Tags: mcovarr/fiss
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v0.16.31 (broadinstitute#155) fiss.py: * attr_delete now works on pairs * mop now recurses into arrays and complex data structures to discover files referenced by attributes * attr_get and attr_list are now reference data aware (matching Terra UI), and can return or elide them from results. Dockerfile: * base image changed to Python 3 __init__.py: * Suppress Python 2 deprecation warning from cryptography module. Co-authored-by: Sushma Chaluvadi <schaluva@broadinstitute.org>
hotfix - re-enabled making methods public. (broadinstitute#150)
v0.16.29 (broadinstitute#149) api.py: * added fields parameter to get_workspace() fiss.py: * space_exists(), attr_get(), attr_copy(), mop(), validate_file_attrs(), and config_validate() updated to use fields parameter in call to get_workspace() py3 compatibility bugfixes: * setup.py: - easy_install removed to enable compatibility with latest setuptools * fccore.py: - tempfile generated in edit_text() now opens in mode 'w' instead of 'w+b' to work with both py2 and py3 str objects. Co-authored-by: Luke Sargent <luke.c.sargent@gmail.com> Co-authored-by: DailyDreaming <lblauvel@ucsc.edu>
v0.16.28 (broadinstitute#145) api.py: * added fields parameter to list_workspaces() fiss.py: * space_list() and space_search() updated to use fields parameter in calls to list_workspaces() * Bugfix: proj_list() - fixed TypeError from appending map to list in py3 Co-authored-by: Ilya Shlyakhter <ilya_shl@alum.mit.edu> Co-authored-by: Luke Sargent <luke.c.sargent@gmail.com>
v0.16.27 (broadinstitute#140) New function validate_file_attrs: * Returns a list of any file (google bucket object) attributes that don't exist or the user does not have access to. Bugfix (Fixes broadinstitute#138): * assign root_url = fcconfig.root_url inside API method calls * While commands existed to modify the default root URL of the API, they only modified the calls to the API if set in the user's .fissconfig. This fix allows it to be set programmatically and via the CLI. Co-authored-by: M. Morgan Taylor (@mmorgantaylor), Michael Baumann (@mikebaumann)
v0.16.26 (broadinstitute#137) Enabled deep copy of objects with a given prefix when cloning a workspace (closes broadinstitute#131). For workflow submissions, enabled running non-data model configs by making entity name optional in the CLI, and not including entity name and type in the API payload when they have not been set. Specifics: api.py * added copyFilesWithPrefix parameter to clone_workspace * create_submission no longer includes entity name and type in its payload when they are not set fiss.py * added copyFilesWithPrefix parameter to space_clone * config_start no longer requires entity to be set Co-authored-by: M. Morgan Taylor <marymorg@broadinstitute.org>
v0.16.25 (broadinstitute#129) Multiple enhancements to mop: * Only delete unreferenced files generated by workflows. (broadinstitute#127 by @Marianie-Simeon) * Ignore more files generated by the execution engine (e.g. rc, script, stdout, stderr). (closes broadinstitute#128) * Report file sizes in summaries and listings. (closes broadinstitute#118) * Allow user to include/exclude files via glob. (closes broadinstitute#116)
Corrected Google Cloud VM error: (broadinstitute#125) On Google Cloud VMs, the user's account email is stored in a different attribute of the Session's Credentials object (service_account_email rather than id_token). The existence of the attributes are also mutually exclusive. This caused an AttributeError when accessing a non-existent attribute, and failure to populate __USER_ID, which broke several functions. Updated api.py to handle the different attribute locations.
v0.16.23 (broadinstitute#124) Enhanced Config/Method Group ACLs and Added Support for Terra Flexible Data Model fiss.py: * group expansion (used for giving method/config ACLs to groups) made recursive to handle nested groups. * Added back entity_tsv with updated logic to detect if content is text to print or an archive for download, and support for specifying ordered attributes and data model. * Updated entity_import to specify data model. api.py: * Updated get_entities_tsv with ability to specify ordered attributes and data model. * Updated upload_entities and upload_entities_tsv to enable use of flexible data model API.
v0.16.22 (broadinstitute#122) api.py: * enabled namespace, name, and snapshot ID filtering for method repository listings * new command whoami returns FireCloud user id fiss.py: * updated listing calls (method_list, config_list) to enable new filters * calls to listings updated to use filters when appropriate * new command set_config_acl for setting ACLs on configs in the methods repo * added capability to set method and config ACLs for groups * meth_list and meth_exists commands updated to use argument method instead of name to be consistent with the rest of the CLI. * config_list updated to work on methods repo when user has a default workspace defined in their ~/.fissconfig setup.py: * google-auth updated to use current release __init__.py: * Added warning filter to silence application default warning Makefile: * publish updated to use twine
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