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Neuron search and switch to scicrunch _dev#19

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Tehsurfer wants to merge 64 commits intoABI-Software:mainfrom
Tehsurfer:scicrunch-doi
Open

Neuron search and switch to scicrunch _dev#19
Tehsurfer wants to merge 64 commits intoABI-Software:mainfrom
Tehsurfer:scicrunch-doi

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@Tehsurfer
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@Tehsurfer Tehsurfer commented Jun 23, 2021

Description

  • Added DOI endpoint
  • Addend enpoint for query string
  • Made changes to switch to _dev index

Changes viewable here:
https://jesses-sparc-science.herokuapp.com/maps

Type of change

Delete those that don't apply.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)

How Has This Been Tested?

Ran locally

Checklist:

  • My code follows the style guidelines of this project
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • I have added unit tests that prove my fix is effective or that my feature works

agarny and others added 30 commits November 12, 2020 11:49
@agarny
Merge remote-tracking branch 'nih/master'.
72f5ecc
@agarny
Merge remote-tracking branch 'upstream/master'.
6cf3c3c
@agarny
Merge remote-tracking branch 'upstream/master'.
60a9276
@agarny
Merge branch 'main' of https://github.com/agarny/sparc-api into main
df7d8ef
@agarny
Merge remote-tracking branch 'upstream/main'.
34eb00d
@agarny
Merge remote-tracking branch 'nih-sparc/master'.
0ab30f9
@agarny
Merge remote-tracking branch 'upstream/main'.
9597f07
@agarny
Prevent the app from crashing if SPARC_PORTAL_AWS_KEY and/or SPARC_PO…
bd472bf 
…RTAL_AWS_SECRET cannot be found.
@agarny
Require the osparc Python package.
1727449
@agarny
Merge branch 'main' into simulation.
471a5e1
@agarny
Retrieve oSPARC-related configuration.
5760f3c
@agarny
Updated the required version of various Python packages.
84e380e 
Indeed, there were various incompatibilities, especially after installing the `osparc` package.
@agarny
Retrieve oSPARC-related configuration.
42b693d 
Although only the staging site is useable, we will be using the official site at some point.
@agarny
Added an endpoint to run a simulation on oSPARC.
1ac51c5 
This requires some configuration information (as JSON), which is currently hard-coded.
@agarny
Pass a model URL to run_simulation().
ebe54e3
@agarny
Some minor cleaning up.
9c8326e
@agarny
Add support for arguments to the run_simulation endpoint.
79c97d9
@agarny
Can now pip install the version we need of the oSPARC API.
1bc81cb
@agarny
Some minor cleaning up.
ebbeb82
@agarny
Use the POST method for our simulation endpoint.
0591f99
@agarny
Slight improvements to README.md.
8c149f8
@agarny
oSPARC: check whether the exception has at least one argument.
943461b 
Indeed, during our testing (`tests/test_osparc.py`), there have been cases where an exception was raised, but not by us, and with no argument...?!
@agarny
Some tests for the /simulation endpoint.
fa5fbca
@Tehsurfer
Working implementation of scaffold search
74badcf
@alan-wu
Merge branch 'master' of https://github.com/nih-sparc/sparc-api into …
ddd66b4 
…main
@Tehsurfer
Add endpoint to retrieve doi from scicrunch
5e35096
@Tehsurfer
switch to more up to date index
9b37fc6
@agarny
Merge remote-tracking branch 'upstream/main'.
3d666ab
@agarny
Merge branch 'main' into simulation.
6f96294
@agarny
Use the latest SciCrunch endpoint we were given.
1e39cff
agarny and others added 16 commits June 3, 2021 18:42
@agarny
Some minor cleaning up.
2a14415
@agarny
Filtering: can now filter for "All xxx".
070169c
@agarny
Simulation filtering: look for either "CellML" or "SED-ML".
56d4d14
@agarny
Simulation filtering: look for either "CellML" or "SED-ML".
60c7ce5 
Not sure why I originally wrote this "SedML"!
@agarny
Added a couple of tests for the scaffolds and simulations filtering.
3ddc1c6
@agarny
Added a couple of tests for the scaffolds and simulations filtering.
0c6df77 
We were searching for "heart" hence our filtering for scaffolds was only returning 3 hits while it should return 14 hits if we want all the scaffolds.
@agarny
Revert the default value of SCI_CRUNCH_HOST.
7698bc7 
If anything, one should create an environment variable for SCI_CRUNCH_HOST on their system.
@agarny
Filtering: use the scaffold MIME type rather an item's name.
ec7d7f0
@Tehsurfer
Add doi endpoint
e89602b
@Tehsurfer
Switch back to stable endpoint
6efca8e
@agarny
Added "pmr_latest_exposure" to retrieve the latest exposure, if any, …
d8547f7 
…of a PMR workspace.
@Tehsurfer
Add endpoint for neuron queries
0a58725
@Tehsurfer
Switch to dev endpoint
61c8771
@Tehsurfer
Adjust query endpoint to be more flexible
17836d4
@Tehsurfer
Bug fix and query change
10ce60f 
 - Bug fix for some datasets not returning _any_ objects
 - Switch scicrunch-query-string from using the route to using URL
   params (this is now implemented in tehsurfer/map-side-bar)
@Tehsurfer
Fix mistake in order of data processing
300a85a
@Tehsurfer Tehsurfer changed the base branch from future-with-hacks to main June 23, 2021 00:14
@Tehsurfer Tehsurfer changed the title Scicrunch doi Neuron search and switch to scicrunch _dev Jun 23, 2021
Tehsurfer and others added 11 commits June 23, 2021 17:47
@Tehsurfer
Switch to using additional mimetypes as intented
2bc2d6a
@alan-wu
Merge branch 'mimetypes-used' of https://github.com/Tehsurfer/sparc-api…
f93de5b 
… into Tehsurfer-mimetypes-used
@alan-wu
Rename genotype to organ.
7f4865e
@alan-wu
Merge branch 'simulation' of https://github.com/agarny/sparc-api into…
e1074b7 
… integrated-feature
@Tehsurfer
Fix to hit processing
6fab9e0 
Previously there was no check to make sure we made it to the end of our
desired attributes. This has now been added along with some comments to
explain what is going on
@alan-wu
Merge branch 'mimetypes-used' of https://github.com/Tehsurfer/sparc-api…
033b9dc 
… into integrated-feature
@alan-wu
Improve filters for dataset with scaffold.
c72739e
@alan-wu
Add test for available scaffolds.
39f43f2
@alan-wu
Change to use the production endpoint.
2f59cf3
@Tehsurfer
Add pubmed proxy
fe65ca7
@Tehsurfer
Merge branch 'main' into scicrunch-doi
e9e4970
dbrnz pushed a commit to dbrnz/sparc-api that referenced this pull request Nov 21, 2021
@JeremyLecoeur
Merge pull request ABI-Software#19 from nih-sparc/test_bio
3878782 
uncommenting biolucida tests
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3 participants

@Tehsurfer @agarny @alan-wu