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replace appVersion param with appType
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Bindu Gajria committed Oct 4, 2024
1 parent caab041 commit a26feef
Showing 1 changed file with 20 additions and 20 deletions.
40 changes: 20 additions & 20 deletions Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand All @@ -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);
}
Expand All @@ -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();
Expand All @@ -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);
}
Expand All @@ -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
Expand All @@ -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);
}
Expand All @@ -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
Expand All @@ -150,15 +150,15 @@ 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);
}

@GET
@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();
Expand All @@ -174,15 +174,15 @@ public Response getJbrowseOrganismSpecificTracks(@PathParam("organismAbbrev") St
command.add(isApollo);
command.add(buildNumber);
command.add(webservicesDir);
command.add(appVersion);
command.add(appType);
return responseFromCommand(command);
}

@GET
@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();
Expand All @@ -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);
}

Expand All @@ -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();
Expand All @@ -228,15 +228,15 @@ 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);
}

@GET
@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();
Expand All @@ -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);
}

Expand Down Expand Up @@ -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())) {
Expand All @@ -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);
}
Expand All @@ -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();
Expand All @@ -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);
Expand Down

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