omero.plugins package¶
Submodules¶
omero.plugins.admin module¶
author: | Josh Moore, josh at glencoesoftware.com |
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OMERO Grid admin controller
This is a python wrapper around icegridregistry/icegridnode for master and various other tools needed for administration.
Copyright 2008-2016 Glencoe Software, Inc. All Rights Reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.admin.
AdminControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.DiagnosticsControl
,omero.plugins.prefs.WriteableConfigControl
,omero.cli.UserGroupControl
-
_cmd
(*command_arguments)¶ Used to generate an icegridadmin command line argument list
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_complete
(text, line, begidx, endidx)¶ Returns a file after “deploy”, “start”, or “startasync” and otherwise delegates to the BaseControl
-
_configure
(parser)¶
-
_descript
(args)¶
-
_get_data_dir
(config)¶
-
_get_etc_dir
()¶ Return path to directory containing configuration files
-
_get_grid_dir
()¶ Return path to directory containing Gridconfiguration files
-
_get_omero_properties
()¶
-
_get_templates_dir
()¶ Return path to directory containing templates
-
_glacier2_icessl_xml
(config_props)¶
-
_node
(omero_node=None)¶ Overrides the regular node() logic to return the value of OMERO_MASTER or “master”
-
_query_service
(svc_name)¶
-
_start_service
(config, descript, svc_name, pasw, user)¶
-
_stop_service
(svc_name)¶
-
can_access
(filepath, mask=6)¶ Check that the given path belongs to or is accessible by the current user on Linux systems.
-
check
(args)¶
-
check_access
(mask=6, config=None)¶ Check that ‘var’ is accessible by the current user.
-
check_internal_cfg
()¶
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check_lock
(config)¶ Issue a warning if any of the top ”.omero” directories contain a lock file. This isn’t a conclusive test this we don’t have access to the DB to get the UUID for this instance. Usually there should only be one though.
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check_node
(args)¶ If the args argparse.Namespace argument has no “node” attribute, then assign one.
-
check_service
(name)¶
-
checkice
(args=None)¶ Checks for Ice version compatibility.
See ticket:2514, ticket:1260
-
checkupgrade
(*args, **kwargs)¶ Checks whether a server upgrade is available, exits with return code 0: this is the latest version 1: an upgrade is available 2: an error occurred whilst checking
-
checkwindows
(args)¶ Checks that the templates file as defined in etcWindows.cfg can be found.
-
cleanse
(*args, **kwargs)¶
-
deploy
(*args, **kwargs)¶
-
diagnostics
(*args, **kwargs)¶
-
email
(args)¶
-
events
(svc_name)¶
-
fixpyramids
(*args, **kwargs)¶
-
getdirsize
(directory)¶
-
ice
(args)¶
-
jvmcfg
(*args, **kwargs)¶ Display JVM settings from the current configuration
-
log
(*args, **kwargs)¶
-
loops_and_wait
(args)¶ If present, get the wait time from the args argument and calculate the number of loops and the wait time needed. If not present in args, use a default value.
-
open_config
(unused=None)¶ Callers are responsible for closing the returned ConfigXml object.
-
reindex
(*args, **kwargs)¶
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removepyramids
(*args, **kwargs)¶
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restart
(*args, **kwargs)¶
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restartasync
(*args, **kwargs)¶
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rewrite
(*args, **kwargs)¶ Regenerate all the template files under the configuration directory
-
session_manager
(communicator)¶
-
sessionlist
(args)¶
-
start
(*args, **kwargs)¶
-
start_service
(name)¶
-
startasync
(*args, **kwargs)¶ First checks for a valid installation, then checks the grid, then registers the action: “node HOST start”
-
status
(*args, **kwargs)¶
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stop
(*args, **kwargs)¶
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stop_service
(name)¶
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stopasync
(*args, **kwargs)¶ Returns true if the server was already stopped
-
wait_for_icedb
(args, config)¶ Since the stop and start are separately protected by the lock on config.xml, we need to wait for some time to hopefully let the icegridnode process release the file locks.
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waitdown
(args)¶ Returns true if the server went down
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waitup
(args)¶ Loops 30 times with 10 second pauses waiting for status() to return 0. If it does not, then ctx.die() is called.
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omero.plugins.basics module¶
load, quit, version, help plugins
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
The load plugin is used to read in files with omero cli commands (omitting the omero). For example,
./omero load some/file.osh
The help, quit, and version plugins are self-explanatory.
Copyright 2008 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.basics.
ErrorsControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
-
_configure
(parser)¶
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class
omero.plugins.basics.
HelpControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
Defined here since the background loading might be too slow to have all help available
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_complete
(text, line, begidx, endidx)¶ This is something of a hack. This should either be a part of the context interface, or we should put it somewhere in a utility. FIXME.
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_configure
(parser)¶
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format_title
(command, sep='-')¶ Create heading for command or topic help
-
print_all_commands_and_topics
(args)¶ Print the help for all commands and topics
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print_command_help
(control, args)¶ Print help for a single command and optionally its subcommand
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print_commands_list
(args)¶ Print a list of all commands
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print_single_command_or_topic
(args)¶ Print the help for a command or a topic
-
print_usage
()¶
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class
omero.plugins.basics.
LoadControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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class
omero.plugins.basics.
QuitControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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class
omero.plugins.basics.
ShellControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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class
omero.plugins.basics.
VersionControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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omero.plugins.chgrp module¶
chgrp plugin
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
omero.plugins.chown module¶
chown plugin
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
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class
omero.plugins.chown.
ChownControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.GraphControl
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_check_command
(command_check)¶ Rewrite higher class method to have command check as well as the possibility to adjust the command.
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_objects
(parser)¶
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_pre_objects
(parser)¶
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_process_request
(req, args, client)¶
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cmd_type
()¶
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populate_target_users
(command_check)¶ Move the Experimenters whose data are to be transferred from targetObjects to targetUsers. The rewritten _check_command method checked these Experimenters when they were in targetObjects, but Chown2 needs them in targetUsers.
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print_chown_response
(rsp)¶
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print_detailed_report
(req, rsp, status)¶
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omero.plugins.db module¶
Plugin for our managing the OMERO database.
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
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class
omero.plugins.db.
DatabaseControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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_copy
(input_path, output, func, cfg=None)¶
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_create
(sql_directory, db_vers, db_patch, password_hash, args, location=None)¶
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_db_profile
()¶
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_get_password_hash
(args, root_pass=None, old_prompt=False)¶
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_has_user_id
(args)¶
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_lookup
(key, defaults, args)¶ Get a value from a flag arg, positional arg, or default properties
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_make_replace
(root_pass, db_vers, db_patch)¶
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_sql_directory
(db_vers, db_patch)¶ See #2689
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loaddefaults
(*args, **kwargs)¶
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password
(*args, **kwargs)¶
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script
(*args, **kwargs)¶
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omero.plugins.delete module¶
Startup plugin for command-line deletes
Copyright 2009-2015 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.delete.
DeleteControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.GraphControl
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cmd_type
()¶
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default_exclude
()¶ Don’t delete these three types of Annotation by default
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print_delete_response
(rsp)¶
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print_detailed_report
(req, rsp, status)¶
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omero.plugins.download module¶
download plugin
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
Copyright 2007 - 2014 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.download.
DownloadControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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get_file
(session, value)¶
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parse_object_id
(object_type, value)¶
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omero.plugins.duplicate module¶
Plugin for duplicating object graphs
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class
omero.plugins.duplicate.
DuplicateControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.GraphControl
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cmd_type
()¶
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print_detailed_report
(req, rsp, status)¶
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print_duplicate_response
(rsp)¶
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omero.plugins.export module¶
Startup plugin for command-line exporter
Copyright 2009 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
omero.plugins.fs module¶
fs plugin for querying repositories, filesets, and the like.
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class
omero.plugins.fs.
Entry
(level, id, path, mimetype)¶ Bases:
tuple
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_asdict
(t)¶ Return a new dict which maps field names to their values
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_fields
= ('level', 'id', 'path', 'mimetype')¶
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classmethod
_make
(iterable, new=<built-in method __new__ of type object>, len=<built-in function len>)¶ Make a new Entry object from a sequence or iterable
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_replace
(_self, **kwds)¶ Return a new Entry object replacing specified fields with new values
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id
¶ itemgetter(item, ...) –> itemgetter object
Return a callable object that fetches the given item(s) from its operand. After, f=itemgetter(2), the call f(r) returns r[2]. After, g=itemgetter(2,5,3), the call g(r) returns (r[2], r[5], r[3])
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level
¶ itemgetter(item, ...) –> itemgetter object
Return a callable object that fetches the given item(s) from its operand. After, f=itemgetter(2), the call f(r) returns r[2]. After, g=itemgetter(2,5,3), the call g(r) returns (r[2], r[5], r[3])
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mimetype
¶ itemgetter(item, ...) –> itemgetter object
Return a callable object that fetches the given item(s) from its operand. After, f=itemgetter(2), the call f(r) returns r[2]. After, g=itemgetter(2,5,3), the call g(r) returns (r[2], r[5], r[3])
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path
¶ itemgetter(item, ...) –> itemgetter object
Return a callable object that fetches the given item(s) from its operand. After, f=itemgetter(2), the call f(r) returns r[2]. After, g=itemgetter(2,5,3), the call g(r) returns (r[2], r[5], r[3])
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class
omero.plugins.fs.
FsControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.CmdControl
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_configure
(parser)¶
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_detailed_usage_report
(req, rsp, status, args)¶ Print a breakdown of disk usage in table form, including user, group and component information according to the args.
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_extended_info
(client, row, values)¶
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_table
(args)¶
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_to_units
(size, units)¶ Convert from bytes to KiB, MiB, GiB, TiB or PiB.
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_usage_obj
(obj)¶ Take the positional arguments and marshal them into a dictionary and a list for the command argument.
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_usage_report
(req, rsp, status, args)¶ Output the total bytes used or the error, optionally provide more details.
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get_managed_repo
(client)¶ For the moment this assumes there’s only one.
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images
(args)¶ List images, filtering for archives, etc.
This command is useful for showing pre-FS (i.e. OMERO 4.4 and before) images which have original data archived with them. It may be possible to convert these to OMERO 5 filesets.
Examples:
bin/omero fs images –archived # List only OMERO4 images bin/omero fs images –order=newest # Default bin/omero fs images –order=largest # Most used space bin/omero fs images –limit=500 # Longer listings bin/omero fs images –extended # More details
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importtime
(args)¶ Find out how long it took to import an existing fileset
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logfile
(args)¶ Return the logfile associated with a fileset
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ls
(args)¶ List all the original files contained in a fileset
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mkdir
(*args, **kwargs)¶ Make a new directory (admin-only)
Creates a new empty directory in the managed repository. A new storage volume may then be mounted at that location and the import template (omero.fs.repo.path) adjusted to target it. Once created, the directory may be deleted from the underlying filesystem and replaced with a symbolic link. Directories that violate the root-owned prefix components of omero.fs.repo.path are all set to be owned by the root user.
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rename
(*args, **kwargs)¶ Moves an existing fileset to a new location (admin-only)
After the import template (omero.fs.repo.path) has been changed, it may be useful to rename an existing fileset to match the new template. By default the original files and import log are also moved.
-
repos
(args)¶ List all repositories.
These repositories are where OMERO stores all binary data for your system. Most useful is likely the “ManagedRepository” where OMERO 5 imports to.
Examples:
bin/omero fs repos # Show all bin/omero fs repos –managed # Show only the managed repo
# Or to print only the directory # under Unix:bin/omero fs repos –managed –style=plain | cut -d, -f5
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sets
(args)¶ List filesets by various criteria
Filesets are bundles of original data imported into OMERO 5 and above which represent 1 or more images.
Examples:
bin/omero fs sets –order=newest # Default bin/omero fs sets –order=oldest bin/omero fs sets –order=largest bin/omero fs sets –without-images # Corrupt filesets bin/omero fs sets –with-transfer=ln_s # Symlinked filesets bin/omero fs sets –check # Proof the checksums
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usage
(args)¶ Shows the disk usage for various objects.
This command shows the total disk usage of various objects including: ExperimenterGroup, Experimenter, Project, Dataset, Folder, Screen, Plate, Well, WellSample, Image, Pixels, Annotation, Job, Fileset, OriginalFile. The total size returned will comprise the disk usage by all related files. Thus an image’s size would typically include the files uploaded to a fileset, import log (Job), thumbnails, and, possibly, associated pixels or original files. These details can be displayed using the –report option.
Examples:
bin/omero fs usage # total usage for current user bin/omero fs usage –report # more detailed usage for current user bin/omero fs usage –groups # total usage for current user’s groups # total usage for five images with minimal output bin/omero fs usage Image:1,2,3,4,5 –size_only # total usage for all images with in a human readable format bin/omero fs usage Image:* –human-readable # total usage for all users broken down by user and group bin/omero fs usage Experimenter:* –report –sum-by user group # total usage for two projects and one dataset Megabytes bin/omero fs usage Project:1,2 Dataset:5 –units M # in this last case if the dataset was within project 1 or 2 # then the size returned would be identical to: bin/omero fs usage Project:1,2 –units M
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-
class
omero.plugins.fs.
ImportTime
(ctx, query)¶ -
get_cache
()¶ Retrieve import metrics from a map annotation on the fileset
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print_report
()¶ Report how long it took to import an existing fileset
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print_summary
()¶ Report import metrics from map annotations on filesets
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print_summary_line
()¶ Report import metrics from the map annotations on a fileset
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query_counts
()¶ Determine values for the per-item counts for the import metrics
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query_durations
()¶ Determine values for the phase durations for the import metrics
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write_cache
(update)¶ Write import metrics to a map annotation on the fileset
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omero.plugins.fs.
contents
(mrepo, path, ctx=None)¶ Yield Entry namedtuples for each return value from treeList for the given path.
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omero.plugins.fs.
get_logfile
(query, fid)¶
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omero.plugins.fs.
prep_directory
(client, mrepo)¶ Create an empty FS directory by performing an import and then deleting the created fileset.
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omero.plugins.fs.
rename_fileset
(client, mrepo, fileset, new_dir, ctx=None)¶ Loads each OriginalFile found under orig_dir and updates its path field to point at new_dir. Files are not yet moved.
omero.plugins.group module¶
Group administration plugin
Copyright 2009-2015 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.group.
GroupControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.UserGroupControl
-
_configure
(parser)¶
-
add
(*args, **kwargs)¶
-
add_permissions_arguments
(parser)¶
-
adduser
(args)¶
-
copyusers
(args)¶
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filter_users
(uids, group, owner=False, join=True)¶
-
info
(args)¶
-
list
(args)¶
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listusers
(args)¶
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parse_groupid
(a, args)¶
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parse_perms
(args)¶
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perms
(args)¶
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removeuser
(args)¶
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omero.plugins.hql module¶
HQL plugin
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
Copyright 2008 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.hql.
HqlControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
-
_configure
(parser)¶
-
display
(rv, cols=None, style=None, idsonly=False)¶
-
filter
(values)¶
-
hql
(args, loop=False)¶
-
project
(querySvc, queryStr, params, ice_map)¶
-
unwrap
(object, cache=None)¶
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omero.plugins.import module¶
Startup plugin for command-line importer.
-
class
omero.plugins.import.
CommandArguments
(ctx, args)¶ Bases:
object
-
accepts
(key)¶
-
add
(key, val=<object object>)¶
-
added_args
()¶
-
append_arg
(cmd_list, key, val=<object object>)¶
-
build_arg_list
(key, val=<object object>)¶
-
initial_args
()¶
-
java_args
()¶
-
open_files
()¶
-
open_log
(file, prefix=None)¶
-
reset_arg
(cmd_list, idx, key, val=<object object>)¶
-
set_login_arguments
(ctx, args)¶ Set the connection arguments
-
set_path
(path)¶
-
set_skip_arguments
(args)¶ Set the arguments to skip steps during import
-
set_skip_values
(skip)¶ Set the arguments to skip steps during import
-
-
class
omero.plugins.import.
ImportControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
-
COMMAND
= ['ome.formats.importer.cli.CommandLineImporter']¶
-
_configure
(parser)¶
-
bulk_import
(command_args, xargs)¶
-
do_import
(command_args, xargs)¶
-
importer
(args)¶
-
parse_bulk
(bulk, command_args)¶
-
parse_csv
(path, delimiter=', ')¶
-
parse_shlex
(path)¶
-
parse_text
(path, parse=False)¶
-
parse_tsv
(path, delimiter='\t')¶
-
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class
omero.plugins.import.
TestEngine
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.plugins.import.ImportControl
-
COMMAND
= ['ome.formats.test.util.TestEngine']¶
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omero.plugins.ldap module¶
User administration plugin (LDAP extension)
Copyright 2011 - 2016 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
-
class
omero.plugins.ldap.
LdapControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.UserGroupControl
-
_configure
(parser)¶
-
active
(*args, **kwargs)¶
-
create
(*args, **kwargs)¶
-
discover
(*args, **kwargs)¶
-
getdn
(*args, **kwargs)¶
-
list
(args)¶
-
setdn
(*args, **kwargs)¶
-
update_group
(*args, **kwargs)¶
-
update_user
(*args, **kwargs)¶
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omero.plugins.metadata module¶
Metadata plugin
Copyright 2015 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
-
class
omero.plugins.metadata.
Metadata
(obj_wrapper)¶ Bases:
object
A general helper object which providers higher-level accessors and mutators for a particular object.
-
get_allanns
(ns=None, anntype=None)¶
-
get_bulkanns
()¶
-
get_id
()¶
-
get_measures
()¶
-
get_name
()¶
-
get_original
()¶
-
get_parent
()¶
-
get_parents
()¶
-
get_roi_count
()¶
-
get_type
()¶
-
wrap
(obj)¶
-
-
class
omero.plugins.metadata.
MetadataControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
-
POPULATE_CONTEXTS
= (('csv', <class 'omero.util.populate_metadata.ParsingContext'>), ('bulkmap', <class 'omero.util.populate_metadata.BulkToMapAnnotationContext'>), ('deletemap', <class 'omero.util.populate_metadata.DeleteMapAnnotationContext'>))¶
-
_clientconn
(args)¶
-
_configure
(parser)¶
-
_format_ann
(md, obj, indent=None)¶ Format an annotation as a string, optionally pretty-printed
-
_load
(args, die_on_failure=True)¶
-
_output_ann
(mdobj, func, parents, indent)¶
-
allanns
(args)¶ Provide a list of all annotations linked to the given object
-
bulkanns
(args)¶ Provide a list of the NSBULKANNOTATION tables linked to the given object
-
mapanns
(args)¶ Provide a list of all MapAnnotations linked to the given object
-
measures
(args)¶ Provide a list of the NSMEASUREMENT tables linked to the given object
-
original
(args)¶ Print the original metadata in ini format
-
pixelsize
(args)¶ Set physical pixel size
-
populate
(args)¶ Add metadata (bulk-annotations) to an object
-
populateroi
(args)¶ Add ROIs to an object
-
rois
(args)¶ Manage ROIs
-
summary
(args)¶ Provide a general summary of available metadata
-
testtables
(args)¶ Tests whether tables can be created and initialized
-
-
exception
omero.plugins.metadata.
ObjectLoadException
(klass, oid)¶ Bases:
exceptions.Exception
Raised when a requested object could not be loaded
-
omero.plugins.metadata.
guess_mimetype
(filename)¶
omero.plugins.node module¶
author: | Josh Moore, josh at glencoesoftware.com |
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OMERO Grid node controller
This is a python wrapper around icegridnode.
Copyright 2008, 2016 Glencoe Software, Inc. All Rights Reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.node.
NodeControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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_handleNZRC
(nzrc)¶ Set the return value from nzrc on the context, and print out the last two lines of any error messages if present.
-
kill
(*args, **kwargs)¶
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start
(*args, **kwargs)¶
-
status
(args)¶
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stop
(*args, **kwargs)¶
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omero.plugins.obj module¶
Plugin for performing OMERO transactional changes (DML) from a simple script. This macro like language is intended to be used simply from the command-line as well as in scripts and tests.
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class
omero.plugins.obj.
ListGetTxAction
(tx_state, tx_cmd)¶ Bases:
omero.plugins.obj.NonFieldTxAction
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on_go
(ctx, args)¶
-
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class
omero.plugins.obj.
MapGetTxAction
(tx_state, tx_cmd)¶ Bases:
omero.plugins.obj.NonFieldTxAction
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on_go
(ctx, args)¶
-
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class
omero.plugins.obj.
MapSetTxAction
(tx_state, tx_cmd)¶ Bases:
omero.plugins.obj.NonFieldTxAction
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on_go
(ctx, args)¶
-
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class
omero.plugins.obj.
NewObjectTxAction
(tx_state, tx_cmd)¶ Bases:
omero.plugins.obj.TxAction
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check_requirements
(ctx, obj, completed)¶
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go
(ctx, args)¶
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class
omero.plugins.obj.
NonFieldTxAction
(tx_state, tx_cmd)¶ Bases:
omero.plugins.obj.TxAction
Base class for use with command actions which don’t take the standard a=b c=d fields.
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go
(ctx, args)¶
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save_and_return
(ctx)¶
-
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class
omero.plugins.obj.
NullTxAction
(tx_state, tx_cmd)¶ Bases:
omero.plugins.obj.NonFieldTxAction
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on_go
(ctx, args)¶
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class
omero.plugins.obj.
ObjControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
Create, Update and Query OMERO objects
The obj command allows inserting any objects into the OMERO database as well as updating and querying existing ones. This is likely useful for preparing datasets for import and similar.
Examples:
$ bin/omero obj new Dataset name=foo Dataset:123 $ bin/omero obj update Dataset:123 description=bar Dataset:123 $ bin/omero obj get Dataset:123 name foo $ bin/omero obj get Dataset:123 description=bar id=123 name=foo version= $ bin/omero obj null Dataset:123 description Dataset:123 $ bin/omero obj get Dataset:123 description
$ bin/omero obj new MapAnnotation ns=example.com MapAnnotation:456 $ bin/omero obj map-set MapAnnotation:456 mapValue foo bar MapAnnotation:456 $ bin/omero obj map-set MapAnnotation:456 mapValue foo MapAnnotation:456 $ bin/omero obj map-set MapAnnotation:456 mapValue fu baa MapAnnotation:456 $ bin/omero obj map-get MapAnnotation:456 mapValue foo bar $ bin/omero obj get MapAnnotation:456 mapValue (foo,bar),(fu,baa) $ bin/omero obj list-get MapAnnotation:456 mapValue 0 (foo,bar)
Bash examples:
$ project=$(bin/omero obj new Project name=’my Project’) $ dataset=$(bin/omero obj new Dataset name=’my Dataset’) $ bin/omero obj new ProjectDatasetLink parent=$project child=$dataset ProjectDatasetLink:456 $ bin/omero import -d $dataset ...-
_configure
(parser)¶
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parse
(tx_state, arg_list=None, line=None)¶ Takes a single command list and turns it into a TxAction object
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process
(args)¶
-
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class
omero.plugins.obj.
ObjGetTxAction
(tx_state, tx_cmd)¶ Bases:
omero.plugins.obj.NonFieldTxAction
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get_field
(field)¶
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on_go
(ctx, args)¶
-
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class
omero.plugins.obj.
TxAction
(tx_state, tx_cmd)¶ Bases:
object
Parsed operation provided by the user chosen based on the first non-variable field of the command. Implementations can choose how they will handle the fields parsed by TxCmd.
-
class_name
(ctx)¶
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go
(ctx, args)¶
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instance
(ctx)¶
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obj_id
()¶
-
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class
omero.plugins.obj.
TxCmd
(tx_state, arg_list=None, line=None)¶ Bases:
object
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VAR_NAME
= '(?P<DEST>[a-zA-Z][a-zA-Z0-9]*)'¶
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VAR_RE
= <_sre.SRE_Pattern object>¶
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_parse_early
()¶
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_parse_late
()¶
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setters
()¶
-
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class
omero.plugins.obj.
TxState
(ctx)¶ Bases:
object
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add
(command)¶
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get_row
(i)¶
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get_var
(key)¶
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set_value
(proxy, dest=None)¶
-
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class
omero.plugins.obj.
UpdateObjectTxAction
(tx_state, tx_cmd)¶ Bases:
omero.plugins.obj.TxAction
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go
(ctx, args)¶
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omero.plugins.perf module¶
Plugin for measuring the performance of an OMERO installation.
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
Copyright 2008, 2016 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.perf.
PerfControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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omero.plugins.prefs module¶
prefs plugin
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
The pref plugin makes use of prefs.class from the common component.
Copyright 2007-2013 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.prefs.
PrefsControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.plugins.prefs.WriteableConfigControl
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_configure
(parser)¶
-
all
(*args, **kwargs)¶
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append
(*args, **kwargs)¶
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assert_valid_property_name
(key)¶
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default
(*args, **kwargs)¶
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drop
(*args, **kwargs)¶
-
edit
(*args, **kwargs)¶
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get
(*args, **kwargs)¶
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get_list_value
(args, config)¶
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get_omeroweb_default
(key)¶
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handle_line
(line, config, keys)¶
-
keys
(*args, **kwargs)¶
-
list
(*args, **kwargs)¶
-
load
(*args, **kwargs)¶
-
lock
(*args, **kwargs)¶
-
old
(args)¶
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open_config
(args)¶
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parse
(args)¶
-
path
(*args, **kwargs)¶
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remove
(*args, **kwargs)¶
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set
(*args, **kwargs)¶
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upgrade
(*args, **kwargs)¶
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version
(*args, **kwargs)¶
-
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class
omero.plugins.prefs.
WriteableConfigControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
Base class for controls which need write access to the OMERO configuration using the @with_rw_config decorator
Note BaseControl should be used for read-only access using @with_config
-
die_on_ro
(config)¶
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run_upgrade_check
(config, agent)¶
-
-
omero.plugins.prefs.
_make_open_and_close_config
(func, allow_readonly)¶
-
omero.plugins.prefs.
getprefs
(args, dir)¶ Kept around temporarily for upgrading users from pre-4.2 configurations.
-
omero.plugins.prefs.
with_config
(func)¶ opens a config and passes it as the second argument.
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omero.plugins.prefs.
with_rw_config
(func)¶ opens a config and passes it as the second argument. Requires that the returned config be writeable
omero.plugins.script module¶
script plugin
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
The script plugin is used to run arbitrary blitz scripts which take as their sole input Ice configuration arguments, including –Ice.Config=file1,file2.
The first parameter, the script itself, should be natively executable on a given platform. I.e. invokable by subprocess.call([file,...])
Copyright 2008 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.script.
ScriptControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_complete
(text, line, begidx, endidx)¶ Returns a file after “upload” and otherwise delegates to the BaseControl
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_configure
(parser)¶
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_file
(args, client)¶
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_parse_inputs
(args, params)¶
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_parse_scripts
(scripts, msg)¶ Parses a list of scripts to self.ctx.out
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_parse_who
(who)¶ Parses who items of the form: “user”, “group”, “user=1”, “group=6”
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cat
(args)¶
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delete
(args)¶
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demo
(args)¶
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disable
(args)¶
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edit
(args)¶
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enable
(args)¶
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foreground_nix
(impl, timeout)¶ Use signal.SIGALRM to wait for the timeout to signal
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foreground_win
(impl, timeout)¶ Note: currently simply fails. An implementation might be possible using msvcrt. See: http://stackoverflow.com/questions/3471461/raw-input-and-timeout/3911560
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help
(args)¶
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jobs
(args)¶
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launch
(args)¶
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list
(args)¶
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log
(args)¶
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params
(args)¶
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replace
(args)¶
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run
(args)¶
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serve
(args)¶
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setmimetype
(args)¶
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upload
(args)¶
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omero.plugins.search module¶
Simple command-line searching. Similar to the hql plugin.
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class
omero.plugins.search.
SearchControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.plugins.hql.HqlControl
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_configure
(parser)¶
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date
(user_string)¶
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search
(args)¶
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omero.plugins.server module¶
Startup plugin for our various server components, called typically by icegridnode after parsing etc/grid/templates.xml.
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
Copyright 2008, 2016 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.server.
ServerControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_checkIceConfig
(*args, **kwargs)¶
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_configure
(parser)¶
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_prop
(data, key)¶
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_xargsAndDebug
(component, xargs_default)¶
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blitz
(args)¶
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help
(*args, **kwargs)¶
-
indexer
(args)¶
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omero.plugins.sessions module¶
Plugin for viewing and controlling active sessions for a local user.
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
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class
omero.plugins.sessions.
SessionsControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.UserGroupControl
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FACTORY
¶ alias of
SessionsStore
-
_configure
(parser)¶
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_configure_dir
(parser)¶
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_configure_login
(login)¶
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_get_server
(store, name, port)¶
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_get_username
(defuser)¶
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static
_parse_conn
(server, default_name)¶ Parse a connection string of form (user@)server(:port)
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_parse_timeout
(timeout, msg='')¶
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_require_tty
(msg)¶
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attach
(store, server, name, uuid, props, exists, set_current=True)¶
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check_and_attach
(store, server, name, uuid, props, check_group=False)¶ Checks for conflicts in the settings for this session, and if there are none, then attempts an “attach()”. If that fails, the session is removed.
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clear
(args)¶
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close
(args)¶
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conn
(properties=None, profile=None, args=None)¶ Either creates or returns the exiting omero.client instance. Uses the comm() method with the same signature.
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file
(args)¶ Return the file associated with the current active session
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group
(args)¶
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handle
(rv, action)¶ Handles a new connection
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help
(args)¶
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keepalive
(args)¶
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key
(args)¶ Return the key associated with the current active session
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list
(args)¶
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login
(args)¶ Login to a given server, and store session key locally.
USER, HOST, and PORT are set as args or in a ssh-style connection string. PASSWORD can be entered interactively, or passed via -w (insecure!). Alternatively, a session KEY can be passed with ‘-k’. Admin users can use –sudo=ADMINUSER to login for others.
- Examples:
- bin/omero login example.com bin/omero login user@example.com bin/omero login user@example.com:24064 bin/omero login -k SESSIONKEY example.com bin/omero login –sudo=root user@example
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logout
(args)¶
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open
(*args, **kwargs)¶
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store
(args)¶
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timeout
(args)¶
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who
(args)¶
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omero.plugins.submit module¶
submit plugin
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
Copyright 2007 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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exception
omero.plugins.submit.
Cancel
¶ Bases:
exceptions.Exception
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exception
omero.plugins.submit.
Save
¶ Bases:
exceptions.Exception
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class
omero.plugins.submit.
SubmitCLI
¶ Bases:
omero.cli.CLI
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do_cancel
(arg)¶
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do_save
(arg)¶
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post_process
()¶
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postcmd
(stop, line)¶
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class
omero.plugins.submit.
SubmitControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_configure
(parser)¶
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omero.plugins.tag module¶
Tag plugin for command-line tag manipulation
author: | Sam Hart <sam@glencoesoftware.com> |
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Copyright (C) 2013-2015 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.tag.
Tag
(tag_id=None, name=None, description=None, owner=None, children=None)¶ Bases:
object
-
class
omero.plugins.tag.
TagCollection
¶ Bases:
object
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class
omero.plugins.tag.
TagControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
-
_configure
(parser)¶
-
add_newtag_params
(parser)¶
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add_standard_params
(parser)¶
-
add_tag_common_params
(parser)¶
-
create
(args)¶ create a tag command.
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create_tag
(name, description, text='tag')¶ Creates a new tag object. Returns the new tag object.
If name parameter is None, the user will be prompted to input it.
The “text” parameter should be the text description to use upon user input. For example, if we were creating a tag, this would be “tag” (the default). If we were creating a tagset, this could be “tag set”.
-
createset
(args)¶ Create a tag set command.
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determine_console_size
()¶ Will attempt to determine console size based upon the current platform.
Returns tuple of width and length.
-
generate_empties
(empties, args)¶ Given a list of empty tagsets, return a list of lines representing the empty tagset output.
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generate_orphans
(orphans, args)¶ Given a list of orphaned tags, return a list of lines representing the orphan output.
Given a dict of tags and mappings for parent/child relationships return a list of lines representing the tagset output.
-
link
(args)¶ Links an object to a tag annotation.
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list
(args)¶ List tags command.
Returns a TagCollection object
Returns a TagCollection object
Returns a TagCollection of just the tagsets.
If tag is provided, will return the tagsets with those tags.
-
listsets
(args)¶ List tag sets command.
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load
(args)¶ Import new tag(s) from json.
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pagetext
(lines)¶
-
pagetext_format
(format, elements)¶
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print_line
(line, index)¶
-
-
omero.plugins.tag.
clip
(s, width)¶ Given a string, s, and a width, will clip the string to that width or fill it with spaces up to that width.
Returns modified string
-
omero.plugins.tag.
exec_command
(cmd)¶ given a command, will execute it in the parent environment Returns a list containing the output
omero.plugins.upload module¶
upload plugin
Plugin read by omero.cli.Cli during initialization. The method(s) defined here will be added to the Cli class for later use.
Copyright 2007-2016 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.upload.
UploadControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.BaseControl
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_complete
(text, line, begidx, endidx)¶ Returns a file after “upload” and otherwise delegates to the BaseControl
-
_configure
(parser)¶
-
upload
(args)¶
-
omero.plugins.user module¶
User administration plugin
Copyright 2009-2014 Glencoe Software, Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
-
class
omero.plugins.user.
UserControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.UserGroupControl
-
_configure
(parser)¶
-
add
(*args, **kwargs)¶
-
email
(args)¶
-
filter_groups
(groups, uid, owner=False, join=True)¶
-
format_name
(exp)¶
-
info
(args)¶
-
joingroup
(args)¶
-
leavegroup
(args)¶
-
list
(args)¶
-
listgroups
(args)¶
-
parse_userid
(a, args)¶
-
password
(args)¶
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omero.plugins.web module¶
Plugin for our configuring the OMERO.web installation
Copyright 2009-2016 University of Dundee. All rights reserved. Use is subject to license terms supplied in LICENSE.txt
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class
omero.plugins.web.
WebControl
(ctx=None, dir=path(u'/opt/hudson/workspace/OMERO-DEV-release/src/dist'))¶ Bases:
omero.cli.DiagnosticsControl
-
_build_run_cmd
(settings)¶
-
_check_pid
(pid, pid_path)¶
-
_configure
(parser)¶
-
_deprecated_args
(args, settings)¶
-
_get_django_pid
(pid_path)¶ Get Django Process ID
-
_get_django_pid_path
()¶
-
_get_fallback_dir
()¶
-
_get_python_dir
()¶
-
_get_web_templates_dir
()¶
-
call
(args)¶
-
clearsessions
(*args, **kwargs)¶ Clean out expired sessions.
-
collectstatic
(*args, **kwargs)¶ Ensure that static media is copied to the correct location
-
config
(*args, **kwargs)¶ Generate a configuration file from a template
-
config_choices
= ('nginx', 'nginx-development', 'nginx-location')¶
-
diagnostics
(args)¶
-
enableapp
(*args, **kwargs)¶
-
gateway
(args)¶
-
help
(*args, **kwargs)¶ Return extended help
-
restart
(args)¶
-
set_environ
(ice_config=None)¶
-
start
(*args, **kwargs)¶
-
status
(*args, **kwargs)¶
-
stop
(*args, **kwargs)¶
-
syncmedia
(args)¶
-
-
omero.plugins.web.
assert_config_argtype
(func)¶ Decorator validating OMERO.web deployment dependencies
-
omero.plugins.web.
config_required
(func)¶ Decorator validating Django dependencies and omeroweb/settings.py