omeroweb.webclient.controller package

Submodules

omeroweb.webclient.controller.container module

class omeroweb.webclient.controller.container.BaseContainer(conn, project=None, dataset=None, image=None, screen=None, plate=None, acquisition=None, well=None, tag=None, tagset=None, file=None, comment=None, annotation=None, index=None, orphaned=None, **kw)

Bases: webclient.controller.BaseController

_get_object()

Since the container is often used to wrap a single Project, Dataset etc, several methods need access to the underlying object. E.g. obj_type(), obj_id(), canAnnotate(), canEdit(). This removes many if statements from the metadata_general.html template for places that are displaying data for a single Object. E.g. Edit Name etc.

acquisition = None

annotationList()

assertNotNone(obj, obj_id, obj_name)

c_size = 0

canAnnotate()

canDownload(objDict=None)

Returns False if any of selected object cannot be downloaded

canEdit()

canExportAsJpg(request, objDict=None)

Can’t export as Jpg, Png, Tiff if bigger than approx 12k * 12k. Limit set by OOM error in omeis.providers.re.RGBIntBuffer

canUseOthersAnns()

Test to see whether other user’s Tags, Files etc should be provided for annotating. Used to ensure that E.g. Group Admins / Owners don’t try to link other user’s Annotations when in a private group (even though they could retrieve those annotations)

channelMetadata(noRE=False)

checkMimetype(file_type)

comment = None

companionFiles()

containers = None

copyDatasetToProject(source, destination=None)

copyDatasetsToProject(datasets, project)

copyImageToDataset(source, destination=None)

copyImagesToDataset(images, dataset)

copyPlateToScreen(source, destination=None)

copyPlatesToScreen(plates, screen)

createAnnotationsLinks(atype, tids, oids, well_index=0)

Links existing annotations to 1 or more objects

@param atype: Annotation type E.g. “tag”, “file” @param tids: Annotation IDs @param oids: Dict of Objects and IDs. E.g. {“Image”: [1,2,3],

“Dataset”, [6]}

createCommentAnnotations(content, oids, well_index=0)

createDataset(name, description=None, img_ids=None)

createFileAnnotations(newFile, oids, well_index=0)

createProject(name, description=None)

createScreen(name, description=None)

createTagAnnotations(tag, desc, oids, well_index=0, tag_group_id=None)

Creates a new tag (with description) OR uses existing tag with the specified name if found. Links the tag to the specified objects. @param tag: Tag text/name @param desc: Tag description @param oids: Dict of Objects and IDs. E.g. {“Image”: [1,2,3],

“Dataset”, [6]}

dataset = None

deleteItem(child=False, anns=False)

deleteObjects(otype, ids, child=False, anns=False)

experimenter = None

file = None

file_annotations = None

formatMetadataLine(l)

getFilesByObject(parent_type=None, parent_ids=None)

getGroupedRatings(rating_annotations=None)

Groups ratings in preparation for display. Picks out the user’s rating and groups the remaining ones by value. NB: This should be called after annotationList() has loaded annotations.

getNumberOfFields()

Applies to Plates (all fields) or PlateAcquisitions

getPermsCss()

Shortcut to get permissions flags, E.g. for css

getPlateId()

Used by templates that display Plates or PlateAcquisitions

getTagCount(eid=None)

getTagsByObject(parent_type=None, parent_ids=None)

image = None

index = None

listContainerHierarchy(eid=None)

listFigureScripts(objDict=None)

This configures all the Figure Scripts, setting their enabled status given the currently selected object (self.image etc) or batch objects (uses objDict).

listImagesInDataset(did, eid=None, page=None, load_pixels=False)

listOrphanedImages(eid=None, page=None)

loadBatchAnnotations(objDict, ann_ids=None, addedByMe=False)

Look up the Tags, Files, Comments, Ratings etc that are on one or more of the objects in objDect.

loadDataByTag()

loadTags(eid=None)

loadTagsRecursive(eid=None, offset=None, limit=1000)

long_annotations = None

move(parent, destination)

obj_id()

obj_type = None

openAstexViewerCompatible()

Is the image suitable to be viewed with the Volume viewer ‘Open Astex Viewer’ applet? Image must be a ‘volume’ of suitable dimensions and not too big.

orphaned = False

paste(destination)

plate = None

project = None

remove(parents, index, tag_owner_id=None)

Removes the current object (file, tag, comment, dataset, plate, image) from its parents by manually deleting the link. For Comments, we check whether it becomes an orphan & delete if true If self.tag and owner_id is specified, only remove the tag if it is owned by that owner

@param parents: List of parent IDs, E.g. [‘image-123’]

removemany(images)

screen = None

tag = None

tags = None

text_annotations = None

txannSize = 0

updateDataset(name, description=None)

updateDescription(o_type, description=None)

updateImage(name, description=None)

updateName(o_type, name)

updatePlate(name, description=None)

updateProject(name, description=None)

updateScreen(name, description=None)

well = None

omeroweb.webclient.controller.help module

class omeroweb.webclient.controller.help.BaseHelp(conn, **kw)

Bases: webclient.controller.BaseController

omeroweb.webclient.controller.history module

class omeroweb.webclient.controller.history.BaseCalendar(conn, year=None, month=None, day=None, eid=None, **kw)

Bases: webclient.controller.BaseController

calendar_items(month, monthrange)

create_calendar()

day = None

get_items(page=None)

last_month = None

last_month_name = None

last_year = None

month = None

month_range(year, month)

next_month = None

next_month_name = None

next_year = None

year = None

omeroweb.webclient.controller.impexp module

class omeroweb.webclient.controller.impexp.BaseImpexp(conn, **kw)

Bases: webclient.controller.BaseController

omeroweb.webclient.controller.index module

class omeroweb.webclient.controller.index.BaseIndex(conn)

Bases: webclient.controller.BaseController

loadLastAcquisitions()

loadMostRecent()

loadTagCloud()

omeroweb.webclient.controller.search module

class omeroweb.webclient.controller.search.BaseSearch(conn, **kw)

Bases: webclient.controller.BaseController

c_size = 0

datasets = None

dsSize = 0

images = None

imgSize = 0

moreResults = False

prSize = 0

projects = None

search(query, onlyTypes, fields, searchGroup, ownedBy, useAcquisitionDate, date=None)

omeroweb.webclient.controller.share module

class omeroweb.webclient.controller.share.BaseShare(conn, share_id=None, **kw)

Bases: webclient.controller.BaseController

addComment(host, comment)

cmSize = None

comments = None

createDiscussion(host, message, members, enable, expiration=None)

createShare(host, images, message, members, enable, expiration=None)

getAllUsers(share_id)

getComments(share_id)

getMembers(share_id)

getShares()

imageInShare = None

imgSize = 0

loadShareContent()

memberShares = None

membersInShare = None

mshSize = 0

obj_id()

Same as BaseContainer. Used to create identifier E.g. share-123 in right-hand panel

obj_type()

Same as BaseContainer. Used to create identifier E.g. share-123 in right-hand panel

oshSize = 0

ownShares = None

removeImage(image_id)

shSize = None

share = None

shares = None

updateShareOrDiscussion(host, message, members, enable, expiration=None)

Module contents

class omeroweb.webclient.controller.BaseController(conn, **kw)

Bases: object

conn = None

doPaging(page, page_size, total_size, limit=200)

getShareId()