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Add fetch-logs and enable Azure log fetching #259

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Add fetch-logs and enable Azure log fetching #259

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09803c1
added fetch wording to logs in README.md
Apr 28, 2023
a53858b
Merge branch 'main' into bs_fetch_logs
May 5, 2023
a2f86e3
first draft of logs refactoring
May 8, 2023
1ec2a85
Added 'azure_storage_account' to config options
May 9, 2023
aad6a58
Add option to download from azure
May 9, 2023
88a5430
update log readme options
May 9, 2023
b0df586
minor edits, removed function that called logs api
May 9, 2023
88077ed
lint fixes
May 9, 2023
a7b82fc
updated requirements.txt to include azure packages
May 9, 2023
09a3859
Minor updates to command.py, added several unit tests for logs command
May 23, 2023
f7ee8cd
Added function to replace uuids in integration tests
Jun 26, 2023
21bfa56
functional integration tests for logs
Jun 26, 2023
4cb1e6c
refractoring logs command.py
Jun 26, 2023
e1d6316
show default status to retrieve in help message
Jun 26, 2023
f6e4977
Allow the user to specify where to download logs if needed
Jun 26, 2023
b826399
made fetch_logs and printing log summary option mutually exclusive op…
Jun 26, 2023
67b0566
linting changes
Jun 26, 2023
a79f0e1
linting changes, fix to path for test function
Jun 27, 2023
00fe4ed
Added more explicit message about using ALL when default 'Failed' log…
Jun 27, 2023
1228b5a
fix integration test
Jun 28, 2023
389eae3
enum for backends
Jun 29, 2023
69ac907
Added reason why the logs api isn't being used by the logs command
Jun 29, 2023
07fa6a2
added unit tests for io utils functions, added warning for azure/gcp …
Jun 30, 2023
5a6f3dc
lint fix
Jul 20, 2023
7a7459e
removed get_gcp_file_content because it requires in git tox test due …
Jul 20, 2023
ff3ff45
lint fix
Jul 20, 2023
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9 changes: 6 additions & 3 deletions README.md
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Expand Up @@ -73,9 +73,12 @@ Cromshell is a CLI for submitting workflows to a Cromwell server and monitoring/

#### Logs
* `logs [workflow-id] [[workflow-id]...]`
* List the log files produced by a workflow.
* [COMING SOON] `fetch-logs [workflow-id] [[workflow-id]...]`
* Download all logs produced by a workflow.
* List the log files produced by a workflow, Defaults to print `Failed` status only.
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indentations seem to be off?

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should be correct.

- command
  - command description
  - command description

* `-f` Download the log files produced by a workflow.
* `-p` Print the log files produced by a workflow.
* `-des` Don't expand the subworkflows.
* `-j` Print the log files produced by a workflow in JSON format.
* `-s [STATUS]` Only print logs for jobs with the given `[STATUS]`.

#### Job Outputs
* `list-outputs [workflow-id] [[workflow-id]...]`
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2 changes: 2 additions & 0 deletions requirements.txt
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@@ -1,3 +1,5 @@
azure-identity>=1.12.0
azure-storage-blob>=12.16.0
gcsfs>=2022.3.0
google-cloud-bigquery>=3.5.0
termcolor>=1.1.0
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