org.jbei.ice.services.rest

Class PartResource

java.lang.Object

org.jbei.ice.services.rest.RestResource

org.jbei.ice.services.rest.PartResource

@Path(value="/parts")
public class PartResource
extends RestResource

Rest resource for interacting representations of biological parts on ICE

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
PartResource()

Method Summary

Modifier and Type	Method and Description
AttachmentInfo	addAttachment(long partId, AttachmentInfo attachment)
javax.ws.rs.core.Response	addSample(String partId, String strainNamePrefix, PartSample partSample)
javax.ws.rs.core.Response	addShotgunSequence(long partId, InputStream fileInputStream, org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)
javax.ws.rs.core.Response	addTraceSequence(long partId, InputStream fileInputStream, org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)
javax.ws.rs.core.Response	create(String sourceId, PartData partData) Creates a new entry.
javax.ws.rs.core.Response	createComment(long partId, UserComment userComment)
javax.ws.rs.core.Response	createLink(String partId, LinkType type, PartData partData) Creates a new link between the referenced part id and the part in the parameter
javax.ws.rs.core.Response	createPartExperiment(String partId, Study study)
AccessPermission	createPermission(String partId, AccessPermission permission)
javax.ws.rs.core.Response	customExport(EntrySelection selection)
javax.ws.rs.core.Response	delete(long partId, long historyId)
javax.ws.rs.core.Response	deleteAttachment(long partId, long attachmentId)
javax.ws.rs.core.Response	deleteLink(String partId, LinkType linkType, long linkedPart) Removes the linkId from id
javax.ws.rs.core.Response	deletePartExperiment(String partId, long experimentId)
javax.ws.rs.core.Response	deleteSample(javax.ws.rs.core.UriInfo info, long partId, long sampleId)
javax.ws.rs.core.Response	deleteSequence(long partId)
javax.ws.rs.core.Response	deleteShotgunSequence(javax.ws.rs.core.UriInfo info, long partId, long shotgunId)
javax.ws.rs.core.Response	deleteTrace(javax.ws.rs.core.UriInfo info, long partId, long traceId)
javax.ws.rs.core.Response	disablePublicAccess(String partId)
javax.ws.rs.core.Response	enablePublicAccess(String partId)
javax.ws.rs.core.Response	get(String type) Retrieves the defaults for the requested entry types.
javax.ws.rs.core.Response	getAllTraces(long partId, String sid)
List<AttachmentInfo>	getAttachments(long partId)
javax.ws.rs.core.Response	getAutoAnnotations(long partId, boolean ownerFeatures)
List<UserComment>	getComments(long partId)
javax.ws.rs.core.Response	getEntryFolders(String id) Returns the folders that an entry is contained in (filtered by permissions).
javax.ws.rs.core.Response	getHistory(long partId, int limit, int offset, boolean asc, String sort)
javax.ws.rs.core.Response	getLinkedParts(String partId, LinkType linkType) Get linked parts
javax.ws.rs.core.Response	getPartExperiments(String partId)
javax.ws.rs.core.Response	getPermissions(String id)
javax.ws.rs.core.Response	getSamples(String partId)
javax.ws.rs.core.Response	getSequence(String partId, boolean isRemote, String remoteUserToken, String remoteUserId, long fid)
ArrayList<ShotgunSequenceDTO>	getShotgunSequences(javax.ws.rs.core.UriInfo info, long partId, int limit, int start)
PartStatistics	getStatistics(long partId)
PartData	getTooltipDetails(String id, boolean isRemote, long fid) Retrieves either a remote or local tooltip
javax.ws.rs.core.Response	getTraces(long partId, int limit, int start)
javax.ws.rs.core.Response	moveToTrash(ArrayList<PartData> list)
javax.ws.rs.core.Response	read(String id, boolean isRemote, String remoteUserToken, String remoteUserId, long fid) Retrieves a part using any of the unique identifiers.
javax.ws.rs.core.Response	removePermission(String partId, long permissionId)
javax.ws.rs.core.Response	transfer(PartData partData)
javax.ws.rs.core.Response	update(long partId, PartData partData) Update the part information at the specified resource identifier
UserComment	updateComment(long partId, long commentId, UserComment userComment)
javax.ws.rs.core.Response	updateEntries(Visibility visibility, List<Long> entryIds)
javax.ws.rs.core.Response	updateSequence(long partId, boolean add, FeaturedDNASequence sequence)

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

PartResource

public PartResource()

Method Detail

read

@GET
 @Produces(value="application/json")
 @Path(value="/{id}")
public javax.ws.rs.core.Response read(@PathParam(value="id")
                                                                                                      String id,
                                                                                                      @DefaultValue(value="false") @QueryParam(value="remote")
                                                                                                      boolean isRemote,
                                                                                                      @QueryParam(value="token")
                                                                                                      String remoteUserToken,
                                                                                                      @QueryParam(value="userId")
                                                                                                      String remoteUserId,
                                                                                                      @QueryParam(value="folderId")
                                                                                                      long fid)

Retrieves a part using any of the unique identifiers. e.g. Part number, synthetic id, or global unique identifier.

get

@GET
 @Produces(value="application/json")
 @Path(value="/defaults/{type}")
public javax.ws.rs.core.Response get(@PathParam(value="type")
                                                                                                                String type)

Retrieves the defaults for the requested entry types.

Parameters:

type - the type of entry i.e. PLASMID, PART, STRAIN or ARABIDOPSIS. Used to retrieve the default values for that entry

getEntryFolders

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/folders")
public javax.ws.rs.core.Response getEntryFolders(@PathParam(value="id")
                                                                                                                         String id)

Returns the folders that an entry is contained in (filtered by permissions).

Parameters:

id - unique identifier for entry whose containing folders are being returned

getTooltipDetails

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/tooltip")
public PartData getTooltipDetails(@PathParam(value="id")
                                                                                                          String id,
                                                                                                          @DefaultValue(value="false") @QueryParam(value="remote")
                                                                                                          boolean isRemote,
                                                                                                          @QueryParam(value="folderId")
                                                                                                          long fid)

Retrieves either a remote or local tooltip

Parameters:

id - unique identifier for entry whose tooltip is to be retrieved

isRemote - if true, a remote tooltip is being retrieved, false, local

fid - required if isRemote is true. The remote entry should be shared in this folder

Returns:

PartData information about the entry with enough information to show the tooltip

getPermissions

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/permissions")
public javax.ws.rs.core.Response getPermissions(@PathParam(value="id")
                                                                                                                            String id)

createPermission

@POST
 @Produces(value="application/json")
 @Path(value="/{id}/permissions")
public AccessPermission createPermission(@PathParam(value="id")
                                                                                                                      String partId,
                                                                                                                      AccessPermission permission)

removePermission

@DELETE
 @Produces(value="application/json")
 @Path(value="/{id}/permissions/{permissionId}")
public javax.ws.rs.core.Response removePermission(@PathParam(value="id")
                                                                                                                                                String partId,
                                                                                                                                                @PathParam(value="permissionId")
                                                                                                                                                long permissionId)

getPartExperiments

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/experiments")
public javax.ws.rs.core.Response getPartExperiments(@PathParam(value="id")
                                                                                                                                String partId)

createPartExperiment

@POST
 @Produces(value="application/json")
 @Path(value="/{id}/experiments")
public javax.ws.rs.core.Response createPartExperiment(@PathParam(value="id")
                                                                                                                                   String partId,
                                                                                                                                   Study study)

deletePartExperiment

@DELETE
 @Path(value="/{id}/experiments/{eid}")
public javax.ws.rs.core.Response deletePartExperiment(@PathParam(value="id")
                                                                                                      String partId,
                                                                                                      @PathParam(value="eid")
                                                                                                      long experimentId)

enablePublicAccess

@PUT
 @Produces(value="application/json")
 @Path(value="/{id}/permissions/public")
public javax.ws.rs.core.Response enablePublicAccess(@PathParam(value="id")
                                                                                                                                       String partId)

disablePublicAccess

@DELETE
 @Produces(value="application/json")
 @Path(value="/{id}/permissions/public")
public javax.ws.rs.core.Response disablePublicAccess(@PathParam(value="id")
                                                                                                                                           String partId)

getStatistics

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/statistics")
public PartStatistics getStatistics(@PathParam(value="id")
                                                                                                               long partId)

getComments

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/comments")
public List<UserComment> getComments(@PathParam(value="id")
                                                                                                              long partId)

createComment

@POST
 @Produces(value="application/json")
 @Path(value="/{id}/comments")
public javax.ws.rs.core.Response createComment(@PathParam(value="id")
                                                                                                                         long partId,
                                                                                                                         UserComment userComment)

updateComment

@PUT
 @Produces(value="application/json")
 @Path(value="/{id}/comments/{commentId}")
public UserComment updateComment(@PathParam(value="id")
                                                                                                                      long partId,
                                                                                                                      @PathParam(value="commentId")
                                                                                                                      long commentId,
                                                                                                                      UserComment userComment)

addAttachment

@POST
 @Produces(value="application/json")
 @Consumes(value="application/json")
 @Path(value="/{id}/attachments")
public AttachmentInfo addAttachment(@PathParam(value="id")
                                                                                                                                                      long partId,
                                                                                                                                                      AttachmentInfo attachment)

getAttachments

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/attachments")
public List<AttachmentInfo> getAttachments(@PathParam(value="id")
                                                                                                                       long partId)

deleteAttachment

@DELETE
 @Path(value="/{id}/attachments/{attachmentId}")
public javax.ws.rs.core.Response deleteAttachment(@PathParam(value="id")
                                                                                                           long partId,
                                                                                                           @PathParam(value="attachmentId")
                                                                                                           long attachmentId)

getHistory

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/history")
public javax.ws.rs.core.Response getHistory(@PathParam(value="id")
                                                                                                                    long partId,
                                                                                                                    @QueryParam(value="limit")
                                                                                                                    int limit,
                                                                                                                    @QueryParam(value="offset")
                                                                                                                    int offset,
                                                                                                                    @QueryParam(value="asc")
                                                                                                                    boolean asc,
                                                                                                                    @QueryParam(value="sort")
                                                                                                                    String sort)

Returns:

history entries for the part

delete

@DELETE
 @Produces(value="application/json")
 @Path(value="/{id}/history/{historyId}")
public javax.ws.rs.core.Response delete(@PathParam(value="id")
                                                                                                                               long partId,
                                                                                                                               @PathParam(value="historyId")
                                                                                                                               long historyId)

getTraces

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/traces")
public javax.ws.rs.core.Response getTraces(@PathParam(value="id")
                                                                                                                  long partId,
                                                                                                                  @DefaultValue(value="100") @QueryParam(value="limit")
                                                                                                                  int limit,
                                                                                                                  @DefaultValue(value="0") @QueryParam(value="start")
                                                                                                                  int start)

Returns:

traces for the part

getAllTraces

@GET
 @Path(value="/{id}/traces/all")
 @Produces(value="application/octet-stream")
public javax.ws.rs.core.Response getAllTraces(@PathParam(value="id")
                                                                                                                                 long partId,
                                                                                                                                 @QueryParam(value="sid")
                                                                                                                                 String sid)

getShotgunSequences

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/shotgunsequences")
public ArrayList<ShotgunSequenceDTO> getShotgunSequences(@Context
                                                                                                                                          javax.ws.rs.core.UriInfo info,
                                                                                                                                          @PathParam(value="id")
                                                                                                                                          long partId,
                                                                                                                                          @DefaultValue(value="100") @QueryParam(value="limit")
                                                                                                                                          int limit,
                                                                                                                                          @DefaultValue(value="0") @QueryParam(value="start")
                                                                                                                                          int start)

addTraceSequence

@POST
 @Produces(value="application/json")
 @Path(value="/{id}/traces")
public javax.ws.rs.core.Response addTraceSequence(@PathParam(value="id")
                                                                                                                          long partId,
                                                                                                                          InputStream fileInputStream,
                                                                                                                          org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)

addShotgunSequence

@POST
 @Produces(value="application/json")
 @Path(value="/{id}/shotgunsequences")
public javax.ws.rs.core.Response addShotgunSequence(@PathParam(value="id")
                                                                                                                                      long partId,
                                                                                                                                      InputStream fileInputStream,
                                                                                                                                      org.glassfish.jersey.media.multipart.FormDataContentDisposition contentDispositionHeader)

deleteTrace

@DELETE
 @Path(value="/{id}/traces/{traceId}")
public javax.ws.rs.core.Response deleteTrace(@Context
                                                                                            javax.ws.rs.core.UriInfo info,
                                                                                            @PathParam(value="id")
                                                                                            long partId,
                                                                                            @PathParam(value="traceId")
                                                                                            long traceId)

deleteShotgunSequence

@DELETE
 @Path(value="/{id}/shotgunsequences/{shotgunId}")
public javax.ws.rs.core.Response deleteShotgunSequence(@Context
                                                                                                                  javax.ws.rs.core.UriInfo info,
                                                                                                                  @PathParam(value="id")
                                                                                                                  long partId,
                                                                                                                  @PathParam(value="shotgunId")
                                                                                                                  long shotgunId)

getSamples

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/samples")
public javax.ws.rs.core.Response getSamples(@PathParam(value="id")
                                                                                                                    String partId)

addSample

@POST
 @Produces(value="application/json")
 @Path(value="/{id}/samples")
public javax.ws.rs.core.Response addSample(@PathParam(value="id")
                                                                                                                    String partId,
                                                                                                                    @QueryParam(value="strainNamePrefix")
                                                                                                                    String strainNamePrefix,
                                                                                                                    PartSample partSample)

deleteSample

@DELETE
 @Produces(value="application/json")
 @Path(value="/{id}/samples/{sampleId}")
public javax.ws.rs.core.Response deleteSample(@Context
                                                                                                                                    javax.ws.rs.core.UriInfo info,
                                                                                                                                    @PathParam(value="id")
                                                                                                                                    long partId,
                                                                                                                                    @PathParam(value="sampleId")
                                                                                                                                    long sampleId)

getSequence

@GET
 @Produces(value="application/json")
 @Path(value="/{id}/sequence")
public javax.ws.rs.core.Response getSequence(@PathParam(value="id")
                                                                                                                      String partId,
                                                                                                                      @DefaultValue(value="false") @QueryParam(value="remote")
                                                                                                                      boolean isRemote,
                                                                                                                      @QueryParam(value="token")
                                                                                                                      String remoteUserToken,
                                                                                                                      @QueryParam(value="userId")
                                                                                                                      String remoteUserId,
                                                                                                                      @QueryParam(value="folderId")
                                                                                                                      long fid)

updateSequence

@POST
 @Produces(value="application/json")
 @Path(value="/{id}/sequence")
public javax.ws.rs.core.Response updateSequence(@PathParam(value="id")
                                                                                                                          long partId,
                                                                                                                          @DefaultValue(value="false") @QueryParam(value="add")
                                                                                                                          boolean add,
                                                                                                                          FeaturedDNASequence sequence)

deleteSequence

@DELETE
 @Path(value="/{id}/sequence")
public javax.ws.rs.core.Response deleteSequence(@PathParam(value="id")
                                                                                       long partId)

create

@POST
 @Consumes(value="application/json")
 @Produces(value="application/json")
public javax.ws.rs.core.Response create(@QueryParam(value="source")
                                                                                                                        String sourceId,
                                                                                                                        PartData partData)

Creates a new entry. If the sourceId parameter is set, the new entry is a copy of the source id (if found) otherwise the new entry is created from the data contained in the partData

Parameters:

sourceId - optional unique identifier for an existing part to copy. If not set, the partData parameter must be set

partData - optional data for creating new entry. if not set, then the sourceId must be set

Returns:

wrapper around identifier for newly created part which can be used to retrieve it

transfer

@PUT
 @Path(value="/transfer")
 @Consumes(value="application/json")
 @Produces(value="application/json")
public javax.ws.rs.core.Response transfer(PartData partData)

update

@PUT
 @Path(value="/{id}")
 @Consumes(value="application/json")
 @Produces(value="application/json")
public javax.ws.rs.core.Response update(@PathParam(value="id")
                                                                                                                                             long partId,
                                                                                                                                             PartData partData)

Update the part information at the specified resource identifier

Parameters:

partId - unique resource identifier for part being updated

partData - data to update part with

moveToTrash

@POST
 @Path(value="/trash")
 @Consumes(value="application/json")
public javax.ws.rs.core.Response moveToTrash(ArrayList<PartData> list)

getLinkedParts

@GET
 @Path(value="/{id}/links")
public javax.ws.rs.core.Response getLinkedParts(@PathParam(value="id")
                                                                                 String partId,
                                                                                 @DefaultValue(value="CHILD") @QueryParam(value="linkType")
                                                                                 LinkType linkType)

Get linked parts

Parameters:

partId - unique identifier for part whose links are to be retrieved

Returns:

list of PartData that represent links

deleteLink

@DELETE
 @Path(value="/{id}/links/{linkedId}")
public javax.ws.rs.core.Response deleteLink(@PathParam(value="id")
                                                                                           String partId,
                                                                                           @DefaultValue(value="CHILD") @QueryParam(value="linkType")
                                                                                           LinkType linkType,
                                                                                           @PathParam(value="linkedId")
                                                                                           long linkedPart)

Removes the linkId from id

createLink

@POST
 @Path(value="/{id}/links")
 @Consumes(value="application/json")
 @Produces(value="application/json")
public javax.ws.rs.core.Response createLink(@PathParam(value="id")
                                                                                                                                                        String partId,
                                                                                                                                                        @DefaultValue(value="CHILD") @QueryParam(value="linkType")
                                                                                                                                                        LinkType type,
                                                                                                                                                        PartData partData)

Creates a new link between the referenced part id and the part in the parameter

Parameters:

partId - part to be linked

partData - should essentially just contain the part Id or details for a new entry that should be created

updateEntries

@PUT
 @Consumes(value="application/json")
 @Produces(value="application/json")
public javax.ws.rs.core.Response updateEntries(@QueryParam(value="visibility")
                                                                                                                              Visibility visibility,
                                                                                                                              List<Long> entryIds)

getAutoAnnotations

@GET
 @Path(value="/{id}/annotations/auto")
 @Produces(value="application/json")
public javax.ws.rs.core.Response getAutoAnnotations(@PathParam(value="id")
                                                                                                                                     long partId,
                                                                                                                                     @QueryParam(value="ownerFeatures")
                                                                                                                                     boolean ownerFeatures)

customExport

@POST
 @Path(value="/custom")
 @Produces(value="application/octet-stream")
public javax.ws.rs.core.Response customExport(EntrySelection selection)