org.jbei.ice.services.rest

Class FileResource

java.lang.Object

org.jbei.ice.services.rest.RestResource

org.jbei.ice.services.rest.FileResource

@Path(value="/file")
public class FileResource
extends RestResource

Resource for accessing files both locally and remotely

Author:

Hector Plahar

Field Summary

Fields inherited from class org.jbei.ice.services.rest.RestResource

API_KEY_CLIENT_ID, API_KEY_TOKEN, API_KEY_USER, apiClientId, apiToken, apiUser, AUTHENTICATION_PARAM_NAME, hmacHeader, querySessionId, REMOTE_USER_ID, REMOTE_USER_TOKEN, remoteUserId, remoteUserToken, request, sessionId, WOR_PARTNER_TOKEN, worPartnerToken

Constructor Summary

Constructors

Constructor and Description
FileResource()

Method Summary

Modifier and Type	Method and Description
javax.ws.rs.core.Response	downloadCSV(List<String> sequenceFormats, List<String> fields, EntrySelection selection) Extracts the csv information and writes it to the temp dir and returns the file uuid.
javax.ws.rs.core.Response	downloadSequence(long partId, String downloadType, long remoteId, String sid)
javax.ws.rs.core.Response	getAsset(String assetName)
javax.ws.rs.core.Response	getAttachment(String fileId)
javax.ws.rs.core.Response	getEntriesInFile(InputStream fileInputStream, org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)
javax.ws.rs.core.Response	getRemoteAttachment(long partnerId, String fileId, String sid)
javax.ws.rs.core.Response	getSBOLVisual(String recordId)
javax.ws.rs.core.Response	getShotgunSequenceFile(String fileId)
javax.ws.rs.core.Response	getTmpFile(String fileId, String fileName) Retrieves a temp file by fileId
javax.ws.rs.core.Response	getTraceSequenceFile(String fileId, String sid)
javax.ws.rs.core.Response	getUploadCSV(String type, String linkedType)
javax.ws.rs.core.Response	post(InputStream fileInputStream, org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)
javax.ws.rs.core.Response	uploadSequence(InputStream fileInputStream, String recordId, String entryType, boolean extractHierarchy, org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader) this creates an entry if an id is not specified in the form data

Methods inherited from class org.jbei.ice.services.rest.RestResource

addHeaders, getThisServer, getUserId, getUserId, getWebPartner, log, requireUserId, requireUserIdOrWebPartner, requireWebPartner, respond, respond, respond, respond

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FileResource

public FileResource()

Method Detail

getAsset

@GET
 @Path(value="asset/{assetName}")
public javax.ws.rs.core.Response getAsset(@PathParam(value="assetName")
                                                                                 String assetName)

post

@POST
 @Path(value="attachment")
 @Consumes(value="multipart/form-data")
 @Produces(value="application/json")
public javax.ws.rs.core.Response post(InputStream fileInputStream,
                                                                                                                                                    org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)

Returns:

Response with attachment info on uploaded file

getTmpFile

@GET
 @Path(value="tmp/{fileId}")
public javax.ws.rs.core.Response getTmpFile(@PathParam(value="fileId")
                                                                              String fileId,
                                                                              @QueryParam(value="filename")
                                                                              String fileName)

Retrieves a temp file by fileId

getAttachment

@GET
 @Path(value="attachment/{fileId}")
public javax.ws.rs.core.Response getAttachment(@PathParam(value="fileId")
                                                                                        String fileId)

getRemoteAttachment

@GET
 @Path(value="remote/{id}/attachment/{fileId}")
public javax.ws.rs.core.Response getRemoteAttachment(@PathParam(value="id")
                                                                                                          long partnerId,
                                                                                                          @PathParam(value="fileId")
                                                                                                          String fileId,
                                                                                                          @QueryParam(value="sid")
                                                                                                          String sid)

getUploadCSV

@GET
 @Path(value="upload/{type}")
public javax.ws.rs.core.Response getUploadCSV(@PathParam(value="type")
                                                                                 String type,
                                                                                 @QueryParam(value="link")
                                                                                 String linkedType)

downloadSequence

@GET
 @Path(value="{partId}/sequence/{type}")
public javax.ws.rs.core.Response downloadSequence(@PathParam(value="partId")
                                                                                                long partId,
                                                                                                @PathParam(value="type")
                                                                                                String downloadType,
                                                                                                @DefaultValue(value="-1") @QueryParam(value="remoteId")
                                                                                                long remoteId,
                                                                                                @QueryParam(value="sid")
                                                                                                String sid)

getTraceSequenceFile

@GET
 @Path(value="trace/{fileId}")
public javax.ws.rs.core.Response getTraceSequenceFile(@PathParam(value="fileId")
                                                                                          String fileId,
                                                                                          @QueryParam(value="sid")
                                                                                          String sid)

getShotgunSequenceFile

@GET
 @Path(value="shotgunsequence/{fileId}")
public javax.ws.rs.core.Response getShotgunSequenceFile(@PathParam(value="fileId")
                                                                                                      String fileId)

getSBOLVisual

@GET
 @Produces(value="image/png")
 @Path(value="sbolVisual/{rid}")
public javax.ws.rs.core.Response getSBOLVisual(@PathParam(value="rid")
                                                                                                                   String recordId)

uploadSequence

@POST
 @Path(value="sequence")
 @Consumes(value="multipart/form-data")
 @Produces(value="application/json")
public javax.ws.rs.core.Response uploadSequence(InputStream fileInputStream,
                                                                                                                                                            String recordId,
                                                                                                                                                            String entryType,
                                                                                                                                                            @DefaultValue(value="false")
                                                                                                                                                            boolean extractHierarchy,
                                                                                                                                                            org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)

this creates an entry if an id is not specified in the form data

downloadCSV

@POST
 @Path(value="csv")
 @Consumes(value="application/json")
 @Produces(value="application/json")
public javax.ws.rs.core.Response downloadCSV(@QueryParam(value="sequenceFormats")
                                                                                                                                                 List<String> sequenceFormats,
                                                                                                                                                 @QueryParam(value="entryFields")
                                                                                                                                                 List<String> fields,
                                                                                                                                                 EntrySelection selection)

Extracts the csv information and writes it to the temp dir and returns the file uuid. Then the client is expected to make another rest call with the uuid in a separate window. This workaround is due to not being able to download files using XHR or sumsuch

getEntriesInFile

@POST
 @Consumes(value="multipart/form-data")
 @Produces(value="application/json")
 @Path(value="entries")
public javax.ws.rs.core.Response getEntriesInFile(InputStream fileInputStream,
                                                                                                                                                             org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)