omeroweb.webclient package
Submodules
omeroweb.webclient.decorators module
Decorators for use with the webclient application.
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class omeroweb.webclient.decorators.login_required(ignore_login_fail=False, setGroupContext=False, login_redirect=None, **kwargs)
Bases: omeroweb.decorators.login_required
webclient specific extension of the OMERO.web login_required() decorator.
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on_logged_in(request, conn)
Called whenever the users is successfully logged in.
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on_not_logged_in(request, url, error=None)
This can be used to fail silently (not return 403, 500 etc. E.g.
keepalive ping)
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prepare_session(request)
Prepares various session variables.
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class omeroweb.webclient.decorators.render_response
Bases: omeroweb.decorators.render_response
Subclass for adding additional data to the ‘context’ dict passed to
templates
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load_settings(request, context, conn)
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prepare_context(request, context, *args, **kwargs)
This allows templates to access the current eventContext and user from
the L{omero.gateway.BlitzGateway}.
E.g. <h1>{{ ome.user.getFullName }}</h1>
If these are not required by the template, then they will not need to
be loaded by the Blitz Gateway.
The results are cached by Blitz Gateway, so repeated calls have no
additional cost.
We also process some values from settings and add these to the
context.
omeroweb.webclient.show module
Generic functionality for handling particular links and “showing” objects
in the OMERO.web tree view.
Bases: exceptions.Exception
Exception to signal that we are on the wrong menu.
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class omeroweb.webclient.show.Show(conn, request, menu)
Bases: object
This object is used by most of the top-level pages. The “show” and
“path” query strings are used by this object to both direct OMERO.web to
the correct locations in the hierarchy and select the correct objects
in that hierarchy.
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PATH_REGEX = <_sre.SRE_Pattern object at 0x142dc6d0>
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SUPPORTED_OBJECT_TYPES = ('project', 'dataset', 'image', 'screen', 'plate', 'tag', 'acquisition', 'run', 'well')
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TOP_LEVEL_PREFIXES = ('project', 'screen')
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WELL_REGEX = <_sre.SRE_Pattern object at 0x18ef78d0>
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_add_if_supported(path)
Adds a path to the initially selected list if it is supported.
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_find_first_selected()
Finds the first selected object.
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_load_first_selected(first_obj, attributes)
Loads the first selected object from the server. Will raise
L{IncorrectMenuError} if the initialized menu was incorrect for
the loaded objects.
@param first_obj Type of the first selected object.
@type first_obj String
@param attributes Set of attributes to filter on.
@type attributes L{dict}
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_load_tag(attributes)
Loads a Tag based on a certain set of attributes from the server.
@param attributes Set of attributes to filter on.
@type attributes L{dict}
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_load_well(attributes)
Loads a Well based on a certain set of attributes from the server.
@param attributes Set of attributes to filter on.
@type attributes L{dict}
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first_selected
Retrieves the first selected object. The first time this method is
invoked on the instance the actual retrieval is performed. All other
invocations retrieve the same instance without server interaction.
Will raise L{IncorrectMenuError} if the initialized menu was
incorrect for the loaded objects.
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get_well_row_column(well)
Retrieves a tuple of row and column as L{int} for a given Well name
(“A1” or “1A”) string.
@param well Well name string to retrieve the row and column tuple for.
@type well L{str}
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initially_open
Retrieves the nodes of the tree that will be initially open based on
the nodes that are initially selected. Should not be invoked until
after first retrieval of the L{Show.first_selected} property.
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initially_open_owner
Retrieves the owner of the node closest to the root of the tree from
the list of initially open nodes. Should not be invoked until
after first retrieval of the L{Show.first_selected} property.
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initially_select
Retrieves the list of “paths” (“type-id”) we have been requested to
show/select in the user interface. May be different than we were
first initialised with due to certain nodes of the Screen-Plate-Well
hierachy not being present in the tree. Should not be invoked until
after first retrieval of the L{Show.first_selected} property.
omeroweb.webclient.tree module
Helper functions for views that handle object trees
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omeroweb.webclient.tree.get_perms(conn, object_type, object_id, object_owner_id, object_group_id, cache)
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omeroweb.webclient.tree.marshal_dataset(conn, row)
Given a Dataset row (list) marshals it into a dictionary. Order
and type of columns in row is:
- id (rlong)
- name (rstring)
- details.owner.id (rlong)
- details.permissions (dict)
- child_count (rlong)
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param row The Dataset row to marshal
@type row L{list}
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omeroweb.webclient.tree.marshal_datasets(conn, experimenter_id)
Marshal datasets for a given user.
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param experimenter_id The Experimenter (user) ID to marshal
Datasets for or None if we are not to filter by a specific user.
@type experimenter_id L{long}
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omeroweb.webclient.tree.marshal_plate(conn, row)
Given a Plate row (list) marshals it into a dictionary. Order and
type of columns in row is:
- id (rlong)
- name (rstring)
- details.owner.id (rlong)
- details.permissions (dict)
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param row The Plate row to marshal
@type row L{list}
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omeroweb.webclient.tree.marshal_plate_acquisition(conn, row)
Given a PlateAcquisition row (list) marshals it into a
dictionary. Order and type of columns in row is:
- id (rlong)
- name (rstring)
- details.owner.id (rlong)
- details.permissions (dict)
- startTime (rtime)
- endTime (rtime)
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param row The PlateAcquisition row to marshal
@type row L{list}
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omeroweb.webclient.tree.marshal_plates(conn, experimenter_id)
Marshal plates for a given user.
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param experimenter_id The Experimenter (user) ID to marshal
Plates for or None if we are not to filter by a specific user.
@type experimenter_id L{long}
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omeroweb.webclient.tree.marshal_projects(conn, experimenter_id)
Marshals projects and contained datasets for a given user.
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param experimenter_id The Experimenter (user) ID to marshal
Projects for or None if we are not to filter by a specific user.
@type experimenter_id L{long}
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omeroweb.webclient.tree.marshal_screens(conn, experimenter_id=None)
Marshals screens and contained plates and aquisitions for a given user.
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param experimenter_id The Experimenter (user) ID to marshal
Screens for or None if we are not to filter by a specific user.
@type experimenter_id L{long}
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omeroweb.webclient.tree.parse_permissions_css(permissions, ownerid, conn)
Parse numeric permissions into a string of space separated
CSS classes.
@param permissions Permissions to parse
@type permissions L{omero.rtypes.rmap}
@param ownerid Owner Id for the object having Permissions
@type ownerId Integer
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
omeroweb.webclient.urls module
omeroweb.webclient.views module
A view functions is simply a Python function that takes a Web request and
returns a Web response. This response can be the HTML contents of a Web page,
or a redirect, or the 404 and 500 error, or an XML document, or an image...
or anything.
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omeroweb.webclient.views.activities(request, *args, **kwargs)
This refreshes callback handles (delete, scripts, chgrp etc) and provides
html to update Activities window & Progressbar.
The returned html contains details for ALL callbacks in web session,
regardless of their status.
We also add counts of jobs, failures and ‘in progress’ to update status
bar.
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omeroweb.webclient.views.activities_update(request, *args, **kwargs)
If the above ‘action’ == ‘clean’ then we clear jobs from
request.session[‘callback’] either a single job (if ‘jobKey’ is specified
in POST) or all jobs (apart from those in progress)
Handle adding Comments to one or more objects
Unbound instance of Comment form not available.
If the form has been submitted, a bound instance of the form
is created using request.POST
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omeroweb.webclient.views.annotate_file(request, *args, **kwargs)
On ‘POST’, This handles attaching an existing file-annotation(s) and/or
upload of a new file to one or more objects
Otherwise it generates the form for choosing file-annotations & local
files.
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omeroweb.webclient.views.annotate_map(request, *args, **kwargs)
Handle adding Map Annotations to one or more objects
POST data “mapAnnotation” should be list of [‘key’:’value’] pairs.
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omeroweb.webclient.views.annotate_rating(request, *args, **kwargs)
Handle adding Rating to one or more objects
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omeroweb.webclient.views.annotate_tags(request, *args, **kwargs)
This handles creation AND submission of Tags form, adding new AND/OR
existing tags to one or more objects
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omeroweb.webclient.views.avatar(request, *args, **kwargs)
Returns the experimenter’s photo
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omeroweb.webclient.views.batch_annotate(request, *args, **kwargs)
This page gives a form for batch annotation.
Local File form and Comment form are loaded. Other forms are loaded via
AJAX
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omeroweb.webclient.views.change_active_group(request, *args, **kwargs)
Simply changes the request.session[‘active_group’] which is then used by
the @login_required decorator to configure conn for any group-based
queries.
Finally this redirects to the ‘url’.
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omeroweb.webclient.views.chgrp(request, *args, **kwargs)
Moves data to a new group, using the chgrp queue.
Handles submission of chgrp form: all data in POST.
Adds the callback handle to the request.session[‘callback’][‘jobId’]
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omeroweb.webclient.views.download_annotation(request, *args, **kwargs)
Returns the file annotation as an http response for download
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omeroweb.webclient.views.download_orig_metadata(request, *args, **kwargs)
Downloads the ‘Original Metadata’ as a text file
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omeroweb.webclient.views.download_placeholder(request, *args, **kwargs)
Page displays a simple “Preparing download...” message and redirects to
the ‘url’.
We construct the url and query string from request: ‘url’ and ‘ids’.
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omeroweb.webclient.views.edit_channel_names(request, *args, **kwargs)
Edit and save channel names
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omeroweb.webclient.views.feed(request, *args, **kwargs)
Viewing this page doesn’t perform any action. All we do here is assemble
various data for display.
Last imports, tag cloud etc are retrived via separate AJAX calls.
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omeroweb.webclient.views.figure_script(request, *args, **kwargs)
Show a UI for running figure scripts
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omeroweb.webclient.views.fileset_check(request, *args, **kwargs)
Check whether Images / Datasets etc contain partial Multi-image filesets.
Used by chgrp or delete dialogs to test whether we can perform this
‘action’.
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omeroweb.webclient.views.getIds(request)
Used by forms to indicate the currently selected objects prepared above
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omeroweb.webclient.views.getObjectUrl(conn, obj)
This provides a url to browse to the specified omero.model.ObjectI P/D/I,
S/P, FileAnnotation etc. used to display results from the scripting
service
E.g webclient/userdata/?path=image-12601
If the object is a file annotation, try to browse to the parent P/D/I
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omeroweb.webclient.views.getObjects(request, conn=None)
Prepare objects for use in the annotation forms.
These objects are required by the form superclass to populate hidden
fields, so we know what we’re annotating on submission
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omeroweb.webclient.views.get_original_file(request, *args, **kwargs)
Returns the specified original file as an http response. Used for
displaying text or png/jpeg etc files in browser
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omeroweb.webclient.views.group_user_content(request, *args, **kwargs)
Loads html content of the Groups/Users drop-down menu on main webclient
pages.
Url should be supplied in request, as target for redirect after switching
group.
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omeroweb.webclient.views.image_as_map(request, *args, **kwargs)
Converts OMERO image into mrc.map file (using tiltpicker utils) and
returns the file
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omeroweb.webclient.views.image_viewer(request, *args, **kwargs)
Delegates to webgateway, using share connection if appropriate
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omeroweb.webclient.views.index_last_imports(request, *args, **kwargs)
Gets the most recent imports - Used in an AJAX call by home page.
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omeroweb.webclient.views.index_most_recent(request, *args, **kwargs)
Gets the most recent ‘shares’ and ‘share’ comments. Used by the homepage
via AJAX call
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omeroweb.webclient.views.index_tag_cloud(request, *args, **kwargs)
Gets the most used Tags. Used by the homepage via AJAX call
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omeroweb.webclient.views.keepalive_ping(request, *args, **kwargs)
Keeps the OMERO session alive by pinging the server
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omeroweb.webclient.views.list_scripts(request, *args, **kwargs)
List the available scripts - Just officical scripts for now
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omeroweb.webclient.views.load_calendar(request, *args, **kwargs)
Loads the calendar which is displayed in the left panel of the history
page.
Shows current month by default. Filter by experimenter
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omeroweb.webclient.views.load_chgrp_groups(request, *args, **kwargs)
Get the potential groups we can move selected data to.
These will be groups that the owner(s) of selected objects is a member of.
Objects are specified by query string like: ?Image=1,2&Dataset=3
If no selected objects are specified, simply list the groups that the
current user is a member of.
Groups list will exclude the ‘current’ group context.
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omeroweb.webclient.views.load_chgrp_target(request, *args, **kwargs)
Loads a tree for user to pick target Project, Dataset or Screen
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omeroweb.webclient.views.load_data(request, *args, **kwargs)
This loads data for the tree, via AJAX calls.
The template is specified by query string. E.g. icon, table, tree.
By default this loads Projects and Datasets.
E.g. /load_data?view=tree provides data for the tree as <li>.
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omeroweb.webclient.views.load_data_by_tag(request, *args, **kwargs)
Loads data for the tag tree and center panel.
Either get the P/D/I etc under tags, or the images etc under a tagged
Dataset or Project.
@param o_type ‘tag’ or ‘project’, ‘dataset’.
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omeroweb.webclient.views.load_history(request, *args, **kwargs)
The data for a particular date that is loaded into the center panel
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omeroweb.webclient.views.load_metadata_acquisition(request, *args, **kwargs)
The acquisition tab of the right-hand panel. Only loaded for images.
TODO: urls regex should make sure that c_type is only ‘image’ OR ‘well’
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omeroweb.webclient.views.load_metadata_details(request, *args, **kwargs)
This page is the right-hand panel ‘general metadata’, first tab only.
Shown for Projects, Datasets, Images, Screens, Plates, Wells, Tags etc.
The data and annotations are loaded by the manager. Display of appropriate
data is handled by the template.
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omeroweb.webclient.views.load_metadata_hierarchy(request, *args, **kwargs)
This loads the ancestors of the specified object and displays them in a
static tree.
Used by an AJAX call from the metadata_general panel.
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omeroweb.webclient.views.load_metadata_preview(request, *args, **kwargs)
This is the image ‘Preview’ tab for the right-hand panel.
Currently this doesn’t do much except launch the view-port plugin using
the image Id (and share Id if necessary)
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omeroweb.webclient.views.load_original_metadata(request, *args, **kwargs)
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omeroweb.webclient.views.load_public(request, *args, **kwargs)
Loads data for the tree in the ‘public’ main page.
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omeroweb.webclient.views.load_searching(request, *args, **kwargs)
Handles AJAX calls to search
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omeroweb.webclient.views.load_template(request, *args, **kwargs)
This view handles most of the top-level pages, as specified by ‘menu’ E.g.
userdata, usertags, history, search etc.
Query string ‘path’ that specifies an object to display in the data tree
is parsed.
We also prepare the list of users in the current group, for the
switch-user form. Change-group form is also prepared.
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omeroweb.webclient.views.login(request)
Webclient Login - Also can be used by other Apps to log in to OMERO. Uses
the ‘server’ id from request to lookup the server-id (index), host and
port from settings. E.g. “localhost”, 4064. Stores these details, along
with username, password etc in the request.session. Resets other data
parameters in the request.session. Tries to get connection to OMERO and
if this works, then we are redirected to the ‘index’ page or url
specified in REQUEST. If we can’t connect, the login page is returned
with appropriate error messages.
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omeroweb.webclient.views.logout(request, *args, **kwargs)
Logout of the session and redirects to the homepage (will redirect to
login first)
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omeroweb.webclient.views.manage_action_containers(request, *args, **kwargs)
Handles many different actions on various objects.
- @param action: “addnewcontainer”, (creates a new Project, Dataset,
- Screen), “editname”, “savename”, “editdescription”,
“savedescription”, (used as GET and POST for in-line
editing), “paste”, “move”, “remove”,
“removefromshare”, (tree P/D/I moving etc)
“delete”, “deletemany” (delete objects)
- @param o_type: “dataset”, “project”, “image”, “screen”, “plate”,
- “acquisition”, “well”,”comment”, “file”, “tag”,
“tagset”,”share”, “sharecomment”
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omeroweb.webclient.views.ome_tiff_info(request, *args, **kwargs)
Query to see if we have an OME-TIFF attached to the image (assume only 1,
since Batch Image Export will delete old ones)
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omeroweb.webclient.views.ome_tiff_script(request, *args, **kwargs)
Uses the scripting service (Batch Image Export script) to generate
OME-TIFF for an image and attach this as a file annotation to the image.
Script will show up in the ‘Activities’ for users to monitor and download
result etc.
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omeroweb.webclient.views.open_astex_viewer(request, *args, **kwargs)
Opens the Open Astex Viewer applet, to display volume masks in a couple of
formats:
- mrc.map files that are attached to images. obj_type = ‘file’
- Convert OMERO image to mrc on the fly. obj_type = ‘image_8bit’ or
- ‘image’
- In this case, we may use ‘scipy’ to scale the image volume.
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omeroweb.webclient.views.run_script(request, conn, sId, inputMap, scriptName='Script')
Starts running a script, adding details to the request.session so that it
shows up in the webclient Activities panel and results are available there
etc.
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omeroweb.webclient.views.script_run(request, *args, **kwargs)
Runs a script using values in a POST
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omeroweb.webclient.views.script_ui(request, *args, **kwargs)
Generates an html form for the parameters of a defined script.
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omeroweb.webclient.views.switch_active_group(request, active_group=None)
Simply changes the request.session[‘active_group’] which is then used by
the @login_required decorator to configure conn for any group-based
queries.
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omeroweb.webclient.views.update_callback(request, cbString, **kwargs)
Update a callback handle with key/value pairs
omeroweb.webclient.webclient_gateway module
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class omeroweb.webclient.webclient_gateway.DatasetWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._DatasetWrapper
omero_model_DatasetI class wrapper overwrite omero.gateway.DatasetWrapper
and extends OmeroWebObjectWrapper.
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annotation_counter = None
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class omeroweb.webclient.webclient_gateway.EventLogWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omero.gateway.BlitzObjectWrapper
omero_model_EventLogI class wrapper extends
omero.gateway.BlitzObjectWrapper.
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LINK_CLASS = 'EventLog'
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class omeroweb.webclient.webclient_gateway.ExperimenterGroupWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._ExperimenterGroupWrapper
omero_model_ExperimenterGroupI class wrapper overwrite
omero.gateway.ExperimenterGroupWrapper
and extend OmeroWebObjectWrapper.
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getMembers(excluded_omename=[], excluded_ids=[])
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getOwners()
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getOwnersNames()
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isEditable()
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isLocked()
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isOwner()
Returns True if current user is Owner of this group
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loadLeadersAndMembers()
Returns lists of ‘leaders’ and ‘members’ of the specified group
(default is current group) as a dict with those keys.
- @return: {‘leaders’: list L{ExperimenterWrapper},
- ‘colleagues’: list L{ExperimenterWrapper}}
@rtype: dict
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class omeroweb.webclient.webclient_gateway.ExperimenterWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._ExperimenterWrapper
omero_model_ExperimenterI class wrapper overwrite
omero.gateway.ExperimenterWrapper and extend OmeroWebObjectWrapper.
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getDefaultGroup()
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getOtherGroups(excluded_names=('user', 'guest'), excluded_ids=[])
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isEditable()
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isLdapUser()
Return DN of the specific experimenter if uses LDAP authentication
(has set dn on password table) or None.
@param eid: experimenter ID
@type eid: L{Long}
@return: Distinguished Name
@rtype: String
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ldapUser = None
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class omeroweb.webclient.webclient_gateway.ImageWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._ImageWrapper
omero_model_ImageI class wrapper overwrite omero.gateway.ImageWrapper
and extends OmeroWebObjectWrapper.
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annotation_counter = None
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getChannels(*args, **kwargs)
This override standard omero.gateway.ImageWrapper.getChannels
and catch exceptions.
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getFilesetImages()
Returns a list of the ‘sibling’ images (including this one) that
belong to this image’s Fileset. Sorted by name.
If Image has no Fileset, return an empty list.
@rtype: List of {ImageWrapper}
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getInplaceImportCmd()
Returns the command used to do import transfer for this image,
E.g. ‘ln’, or empty string if not in-place imported.
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getPixelSizeUnits()
We use the pixelSizeX to find the appropriate units.
By default, we get the actual size in Microns, then use the
lengthunit filter to pick the most suitable size (same logic
is used for doing the length conversions).
However, if unit can’t be converted, then we just return the
current unit’s symbol.
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getPixelSizeXMicrons()
Helper for calling getPixelSizeX(units=”MICROMETER”) in templates
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getPixelSizeYMicrons()
Helper for calling getPixelSizeX(units=”MICROMETER”) in templates
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getPixelSizeZMicrons()
Helper for calling getPixelSizeX(units=”MICROMETER”) in templates
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showOriginalFilePaths()
This determines whether we want to show the paths of
Original Imported Files.
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class omeroweb.webclient.webclient_gateway.OmeroWebGateway(*args, **kwargs)
Bases: omero.gateway._BlitzGateway
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changeActiveGroup(gid)
Every time session is created default group becomes active group
and is loaded with the security for the current user and thread.
Public data has to be created in the context of the group where user,
who would like to look at these data, is a member of.
Public data can be only visible by the member of group and owners.
@param gid: New active group ID
@type gid: Long
@return: Boolean
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changeMyPassword(password, old_password)
Change the password for the current user by passing the old password.
- @param password Must pass validation in the security
- sub-system.
@type password String
@param old_password Old password
@type old_password String
@return None or error message if password could not be
changed
@rtype String
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changeUserPassword(omeName, password, my_password)
Change the password for the a given user.
@param omeName Experimetner omename
@type omeName String
@param password Must pass validation in the security sub-system.
@type password String
@param my_password Must pass validation in the security sub-system.
@type my_password String
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checkEmail(email, old_email=None)
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checkGroupName(name, old_name=None)
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checkOmeName(ome_name, old_omeName=None)
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countDataByPeriod(start, end, eid, otype=None)
Counts given data objects by the given period of time
controlled by the security system.
@param start Starting data
@type start Long
@param end Finishing data
@type end Long
@param otype Data type: Project, Dataset, Image
@type otype String
@return: Counter
@rtype: Long
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countOrphans(obj_type, eid=None)
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createContainer(dtype, name, description=None)
Creates new Project, Dataset or Screen and returns ID
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createDataset(name, description=None, img_ids=None)
Creates a Dataset and adds images if img_ids is specified.
Returns the new Dataset ID.
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createExperimenter(omeName, firstName, lastName, email, isAdmin, isActive, defaultGroup, otherGroups, password, middleName=None, institution=None)
Create and return a new user in the given groups with password.
@param omeName A new username.
@type omeName String
@param firstName A new first name.
@type firstName String
@param lastName A new last name.
@type lastName String
@param email A new email.
@type email String
@param isAdmin An Admin permission.
@type isAdmin Boolean
@param isActive Active user (user can log in).
@type isActive Boolean
@param defaultGroup Instance of ExperimenterGroup selected as a first
active group.
@type defaultGroup ExperimenterGroupI
@param otherGroups List of ExperimenterGroup instances. Can be empty.
@type otherGroups L{ExperimenterGroupI}
@param password Must pass validation in the security sub-system.
@type password String
@param middleName A middle name.
@type middleName String
@param institution An institution.
@type institution String
@return ID of the newly created Experimenter Not null.
@rtype Long
-
createGroup(name, permissions, owners=[], description=None)
Create and return a new group with the given owners.
@param group A new ExperimenterGroup instance.
@type group ExperimenterGroupI
@param owners List of Experimenter instances. Can be empty.
@type owners L{ExperimenterI}
@param permissions Permissions instances.
@type permissions L{PermissionsI}
@return ID of the newly created ExperimenterGroup Not
null.
@rtype Long
-
createProject(name, description=None)
Creates new Project and returns ID
-
createScreen(name, description=None)
Creates new Screen and returns ID
-
createShare(host, images, message, members, enable, expiration=None)
-
cropExperimenterPhoto(box, oid=None)
Crop File annotation with the namespace:
“openmicroscopy.org/omero/experimenter/photo” (NSEXPERIMENTERPHOTO)
linked to the given user ID. If user id not set, owned by the current
user.
New dimensions are defined by squer positions box = (x1,y1,x2,y2)
@param box tuple of new square positions
@type box Tuple
@param oid experimenter ID
@type oid Long
-
deleteExperimenterPhoto(oid=None)
-
findTag(name, desc=None)
Retrieves Tag by given Name and description
@param name name of tag
@type name String
@param desc description of tag
@type desc String
@return: TagAnnotation
@rtype: AnnotationWrapper
-
findWellInPlate(plate_name, row, column)
-
getAllGuests(share_id)
Get the email addresses for all share guests.
@param share_id: share ID
@type share_id: Long
@return: List of e-mail addresses
@rtype: List of Strings
-
getAllMembers(share_id)
Get all {@link Experimenter users} who are a member of the share.
@param share_id: share ID
@type share_id: Long
@return: Members of share
@rtype: L{ExperimenterWrapper} generator
-
getAllUsers(share_id)
Get a single set containing the login names of the users as well email
addresses for guests.
@param share_id: share ID
@type share_id: Long
@return: List of usernames and e-mail addresses
@rtype: List of Strings
-
getCollectionCount(parent, child, ids)
Counts the number of members in a collection for a given object.
- @param parent The fully-qualified classname of the object to be
- tested
@type parent String
@param child Name of the property on that class, omitting
getters and setters.
@type child String
@param ids Set of Longs, the ids of the objects to test
@type ids L{Long}
@return A map from id integer to count integer
@rtype L{(Long, Long)}
Returns a map from share id to comment count.
@param share_ids: List of IDs
@type share_ids: List of Longs
@return: Dict of shareId: comment-count
@rtype: Dict of long: long
Looks up all comments which belong to the share, wrapped in object
wrapper
@param share_id: share ID
@type share_id: Long
@return: Share comments
@rtype: L{AnnotationWrapper} generator
-
getContents(share_id)
Looks up all items belonging to the share, wrapped in object wrapper
@param share_id: share ID
@type share_id: Long
@return: Share contents
@rtype: L{omero.gateway.BlitzObjectWrapper} generator
-
getDataByPeriod(start, end, eid, otype=None, page=None)
Retrieve given data objects by the given period of time
controlled by the security system.
@param start Starting data
@type start Long
@param end Finishing data
@type end Long
@param otype Data type: Project, Dataset, Image
@type otype String
@return: Map of project, dataset and image lists
@rtype: Map
-
getEmailSettings()
Retrieves a configuration value “omero.mail.config” from the backend
store.
@return: String
-
getEventsByPeriod(start, end, eid)
Retrieve event log objects by the given period of time
controlled by the security system.
@param start Starting data
@type start Long
@param end Finishing data
@type end Long
@return: List of event logs
@rtype: List
-
getExperimenterDefaultPhoto()
If file annotation with the namespace:
“openmicroscopy.org/omero/experimenter/photo” (NSEXPERIMENTERPHOTO)
is not linked to experimenter this method generate default picture of
the person.
@return Data from the image.
@rtype String
-
getExperimenterPhoto(oid=None)
Get File annotation with the namespace:
“openmicroscopy.org/omero/experimenter/photo” (NSEXPERIMENTERPHOTO)
linked to the given user ID. If user id not set, owned by the current
user.
@param oid experimenter ID
@type oid Long
@return Data from the image.
@rtype String
-
getExperimenterPhotoSize(oid=None)
Get size of File annotation with the namespace:
“openmicroscopy.org/omero/experimenter/photo” (NSEXPERIMENTERPHOTO)
linked to the given user ID. If user id not set, owned by the current
user.
@param oid experimenter ID
@type oid Long
@return Tuple including dimention and size of the file
@rtype Tuple
-
getExperimenters()
Return all experimenters apart from current user.
@return: Generator yielding experimetners list
@rtype: L{ExperimenterWrapper} generator
-
getFileFormat(format)
Get file annotation format for the given value.
@return Omero File format
@rtype String
-
getLdapAuthExperimenter(eid)
Return DN of the specific experimenter if uses LDAP authentication
(has set dn on password table) or None.
@param eid: experimenter ID
@type eid: L{Long}
@return: Distinguished Name
@rtype: String
-
getMemberCount(share_ids)
Returns a map from share id to the count of total members (including
the owner). This is represented by ome.model.meta.ShareMember links.
@param share_ids: List of IDs
@type share_ids: List of Longs
@return: Dict of shareId: member-count
@rtype: Dict of long: long
-
getMemberShares()
Gets all shares where current user is a member.
@return: Shares that user is a member of
@rtype: L{ShareWrapper} generator
-
getOrphanedContainerSettings()
-
getOwnShares()
Gets all owned shares for the current user.
@return: Shares that user owns
@rtype: L{ShareWrapper} generator
-
getServerVersion()
Retrieves a configuration value “omero.version” from the backend
store.
@return: String
-
getShare(oid)
Gets share for the given share id.
@param oid: Share ID.
@type oid: Long
@return: ShareWrapper or None
@rtype: L{ShareWrapper}
-
getShareId()
Returns active share id .
@return: Share ID
@rtype: Long
-
getTagCount(eid=None)
-
getUpgradesUrl()
Retrieves a configuration value “omero.upgrades.url” from
the backend store.
@return: String
-
hasExperimenterPhoto(oid=None)
Check if File annotation with the namespace:
“openmicroscopy.org/omero/experimenter/photo” (NSEXPERIMENTERPHOTO) is
linked to the given user ID. If user id not set, owned by the current
user.
@param oid experimenter ID
@type oid Long
@return True or False
@rtype Boolean
-
isAnythingCreated()
Checks if any of the experimenter was created before
@return: Boolean
-
listImagesInDataset(oid, eid=None, page=None, load_pixels=False)
List Images in the given Dataset.
Optinally filter by experimenter ‘eid’
@param eid: experimenter id
@type eid: Long
@param page: page number
@type page: Long
@return: Generator yielding Images
@rtype: L{ImageWrapper} generator
-
listLastImportedImages()
Retrieve most recent imported images
controlled by the security system.
@return: Generator yielding Images
@rtype: L{ImageWrapper} generator
-
listLdapAuthExperimenters()
Lists all IDs of experimenters who are authenticated by LDAP
(has set dn on password table).
@return: List of experimetner IDs
@rtype: L{Dict of String: Long}
Retrieve most recent comment annotations
controlled by the security system.
@return: Generator yielding BlitzObjectWrapper
@rtype: L{BlitzObjectWrapper} generator
Retrieve most recent share comments
controlled by the security system.
@return: Generator yielding SessionAnnotationLink
@rtype: L{SessionCommentWrapper} generator
-
listMostRecentShares()
Retrieve most recent shares
controlled by the security system.
@return: Generator yielding SessionAnnotationLink
@rtype: L{ShareWrapper} generator
-
listMostRecentTags()
Retrieve most recent tag annotations
controlled by the security system.
@return: Generator yielding BlitzObjectWrapper
@rtype: L{BlitzObjectWrapper} generator
-
listTags(eid=None)
-
listTagsRecursive(eid=None, offset=None, limit=1000)
Returns a two-element tuple:
* A list of tags, where each tag is a list with the following
elements:
0: id
1: description
2: text
3: owner id
4: list of child tag ids (possibly empty), or 0 if this is not a tag
set
- A dictionary of user ids mapped to user names
-
regroupFilesets(dsIds, fsIds)
For each Fileset, make sure all the Images are in the same Dataset
as each other.
We choose a ‘target’ Dataset that already has one of the Fileset
Images in it, and is in the dsIds list.
This method is used when preparing to chgrp the specified datasets
-
removeImage(share_id, image_id)
-
saveAndReturnFile(binary, oFile_id)
Provide method for directly updating a file object and return binary.
Assumes that the checksum algorithm used for file integrity
verification is SHA-1.
@param binary Binary. Not null.
@type binary String
@param oFile_id File Id in order to manage the state of the
service. Not null.
@type oFile_id Long
@return Shallow copy of file.
-
saveAndReturnId(obj)
Provide method for directly updating object graphs and return ID. Act
recursively on the entire object graph, replacing placeholders and
details where necessary, and then “merging” the final graph. This
means that the objects that are passed into methods are copied over to
new instances which are then returned.
The original objects should be discarded.
- @param obj An entity or an unloaded reference to an entity. Not
- null.
@type obj ObjectI
@return ID of saved object
@rtype Long
-
saveAndReturnObject(obj)
Provide method for directly updating object graphs and return it. Act
recursively on the entire object graph, replacing placeholders and
details where necessary, and then “merging” the final graph. This
means that the objects that are passed into methods are copied over to
new instances which are then returned.
The original objects should be discarded.
- @param obj An entity or an unloaded reference to an entity. Not
- null.
@type obj ObjectI
@return Saved object
@rtype ObjectI
-
saveArray(objs)
Provide method for directly updating list of object graphs. Act
recursively on the entire object graph, replacing placeholders and
details where necessary, and then “merging” the final graph. This
means that the objects that are passed into methods are copied over to
new instances which are then returned.
The original objects should be discarded.
- @param obj List of entities or an unloaded references to an
- entity. Not null.
@type obj L{ObjectI}
-
saveObject(obj)
Provide method for directly updating object graphs. Act recursively on
the entire object graph, replacing placeholders and details where
necessary, and then “merging” the final graph. This means that the
objects that are passed into methods are copied over to new instances
which are then returned.
The original objects should be discarded.
- @param obj An entity or an unloaded reference to an entity. Not
- null.
@type obj ObjectI
-
setDefaultGroup(group_id, exp_id=None)
Sets the default group for the specified experimenter, or current user
if not specified.
-
setMembersOfGroup(group, new_members)
Change members of the group. Returns a list of existing group members
that could not be removed from the group because it is their only
group.
@param group An existing ExperimenterGroup instance.
@type group ExperimenterGroupI
@param new_members List of new new Experimenter Ids.
@type new_members L{Long}
@return List of Experimenters not removed from group
@rtype List of L{ExperimenterWrapper}
-
setOwnersOfGroup(group, new_owners)
Change members of the group.
@param group An existing ExperimenterGroup instance.
@type group ExperimenterGroupI
@param new_members List of new new Experimenter Ids.
@type new_members L{Long}
-
updateExperimenter(experimenter, omeName, firstName, lastName, email, isAdmin, isActive, defaultGroup, otherGroups, middleName=None, institution=None)
Update an existing user including groups user is a member of.
Password cannot be changed by calling that method.
@param experimenter An existing Experimenter instance.
@type experimenter ExperimenterWrapper
@param omeName A new username.
@type omeName String
@param firstName A new first name.
@type firstName String
@param lastName A new last name.
@type lastName String
@param email A new email.
@type email String
@param isAdmin An Admin permission.
@type isAdmin Boolean
@param isActive Active user (user can log in).
@type isActive Boolean
@param defaultGroup Instance of ExperimenterGroup selected as a first
active group.
@type defaultGroup ExperimenterGroupI
@param otherGroups List of ExperimenterGroup instances. Can be empty.
@type otherGroups L{ExperimenterGroupI}
@param middleName A middle name.
@type middleName String
@param institution An institution.
@type institution String
-
updateGroup(group, name, permissions, owners=[], description=None)
Update an existing user including groups user is a member of.
Password cannot be changed by calling that method.
@param group A new ExperimenterGroup instance.
@type group ExperimenterGroupI
@param name A new group name.
@type name String
@param permissions Permissions instances.
@type permissions L{PermissionsI}
@param owners List of Experimenter instances. Can be empty.
@type owners L{ExperimenterI}
@param description A description.
@type description String
-
updateMyAccount(experimenter, firstName, lastName, email, defaultGroupId, middleName=None, institution=None)
Allows a user to update his/her own information and set the default
group for a given user.
@param experimenter A data transfer object. Only the fields:
firstName, middleName, lastName, email, and
institution are checked. Not null.
@type experimenter ExperimenterWrapper
@param firstName A new first name.
@type firstName String
@param lastName A new last name.
@type lastName String
@param email A new email.
@type email String
@param defaultGroup Instance of ExperimenterGroup selected as a
first active group.
@type defaultGroup ExperimenterGroupI
@param middleName A middle name.
@type middleName String
@param institution An institution.
@type institution String
-
updatePermissions(group, permissions)
Allow to change the permission of the group.
- @param group A wrapped entity or an unloaded reference to an
- entity. Not null.
@type group BlitzObjectWrapper
@param perm The permissions value for this entity. Not null.
@type perm PermissionsI
-
updateShareOrDiscussion(host, share_id, message, add_members, rm_members, enable, expiration=None)
-
uploadMyUserPhoto(filename, format, data)
Uploads a photo for the user which will be displayed on his/her
profile.
This photo will be saved as an OriginalFile object
with the given format, and attached to the user’s Experimenter
object via an File Annotation with
the namespace: “openmicroscopy.org/omero/experimenter/photo”
(NSEXPERIMENTERPHOTO).
If such an OriginalFile instance already exists,
it will be overwritten. If more than one photo is present, the oldest
version will be modified (i.e. the highest updateEvent id).
Note: as outlined in ticket:1794, this photo will be placed in the
“user” group and therefore will be visible to everyone on the system.
@param filename name which will be used.
@type filename String
@param format Format.value string. ‘image/jpeg’ and ‘image/png’
are common values.
@type format String
@param data Data from the image. This will be written to disk.
@type data String
- @return ID of the overwritten or newly created user photo
- OriginalFile object.
@rtype Long
-
class omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper
Bases: object
-
annotation_counter = None
-
countAnnotations()
Count on annotations linked to the object and set the value
on the custom fiels ‘annotation_counter’.
@return Counter
-
countParents()
-
getPermissions()
-
getPermsCss()
Returns a string that can be used as classes on an html element to
indicate the permissions flags of the object. E.g. “canEdit canLink”
Flags/classes are canEdit, canAnnotate, canLink, canDelete
-
setRating(rating)
Add a rating (long) annotation to the object, or update an existing
rating.
If rating is zero, we remove any existing rating annotation.
-
warpName()
Warp name of the object if names is longer then 30 characters.
@return Warped string.
-
class omeroweb.webclient.webclient_gateway.OmeroWebSafeCallWrapper(proxyObjectWrapper, attr, f)
Bases: omero.gateway.OmeroGatewaySafeCallWrapper
Function or method wrapper that handles L{Ice.ObjectNotExistException}
by re-creating the server side proxy.
-
handle_exception(e, *args, **kwargs)
-
class omeroweb.webclient.webclient_gateway.PlateAcquisitionWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._PlateAcquisitionWrapper
omero_model_PlateI class wrapper overwrite omero.gateway.PlateWrapper
and extends OmeroWebObjectWrapper.
-
annotation_counter = None
-
class omeroweb.webclient.webclient_gateway.PlateWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._PlateWrapper
omero_model_PlateI class wrapper overwrite omero.gateway.PlateWrapper
and extends OmeroWebObjectWrapper.
-
annotation_counter = None
-
class omeroweb.webclient.webclient_gateway.ProjectWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._ProjectWrapper
omero_model_ProjectI class wrapper overwrite omero.gateway.ProjectWrapper
and extend OmeroWebObjectWrapper.
-
annotation_counter = None
-
class omeroweb.webclient.webclient_gateway.ScreenWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._ScreenWrapper
omero_model_ScreenI class wrapper overwrite omero.gateway.ScreenWrapper
and extends OmeroWebObjectWrapper.
-
annotation_counter = None
-
class omeroweb.webclient.webclient_gateway.ShareWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omero.gateway.BlitzObjectWrapper
omero_model_ShareI class wrapper extends BlitzObjectWrapper.
-
getExpireDate()
Gets the end date for the share
@return: End Date-time
@rtype: datetime object
-
getOwner()
The owner of this share
@return: Owner
@rtype: L{ExperimenterWrapper}
-
getShareType()
-
getStartDate()
Gets the start date of the share
@return: Start Date-time
@rtype: datetime object
-
isEmpty()
-
isExpired()
Returns True if we are past the end date of the share
@return: True if share expired
@rtype: Boolean
-
isOwned()
Returns True if share is owned by the current user
@return: True if owned
@rtype: Boolean
-
class omeroweb.webclient.webclient_gateway.TagWrapper(*args, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway.TagAnnotationWrapper
omero_model_TagAnnotationI class wrapper overwrite
omero.gateway.TagAnnotationWrapper and extends OmeroWebObjectWrapper.
-
class omeroweb.webclient.webclient_gateway.WellWrapper(conn=None, obj=None, cache=None, **kwargs)
Bases: omeroweb.webclient.webclient_gateway.OmeroWebObjectWrapper, omero.gateway._WellWrapper
omero_model_ImageI class wrapper overwrite omero.gateway.ImageWrapper
and extends OmeroWebObjectWrapper.
-
annotation_counter = None
-
omeroweb.webclient.webclient_gateway.defaultThumbnail(size=(120, 120))
omeroweb.webclient.webclient_utils module
-
omeroweb.webclient.webclient_utils._formatReport(callback)
Added as workaround to the changes made in #3006.
-
omeroweb.webclient.webclient_utils._purgeCallback(request)
-
omeroweb.webclient.webclient_utils.formatPercentFraction(value)
Formats a fraction as a percentage for display
Module contents
