Migrate LIMS to use requests library

BICCN / cell-locator

manually align specimens to annotated 3D spaces

https://cell-locator.readthedocs.io

Other

19 stars 7 forks source link

Migrate LIMS to use requests library #133

Closed allemangD closed 4 years ago

allemangD commented 4 years ago

Note that this is based on the changes in https://github.com/BICCN/cell-locator/pull/131 so shouldn't be merged until those changes are resolved (or should be merged into that PR). I'm just creating a PR here for ease in creating a test installer.

This addresses the feedback in https://github.com/BICCN/cell-locator/issues/93.

Switch to the requests library to properly handle request headers. POST requests use the json argument, which sets Content-Type: application/json.
Change failure messages to be more helpful. Now includes the error status code and message. For example: Failed to load annotations for LIMS specimen <ID>. Error <STATUS>: '<REASON>'
Current LIMS specimen ID is shown in the file path box below "Save to LIMS" (screenshot below)

lims-specimen-display

allemangD commented 4 years ago

Marked as draft to indicate this should be merged until https://github.com/BICCN/cell-locator/pull/131 is.

jcfr commented 4 years ago

Could you add an entry to the CHANGES.md, something like this will do it:

Fixes:

* Improve LIMS integration to address the feedback in [#93](https://github.com/BICCN/cell-locator/issues/93#issuecomment-675102826).
  * Switch to the `requests` library to properly handle request headers. POST requests use the `json` argument, which sets `Content-Type: application/json`.
  * Change failure messages to be more helpful. Now includes the error status code and message.
  For example: `Failed to load annotations for LIMS specimen <ID>. Error <STATUS>: '<REASON>'`
  * Current LIMS specimen ID is shown in the file path box below "Save to LIMS".

jcfr commented 4 years ago

Also, it may be worth updating https://github.com/KitwareMedical/AllenInstituteMockLIMS as well. I created few issues: