbbrev, - @DefaultValue("1") @QueryParam("appVersion") String appVersion, + @DefaultValue("1") @QueryParam("appType") String appType, @PathParam("tracks") String tracks) throws IOException { //NOTE: this service call is public facing so we use the publicOrganismAbbrev here @@ -150,7 +150,7 @@ public Response getJbrowseTracks(@PathParam("publicOrganismAbbrev") String publi command.add(projectId); command.add(String.valueOf(isPbrowse)); command.add(tracks); - command.add(appVersion); + command.add(appType); return responseFromCommand(command); } @@ -158,7 +158,7 @@ public Response getJbrowseTracks(@PathParam("publicOrganismAbbrev") String publi @Path("organismSpecific/{organismAbbrev}") @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseOrganismSpecificTracks(@PathParam("organismAbbrev") String organismAbbrev, - @DefaultValue("1") @QueryParam("appVersion") String appVersion, + @DefaultValue("1") @QueryParam("appType") String appType, @DefaultValue("0") @QueryParam("isApollo") String isApollo) throws IOException { String gusHome = getWdkModel().getGusHome(); @@ -174,7 +174,7 @@ public Response getJbrowseOrganismSpecificTracks(@PathParam("organismAbbrev") St command.add(isApollo); command.add(buildNumber); command.add(webservicesDir); - command.add(appVersion); + command.add(appType); return responseFromCommand(command); } @@ -182,7 +182,7 @@ public Response getJbrowseOrganismSpecificTracks(@PathParam("organismAbbrev") St @Path("organismSpecificPbrowse/{organismAbbrev}") @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseOrganismSpecificPbrowseTracks(@PathParam("organismAbbrev") String organismAbbrev, - @DefaultValue("1") @QueryParam("appVersion") String appVersion) throws IOException { + @DefaultValue("1") @QueryParam("appType") String appType) throws IOException { String gusHome = getWdkModel().getGusHome(); String projectId = getWdkModel().getProjectId(); @@ -191,7 +191,7 @@ public Response getJbrowseOrganismSpecificPbrowseTracks(@PathParam("organismAbbr command.add(gusHome + "/bin/jbrowseOrganismSpecificPbrowseTracks"); command.add(organismAbbrev); command.add(projectId); - command.add(appVersion); + command.add(appType); return responseFromCommand(command); } @@ -214,7 +214,7 @@ public Response getOrganismList() throws IOException { @Path("rnaseq/{organismAbbrev}") @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseRNASeqTracks(@PathParam("organismAbbrev") String organismAbbrev, - @DefaultValue("1") @QueryParam("appVersion") String appVersion) throws IOException { + @DefaultValue("1") @QueryParam("appType") String appType) throws IOException { String gusHome = getWdkModel().getGusHome(); String projectId = getWdkModel().getProjectId(); @@ -228,7 +228,7 @@ public Response getJbrowseRNASeqTracks(@PathParam("organismAbbrev") String organ command.add(buildNumber); command.add(webservicesDir); command.add("RNASeq"); - command.add(appVersion); + command.add(appType); return responseFromCommand(command); } @@ -236,7 +236,7 @@ public Response getJbrowseRNASeqTracks(@PathParam("organismAbbrev") String organ @Path("chipseq/{organismAbbrev}") @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseChIPSeqTracks(@PathParam("organismAbbrev") String organismAbbrev, - @DefaultValue("1") @QueryParam("appVersion") String appVersion) throws IOException { + @DefaultValue("1") @QueryParam("appType") String appType) throws IOException { String gusHome = getWdkModel().getGusHome(); String projectId = getWdkModel().getProjectId(); @@ -250,7 +250,7 @@ public Response getJbrowseChIPSeqTracks(@PathParam("organismAbbrev") String orga command.add(buildNumber); command.add(webservicesDir); command.add("ChIPSeq"); - command.add(appVersion); + command.add(appType); return responseFromCommand(command); } @@ -342,7 +342,7 @@ private static String checkPath(String fileSystemPath) { @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseNames(@PathParam("organismAbbrev") String organismAbbrev, @QueryParam("equals") String eq, - @DefaultValue("1") @QueryParam("appVersion") String appVersion, + @DefaultValue("1") @QueryParam("appType") String appType, @QueryParam("startswith") String startsWith) throws IOException { if ((startsWith == null || startsWith.isBlank()) && (eq == null || eq.isBlank())) { @@ -367,7 +367,7 @@ public Response getJbrowseNames(@PathParam("organismAbbrev") String organismAbbr command.add(organismAbbrev); command.add("genomic"); command.add(String.valueOf(isPartial)); - command.add(appVersion); + command.add(appType); command.add(sourceId); return responseFromCommand(command); } @@ -377,7 +377,7 @@ public Response getJbrowseNames(@PathParam("organismAbbrev") String organismAbbr @Produces(MediaType.APPLICATION_JSON) public Response getJbrowseAaNames(@PathParam("organismAbbrev") String organismAbbrev, @QueryParam("equals") String eq, - @DefaultValue("1") @QueryParam("appVersion") String appVersion, + @DefaultValue("1") @QueryParam("appType") String appType, @QueryParam("startswith") String startsWith) throws IOException { String gusHome = getWdkModel().getGusHome(); @@ -398,7 +398,7 @@ public Response getJbrowseAaNames(@PathParam("organismAbbrev") String organismAb command.add(organismAbbrev); command.add("protein"); command.add(String.valueOf(isPartial)); - command.add(appVersion); + command.add(appType); command.add(sourceId); return responseFromCommand(command);