hrm-omero-0.4.0

Improvements

• Uploading images to OMERO into another group than the user's default one is now properly supported.
• HRM job parameter summaries are now being added as OMERO ["Map Annotations"][c4] instead of simply being a comment string.
• Formats like e.g. Olympus .vsi requiring their files to be placed in a specific directory structure are now properly supported.
• Tree levels (users, projects, ...) are now sorted alphabetically instead of the (seemingly) random order as they are returned by OMERO with the exception of the current user always being listed first on the group level, followed by their colleagues.
• Datasets in OMERO that are not associated to a Project will no longer be ignored but rather be shown on the same level than the user's projects, just as OMERO.web and OMERO.insight are doing it.
• The target directory for downloading preview thumbnails from OMERO will be created automatically in case it doesn't exist yet.
• The command line parameter --password (or -w) is now deprecated in favor of using the environment variable described above.
• The following functions are now deprecated and will be removed in a future release.
  • hrm_omero.omero.connect()
  • hrm_omero.cli.parse_arguments()
• Functions hrm_omero.transfer.to_omero() and hrm_omero.transfer.from_omero() are now raising a ValueError in case the provided id_str is malformed.
• Unit string literal µm is no longer converted to um in parameter summaries.
• New dependencies: [Pillow][c1]

New Features

• An environment variable OMERO_PASSWORD can (and should!) now be used to supply the sensitive part of the user credentials that are necessary to connect to OMERO. This avoids having the password as plain-text in the system's process list (e.g. when calling ps fu -e or similar) and also prevents it from showing up in an annotated stack trace in case an uncaught exception is raised.
• Log level of the HRM-OMERO connector itself can now be set through the configuration option OMERO_CONNECTOR_LOGLEVEL in the HRM config file.
• Log messages of the connector will also be placed in a separate log file in the default location defined via HRM_LOG in the HRM config file. his can be disabled by setting OMERO_CONNECTOR_LOGFILE_DISABLED=true.
• Debug logging for the OMERO import call can now be requested be setting the configuration option OMERO_DEBUG_LOG in the HRM config file.
• hrm_omero.hrm.parse_summary() has been added to provide a function for parsing the parameter summary from an HRM job into a (nested) dict.
• hrm_omero.hrm.parse_job_basename() has been added to identify the base name of all files that belong to the set of results from a certain HRM job.
• hrm_omero.omero.add_annotation_keyvalue() can be used to add so-called [Map Annotations][c4] (key-value pairs) to objects in OMERO.
• hrm_omero.omero.find_recently_imported() tries to identify an image in OMERO using the import timestamp and the object label as criteria.
• A decorator hrm_omero.decorators.connect_and_set_group() is now available that can be used with functions that require a valid connection plus an OMERO object identifier pair (submitted on the command line as "G:4:Image:12345" or similar, passed on to the decorated function as obj_type and obj_id).
• hrm_omero.misc.printlog() can be used to push a message to the log and stdout.
• A class hrm_omero.misc.OmeroId provides parsing, validation and access to all group-qualified OMERO object IDs (commonly passed as function parameter id_str throughout the existing code).
• The CLI has a new optional parameter --dry-run that prevents any action from being performed, instead the name of the function and the corresponding parameters that would be called are printed to stdout.
• Unit tests using [pytest][c2] and [pytest-cov][c3].

Fixes

• Thumbnail download has been adapted to recent code changes in OMERO.

hrm-omero-0.3.1

No functional changes, only (PyPI) metadata.

hrm-omero-0.3.0

First public release of hrm-omero.