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import firecloud.api broken in Python 3.10 #170

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amstilp opened this issue Feb 9, 2022 · 2 comments · Fixed by #175
Closed

import firecloud.api broken in Python 3.10 #170

amstilp opened this issue Feb 9, 2022 · 2 comments · Fixed by #175

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@amstilp
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amstilp commented Feb 9, 2022 •
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Python 3.10 changed the collections module, which breaks the firecloud/api.py file.

In a new venv with Python 3.10.2:

python -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install firecloud
python -c 'import firecloud.api as fapi'

gives this error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/amstilp/venv310/lib/python3.10/site-packages/firecloud/api.py", line 16, in <module>
    from collections import Iterable
ImportError: cannot import name 'Iterable' from 'collections' (/opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/collections/__init__.py)

import firecloud.api as fapi works without error in Python 3.9.10.
@amstilp amstilp mentioned this issue Feb 17, 2022
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@DailyDreaming
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I'm also having this issue. Seems like an easy fix. Since FISS seems to no longer be maintained, I may just move off of the FISS dependency and call the API directly then.

This was referenced Jun 30, 2022
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@dheiman
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dheiman commented Jul 1, 2022 via email

dheiman added a commit that referenced this issue Jul 25, 2022
@dheiman
v0.16.32 - initial commit
12d3fd7 
* Changed Dockerfile base image to python 3.10
* Fixed Python 3.10 incompatibility issues (fixes #170)
* pylint set to minimum version 2.0.0 (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 `deleteIntermediateOutputFiles`,
`useReferenceDisks`, `memoryRetryMultiplier`, `workflowFailureMode`, and
`userComment` fields (fixes #165, #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 functionss `_attr_ladd()` and
`_attr_lrem()`
* new functions:
   - `delete_entities_of_type()`
   - `rename_entity()`
   - `rename_entity_type()`
   - `rename_entity_type_attribute()`
* 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
* 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()`.
dheiman pushed a commit that referenced this issue Jul 26, 2022
@DailyDreaming
Fix Iterable import. (#174)
3183a60 
Fixes #170
@dheiman dheiman mentioned this issue Jul 26, 2022
Merged
dheiman added a commit that referenced this issue Jul 26, 2022
@dheiman
v0.16.32 (#175)
bf77785 
* Changed Dockerfile base image to python 3.10
* Fixed Python 3.10 incompatibility issues (fixes #170)
* pylint set to minimum version 2.0.0 (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 attributes 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()`
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v0.16.32 broadinstitute/fiss
3 participants
@dheiman @amstilp @DailyDreaming