Releases | Open Source Science

https://github.com/broadinstitute/fiss - v0.16.38

`api.py`:

get_storage_cost and get_bucket_usage updated to use the new getStorageCostEstimateV2 API (original APIs deprecated)

`fiss.py`:

updated space_size and space_cost to return the applicable fields.

Full Changelog: https://github.com/broadinstitute/fiss/compare/v0.16.37...v0.16.38

- Python
Published by dheiman over 1 year ago

https://github.com/broadinstitute/fiss - v0.16.37

`api.py`

get_workflow_metadata updated to include the arguments include_key, exclude_key, and expand_sub_workflows.

- Python
Published by dheiman over 2 years ago

https://github.com/broadinstitute/fiss - v0.16.36

Hotfix: the old Terra billing API (profile/billing) is being removed, fiss.py and api.py updated to use the new one (billing/v2); Makefile updated to ensure image is built for linux/amd64; Dockerfile updated to use latest Python-3.10.

What's Changed

FISS v0.16.36 by @dheiman in https://github.com/broadinstitute/fiss/pull/183

Full Changelog: https://github.com/broadinstitute/fiss/compare/v0.16.35...v0.16.36

- Python
Published by dheiman over 2 years ago

https://github.com/broadinstitute/fiss - v0.16.35

Hotfix

mop was failing for Python 2.7 installations when the user didn't set a default project, and the bucket listing error message was broken. To fix this, bucket listing was updated to use the workspace billing project, and the bucket listing exception catching code was corrected.

- Python
Published by dheiman almost 4 years ago

https://github.com/broadinstitute/fiss - v0.16.34

`api.py`

check for presence of clock skew argument rather than check google.auth.__version__ #### fiss.py
meth_acl/config_acl
- changed map(f(x),iterable) returns into list comprehensions to make py2/3 consistent
mop updated to account for change in Terra output directory structure #### fccore.py
removed version string parser in favor of above check for the clock skew argument

- Python
Published by dheiman almost 4 years ago

https://github.com/broadinstitute/fiss - v0.16.33

`fccore.py`:

Added function to extract release tuple from a standard version string (based on PEP 440)

`api.py`:

parameter added to allow for clock skew in Oauth call
added version check of google.auth to determine availability of clock skew parameter

`fiss.py`:

added space_size()
added space_cost()
removed Python 3 syntax that broke Python 2 compatibility

`setup.py`:

blocked versions of google.auth with restrictive clock skew defaults and no way to modify them (2.1.0-2.3.1)

- Python
Published by dheiman almost 4 years ago

https://github.com/broadinstitute/fiss - v0.16.32

Changed Dockerfile base image to python 3.10
Fixed Python 3.10 incompatibility issues (fixes #170)
pylint set to minimum version 1.9.5 (fixes #168)

`api.py`:

added __patch() helper to simplify adding wrappers for PATCH API calls
enhanced error checking to use the more robust json decoder in the requests module
upload_entities(): added delete_empty parameter
get_entities_query(): added filter_operator and fields parameters
create_submission(): added delete_intermediate_output_files, use_reference_disks, memory_retry_multiplier, workflow_failure_mode, and user_comment fields (fixes #165, fixes #169)
create_workspace(): added noWorkspaceOwner and bucketLocation fields and enabled use of multiple authorization domains (fixes #171)
new helper functions: _attr_vlcreate() and _attr_erlcreate() for creating list attribute via update_workspace_attributes() and update_entity() (resolves #99)
fixed bugs in existing helper functions _attr_ladd() and _attr_lrem()
new functions:
- delete_entities_of_type()
- rename_entity()
- rename_entity_type()
- rename_entity_type_attribute()
- get_proxy_group()
- get_storage_cost()
- get_bucket_usage()
- get_workflow_cost() (resolves #144)
updated and cleaned up documentation for multiple functions

`fiss.py`:

new functions:
- entity_rename()
- attr_rename()
function updates:
- helper _entity_paginator() updated to take advantage of the fields parameter to speed up queries
- config_start() updated to use new api.create_submission() fields
- attr_get() now returns formatted arrays for list attributes in workspaces
- attr_set() updated to enable creation of value and reference list attributes
- attr_delete() updated to be completely type agnostic (previously only guaranteed to work on entity types in the firecloud model)
- space_new() updated to allow multiple authorization domains and set the bucket region for the new workspace
- mop():
  - Added submission ID filtering (resolves #158)
  - Now uses google-cloud-storage API for file listing rather than gsutil CLI
Cleaned up return of Terra errors to be more human-readable

`highlevel_tests.py`:

updated include new rename functions
fixed bugs that were due to inaccurate API docs

`lowlevel_tests.py`:

added test for get_entities_query().
added test for get_proxy_group()

- Python
Published by dheiman almost 4 years ago

https://github.com/broadinstitute/fiss - v0.16.31

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.

- Python
Published by dheiman over 5 years ago

https://github.com/broadinstitute/fiss - v0.16.30

Hotfix - re-enabled making methods public.

- Python
Published by dheiman almost 6 years ago

https://github.com/broadinstitute/fiss - v0.16.29

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.

- Python
Published by dheiman almost 6 years ago

https://github.com/broadinstitute/fiss - v0.16.28

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

- Python
Published by dheiman almost 6 years ago

https://github.com/broadinstitute/fiss - v0.16.27

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 #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.

Bugfix Co-authored-by: M. Morgan Taylor (@mmorgantaylor), Michael Baumann (@mikebaumann)

- Python
Published by dheiman about 6 years ago

https://github.com/broadinstitute/fiss - v0.16.26

Enabled deep copy of objects with a given prefix when cloning a workspace (closes #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

- Python
Published by dheiman over 6 years ago

https://github.com/broadinstitute/fiss - v0.16.25

Multiple enhancements to mop: * Only delete unreferenced files generated by workflows. * Ignore more files generated by the execution engine (e.g. rc, script, stdout, stderr). * Report file sizes in summaries and listings. * Allow user to include/exclude files via glob.

- Python
Published by dheiman almost 7 years ago

https://github.com/broadinstitute/fiss - v0.16.24

Hotfix * Fixed bug causing errors when run on Google Cloud VMs. Local execution was unaffected by the bug. * setup.py updated to explicitly designate long_description_content_type as text/plain to re-enable publishing to PyPI.

- Python
Published by dheiman about 7 years ago

https://github.com/broadinstitute/fiss - v0.16.23

Enhanced Config/Method Group ACLs and 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.

- Python
Published by dheiman about 7 years ago

https://github.com/broadinstitute/fiss - v0.16.22

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

- Python
Published by dheiman over 7 years ago

https://github.com/broadinstitute/fiss - v0.16.21

The Groups API has been added to api.py
Upon a refresh error, api.py will attempt to re-authenticate
Typo fixes on help descriptions of several high level commands
setup.py now requires a minimum version of setuptools (40.3.0)

- Python
Published by dheiman over 7 years ago

https://github.com/broadinstitute/fiss - v0.16.20

Added WDL extraction capabilities to CLI * Updated API command get_repository_method * added documentation link * added new parameter wdlonly * New CLI commands `configwdlandmeth_wdl` * use the updated API command to retrieve WDL from the workspace config and method repository respectively

- Python
Published by dheiman over 7 years ago

https://github.com/broadinstitute/fiss - v0.16.19

Added config_diff HL command.
HL command mop updated to work in Python 3 and fail with proper error message when workspace bucket is inaccessible.

- Python
Published by dheiman over 7 years ago

https://github.com/broadinstitute/fiss - v0.16.18

added HL export commands for sample, pair and participant sets

- Python
Published by noblem almost 8 years ago

https://github.com/broadinstitute/fiss - v0.16.17

do for pairlist and participantlist what was done for sample_list in 0.16.16; extended tests accordingly

- Python
Published by noblem almost 8 years ago

https://github.com/broadinstitute/fiss - v0.16.16

Added pairlist HL command; enlarged scope of applicability of samplelis HL commandt, to not only workspaces but all sample container types: pair, sampleset, workspace, participant; added pairlist HL function and new tests for both [pair,sample]list; internal HL function _getentities now paginates by default, to enable more calls to complete robustly; HL tests can now REUSESPACE for faster execution during repeated testing

- Python
Published by noblem almost 8 years ago