Trees | Indices | Help |
|
---|
|
Connection wrapper. Handles connecting and keeping the session alive, creation of various services, context switching, security privilidges etc.
|
|||
|
|||
Boolean |
|
||
|
|||
_BlitzGateway |
|
||
|
|||
_BlitzGateway or None if not admin or username unknown |
|
||
Boolean |
|
||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
omero.sys.EventContext
|
|
||
ExperimenterWrapper |
|
||
|
|||
|
|||
|
|||
|
|||
|
|||
omero.model.session
|
|
||
Boolean |
|
||
Boolean |
|
||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
omero.gateway.ProxyObjectWrapper |
|
||
|
|||
|
|||
|
|||
|
|||
|
|||
ProjectWrapper list |
|
||
ProjectWrapper list |
|
||
ExperimenterWrapper generator |
|
||
ExperimenterGroupWrapper |
|
||
ExperimenterGroupWrapper generator |
|
||
ExperimenterGroupWrapper generator |
|
||
ExperimenterGroupWrapper generator |
|
||
ExperimenterWrapper generator |
|
||
ExperimenterWrapper generator |
|
||
ExperimenterWrapper generator |
|
||
ExperimenterWrapper generator |
|
||
ExperimenterGroupWrapper generator |
|
||
Int |
|
||
ImageWrapper generator |
|
||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
BlitzObjectWrapper generator |
|
||
EnumerationWrapper generator |
|
||
EnumerationWrapper |
|
||
EnumerationWrapper |
|
||
Dict of <string: EnumerationWrapper list > |
|
||
List of Strings |
|
||
Dict of <string: EnumerationWrapper list > |
|
||
|
|||
|
|||
|
|||
|
|||
|
|||
omero.api.delete.DeleteHandle
|
|
||
|
|||
Inherited from |
|
|||
CONFIG = {} Holder for class wide configuration properties: |
|||
ICE_CONFIG = None ICE_CONFIG - Defines the path to the Ice configuration |
|
|||
Inherited from |
|
Create the connection wrapper. Does not attempt to connect at this stage Initialises the omero.client
|
Returns the anonymous flag
|
Returns named property of the wrapped omero.client
|
Returns a new instance of this class, with all matching properties. TODO: Add anonymous and userAgent parameters?
|
Saves the username and password for later use, creating session etc
|
If current user isAdmin, return new connection owned by 'username'
|
Keeps service alive. Returns True if connected. If connection was lost, reconnecting. If connection failed, returns False and error is logged.
|
Terminates connection with killSession(). If softclose is False, the session is really terminate disregarding its connection refcount.
|
Creates proxies to the server services. Called on connection or security switch. Doesn't actually create any services themselves. Created if/when needed. If proxies have been created already, they are resynced and reused. |
Switches between SSL and insecure (faster) connections to Blitz. The gateway must already be connected.
|
Creates a new session for the principal given in the constructor. Used during connect method |
Creates or retrieves connection for the given sessionUuid. Returns True if connected.
|
Returns error if thrown by _BlitzGateway.connect connect.
|
Returns last status of connection.
|
Returns omero_System_ice.EventContext. It containes: shareId, sessionId, sessionUuid, userId, userName, groupId, groupName, isAdmin, isReadOnly, eventId, eventType, eventType, memberOfGroups, leaderOfGroups Also saves context to self._ctx
|
Returns current Experimenter.
|
Returns current omero_model_ExperimenterGroupI.
|
Checks if a user has administration privileges.
|
Checks if a user is in system group, i.e. can have administration privileges.
|
Checks if a user has owner privileges of a particular group or any group if gid is not specified.
|
Checks if a user has write privileges to the given object.
|
Returns the existing session, or creates a new one if needed
|
Looks up the group by name, then delegates to setGroupForSession, returning the result
|
Sets the security context of this connection to the specified group
|
Gets reference to the admin service from ProxyObjectWrapper.
|
Gets reference to the query service from ProxyObjectWrapper.
|
Gets reference to the container service from ProxyObjectWrapper.
|
Gets reference to the pixels service from ProxyObjectWrapper.
|
Gets reference to the metadata service from ProxyObjectWrapper.
|
Gets ROI service.
|
Gets script service.
|
Creates a new raw file store. This service is special in that it does not get cached inside BlitzGateway so every call to this function returns a new object, avoiding unexpected inherited states.
|
Gets reference to the repository info service from ProxyObjectWrapper.
|
Gets reference to the share service from ProxyObjectWrapper.
|
Gets reference to the sharedresources from ProxyObjectWrapper.
|
Gets reference to the timeline service from ProxyObjectWrapper.
|
Gets reference to the types service from ProxyObjectWrapper.
|
Gets reference to the config service from ProxyObjectWrapper.
|
Creates a new rendering engine. This service is special in that it does not get cached inside BlitzGateway so every call to this function returns a new object, avoiding unexpected inherited states.
|
Gets reference to the rendering settings service from ProxyObjectWrapper.
|
Creates a new raw pixels store. This service is special in that it does not get cached inside BlitzGateway so every call to this function returns a new object, avoiding unexpected inherited states.
|
Gets a reference to the thumbnail store on this connection object or creates a new one if none exists.
|
Gets a reference to the searching service on this connection object or creates a new one if none exists.
|
Gets reference to the update service from ProxyObjectWrapper.
|
Gets reference to the delete service from ProxyObjectWrapper.
|
Gets reference to the session service from ProxyObjectWrapper.
|
New instance of non cached Exporter, wrapped in ProxyObjectWrapper.
|
List every Project controlled by the security system.
|
List every Screens controlled by the security system.
|
Look up all experimenters and related groups. Groups are also loaded
|
Retrieve the default group for the given user id.
|
Fetch all groups of which the given user is a member. The returned groups will have all fields filled in and all collections unloaded.
|
Look up Groups where current user is a leader of.
|
Look up Groups where current user is a member of (except "user" group).
|
Return a generator for all Experimenters whose omeName starts with 'start'. Experimenters ordered by omeName.
|
Fetch all users contained in this group. The returned users will have all fields filled in and all collections unloaded.
|
Look up users who are a member of the current user active group. Returns None if the group is private and isn't lead by the current user
|
Look up users who are members of groups lead by the current user.
|
Looks up owned groups for the logged user.
|
Returns the free or available space on this file system including nested subdirectories.
|
List images based on their creation times. If both tfrom and tto are None, grab the most recent batch.
|
Retrieve single Object by type E.g. "Image" or None if not found. If more than one object found, raises ome.conditions.ApiUsageException See getObjects for more info.
|
Retrieve Objects by type E.g. "Image" Returns generator of appropriate BlitzObjectWrapper type. E.g. ImageWrapper. If ids is None, all available objects will be returned. i.e. listObjects() Filter objects by attributes. E.g. attributes={'name':name}
|
Prepares a query for iQuery. Also prepares params and determines appropriate wrapper for result Returns (query, params, wrapper) which can be used with the appropriate query method. Used by getObjects and getObject above.
|
Lists FileAnnotations created by users, filtering by namespaces if specified. If NO namespaces are specified, then 'known' namespaces are excluded by default, such as original files and companion files etc. File objects are loaded so E.g. file name is available without lazy loading.
|
Retrieve Annotation Links by parent_type E.g. "Image". Not Ordered. Returns generator of AnnotationLinkWrapper If parent_ids is None, all available objects will be returned. i.e. listObjects()
|
Creates a new multi-dimensional image from the sequence of 2D numpy arrays in zctPlanes. zctPlanes should be a generator of numpy 2D arrays of shape (sizeY, sizeX) ordered to iterate through T first, then C then Z. Example usage: original = conn.getObject("Image", 1) sizeZ = original.getSizeZ() sizeC = original.getSizeC() sizeT = original.getSizeT() zctList = [] for z in range(sizeZ): for c in range(sizeC): for t in range(sizeT): zctList.append( (z,c,t) ) def planeGen(): planes = original.getPrimaryPixels().getPlanes(zctList) for p in planes: # perform some manipulation on each plane yield p createImageFromNumpySeq (planeGen(), imageName, sizeZ=sizeZ, sizeC=sizeC, sizeT=sizeT @param session An OMERO service factory or equivalent with getQueryService() etc. @param zctPlanes A generator of numpy 2D arrays, corresponding to Z-planes of new image. @param imageName Name of new image @param description Description for the new image @param dataset If specified, put the image in this dataset. omero.model.Dataset object @return The new OMERO image: omero.model.ImageI |
Class method to create a FileAnnotationWrapper from a local file. File is uploaded to create an omero.model.OriginalFileI referenced from this File Annotation. Returns a new FileAnnotationWrapper
|
Retrieve objects linked to the given annotation IDs controlled by the security system.
|
Get all enumerations by class
|
Get enumeration by class and value
|
Get enumeration by class and ID
|
Gets original enumerations. Returns a dictionary of enumeration class: list of Enumerations
|
Gets list of enumeration types
|
Get enumeration types, with lists of Enum entries
|
Deletes an enumeration object
|
Create an enumeration with given object
|
Resets the enumerations by type
|
Updates enumerations with new entries
|
Directly Delete object (removes row from database). This may fail with various constraint violations if the object is linked to others in the database
|
Generic method for deleting using the delete queue. Supports deletion of 'Project', 'Dataset', 'Image', 'Screen', 'Plate', 'Well', 'Annotation'. Options allow to delete 'independent' Annotations (Tag, Term, File) and to delete child objects.
|
Search objects of type "Project", "Dataset", "Image", "Screen", "Plate" Returns a list of results
|
|
CONFIGHolder for class wide configuration properties:
One good place to define this is on the extending class' connect() method.
|
Trees | Indices | Help |
|
---|
Generated by Epydoc 3.0.1 on Tue Jan 24 19:48:51 2012 | http://epydoc.sourceforge.net |