Make datman easier to install and use by DESm1th · Pull Request #303 · TIGRLab/datman

DESm1th · 2021-04-30T16:59:01Z

This pull request adds:

Fixes for some bugs that arise when running without a dashboard
Well commented configuration templates in assets/config_templates that can be used by anyone who doesnt have access to our datman-config repo
A dockerfile documenting how tigrlab/datman:0.1 was built
Updates and fixes to our documentation pages on how to install and configure datman

Due to the fact that datman.utils.update_checklist was expecting subject IDs without the repeat/session number, these scripts were causing exceptions to be raised on checklist update when the dashboard wasnt installed.

when running without dashboard

- Started to remove hard-coded redcap config - Updated documentation on configuration and installation

pep8speaks · 2021-04-30T16:59:10Z

Hello @DESm1th, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, pip install flake8 and then run flake8 datman.

Comment last updated at 2022-02-23 19:46:55 UTC

josephmje

Thanks for this @DESm1th! Especially all of that reformatting of the docs. I've yet to go over the config files but had 2 minor comments to start.

Co-authored-by: Michael Joseph <josephmje.22@gmail.com>

DESm1th · 2021-05-04T15:52:07Z

Thanks for the feedback Mike! :)

jerdra

Thanks for putting this together Dawn! Just had a few verrry minor items that could maybe be addressed in a separate PR but i thought would be worth mentioning!

jerdra · 2021-10-05T15:22:39Z

    ch = logging.StreamHandler(sys.stdout)
    ch.setLevel(logging.WARN)
    logger.setLevel(logging.WARN)


Is there a reason to have varying logging set-ups across scripts?

Nope, none at all (except in places where we add a server log handler). This is just a historical thing leftover from the days when we joe/tom/I had three different ideas about how it should be done. I've always meant to clean up these old instances where basicConfig wasnt used though

jerdra · 2021-10-05T15:23:37Z

+def get_setting(key, default=None):
+    try:
+        return cfg.get_key(key)
+    except datman.config.UndefinedSetting as e:
+        if not default:
+            raise e
+        return default
+


should get_setting be defined in the Config object instead?

I think there was a good reason at the time why I put it here and not in config.py, but I can't currently remember what that was. So maybe I should move it over? I'll try to job my memory on this one

Co-authored-by: Jerry Jeyachandra <jerrold.jeyachandra@gmail.com>

josephmje · 2021-12-20T18:51:53Z

Sorry about the delay on this @DESm1th! Is this now ready for review?

DESm1th · 2022-01-04T19:17:07Z

Sorry about the delay on this @DESm1th! Is this now ready for review?

It is!

josephmje · 2022-02-09T16:38:44Z

+    ln -s pip3 pip && \
+    pip install --upgrade pip
+
+# Install dcm2niix/v1.0.20210317


Could we upgrade the version of dcm2niix here?

Absolutely! Thanks for catching that. What version should I add here? Just the newest?

Hey Dawn, sorry for the late reply. Yes, it would be v1.0.20211006

@jerdra Do you know if this latest version is correct or the 2019 version RE the OPT slice timing?

its probably fine given that we don't use slice-timing for fMRI scans anyway. The diffusion scans aren't affected

ok! I updated the version used

…f now)

DESm1th added 28 commits February 5, 2021 14:09

[FIX] linking scripts raised exceptions when dashboard missing.

643459f

Due to the fact that datman.utils.update_checklist was expecting subject IDs without the repeat/session number, these scripts were causing exceptions to be raised on checklist update when the dashboard wasnt installed.

[FIX] Undo code regression from merging

727964c

[FIX] Stop regex from only reading first three characters of a line

838d19f

[FIX] Allow a site to not define an XnatArchive (needed for SPN02)

8731dbb

[FIX] Add better repr for config objects

df635d0

[FIX] Removed handler which caused duplicate log messages

514bab4

[FIX] Update dm_task_file to run without the dashboard

20e981a

[FIX] Fix bug when running with dashboard + filter out phantoms

6d58ecc

when running without dashboard

[FIX] Update deprecated logging method

2b59589

Fixed some rst formatting issues

907d0ae

[ENH] Updated installation docs, added documented config templates

7d4b32b

[FIX] Prevent duplicate log messages due to multiple formatters

64cea73

[FIX] Re-arrange content of template files

8d9c2d2

Updated config template to remove unneeded paths + fix queue values

714a22f

[FIX] Add missing config key

55720e8

[FIX] Removed some hard-coding and updated some documentation

d26a750

- Started to remove hard-coded redcap config - Updated documentation on configuration and installation

Added datman dockerfile + a config template for docker

e5cf728

Fixed error when running dm_sftp.py without a study directory

2bb5a67

[FIX] attempt to fix exceptions when connecting to new server

93fc24d

[FIX] Fix dm_sftp problems with hostkeys

bec8c32

[FIX] Corrected variable name

59002c2

Add workdir just to be explicit about directory scripts run from

78cfbb8

Updated installation for docker usage, removed un-needed docker template

7ce5a53

Added missing sections and made some edits

36adbf8

[FIX] Added known_hosts fix when running as root

df08e6d

Removed lines only used during testing

b97dd31

Merge remote-tracking branch 'upstream/master' into easybake_datman

4cf8414

Removed old comment

cd5bb04

auto-assign bot requested review from edickie and jerdra April 30, 2021 16:59

auto-assign bot requested a review from josephmje April 30, 2021 16:59

DESm1th added 3 commits April 30, 2021 13:07

Fixed f string + made quotes consistent

c03acd0

Fixed indentation

efb24c7

Fixed rst syntax errors

9b143eb

josephmje reviewed May 4, 2021

View reviewed changes

Comment thread Dockerfile Outdated

Comment thread assets/config_templates/main_config.yml Outdated

DESm1th and others added 2 commits May 4, 2021 11:51

Update ubuntu base image version

754bd6d

Co-authored-by: Michael Joseph <josephmje.22@gmail.com>

Update wording in main_config.yml template

9703ec2

Co-authored-by: Michael Joseph <josephmje.22@gmail.com>

josephmje previously approved these changes May 4, 2021

View reviewed changes

jerdra reviewed Oct 5, 2021

View reviewed changes

Correct qcmon URL

6f12dba

Co-authored-by: Jerry Jeyachandra <jerrold.jeyachandra@gmail.com>

DESm1th dismissed josephmje’s stale review via 6f12dba October 5, 2021 19:23

josephmje requested changes Feb 9, 2022

View reviewed changes

[FIX] Update dcm2niix version, remove pip link (package adds it itsel…

476bb19

…f now)

josephmje approved these changes Feb 23, 2022

View reviewed changes

jerdra approved these changes Apr 22, 2022

View reviewed changes

DESm1th merged commit 6ac4827 into TIGRLab:master Apr 25, 2022

DESm1th deleted the easybake_datman branch April 25, 2022 17:48

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Comment last updated at 2022-02-23 19:46:55 UTC

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DESm1th commented Apr 30, 2021 •

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