Remove Girder support #588
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Codecov Report
@@ Coverage Diff @@
## master #588 +/- ##
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+ Coverage 81.26% 82.88% +1.62%
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Files 62 59 -3
Lines 6651 5710 -941
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- Hits 5405 4733 -672
+ Misses 1246 977 -269
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pushed a CPed fix from #591 ... will probably proceed with that PR for now for a minimal fix to get client working for migration; added a TODO in description on docker compose recipe |
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@jwodder - as part of this we can also remove migrating to new schema perhaps for the dandiset metadata. the asset related stuff can stay. |
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@satra File that as a separate issue. It'll require changes to |
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@yarikoptic While we wait for dandi/dandi-archive#251 to be merged, I'd appreciate if it you'd take a look at what's left of |
Why do we need to wait on it - even if docker compose ships girder, we can just not use it (i.e. nothing in dandi-cli somehow senses for girder to be present etc), can't we? |
git grep -i girder | grep -v -e CHANGELOG -e README -e docker-compose -e '^tools/'.github/workflows/test.yml: run: echo DANDI_LOG_GIRDER=1 >> "$GITHUB_ENV"
DEVELOPMENT.md:dandiarchive (both with our web frontend, and girder backend).
DEVELOPMENT.md:as `local-docker` (as opposed from `local` for a plain girder instance). See note
DEVELOPMENT.md: such as explicit specification of the girder instance, collection, etc.
DEVELOPMENT.md:- `DANDI_GIRDER_API_KEY` -- avoids using keyrings, thus making it possible to
DEVELOPMENT.md: "temporarily" use another account etc for the Girder version of the server.
DEVELOPMENT.md:- `DANDI_LOG_GIRDER` -- log REST requests.
dandi/cli/__init__.py: e.g. girder-client
dandi/consts.py:# Chunk size when iterating a download (and upload) body. Taken from girder-cli
dandi/core/digests/dandietag.py:# Derived from <https://github.com/girder/django-s3-file-field/blob/master/
dandi/dandiapi.py:# Following class is loosely based on GirderClient, with authentication etc
dandi/dandiapi.py: girder and DANDI api clients.
dandi/dandiarchive.py:Interactions with DANDI archive ATM go either through Girder or through DANDI API.
dandi/dandiarchive.py:Eventually it is largely to be "dissolved" whenever we stop talking to girder.
dandi/dandiarchive.py: old (girder inflicted): https://gui.dandiarchive.org/#/folder/5e5593cc1a343161ff7c5a92
dandi/dandiarchive.py: old (girder inflicted): https://gui.dandiarchive.org/#/folder/5dab0830f377535c7d96c2b4
dandi/dandiarchive.py: old (girder inflicted): https://gui.dandiarchive.org/#/dandiset/5e6d5c6976569eb93f451e4f
dandi/dandiarchive.py: gui.dandiarchive.org ones into girder.
dandi/dandiset.py: # girder-based, used before migration to API TODO: API-migration-remove
dandi/download.py: # by server while establishing downloader... but it seems that girder itself
dandi/download.py: A backend (girder or api) specific fixture for downloading some file into
dandi/download.py: # both girder and we use HttpError
dandi/download.py: # It seems that girder might not care about setting either mtime, so we will do if we know
dandi/metadata.py:The following section converts metadata schema from the current girder dandiset
dandi/tests/fixtures.py: GIRDER_URL = "http://localhost:8081"
dandi/tests/fixtures.py: f"{GIRDER_URL}/api/v1/user/authentication", auth=("admin", "letmein")
dandi/tests/fixtures.py: f"{GIRDER_URL}/api/v1/api_key",
dandi/tests/fixtures.py: headers={"Girder-Token": initial_api_key},
dandi/tests/fixtures.py: f"{GIRDER_URL}/api/v1/user",
dandi/tests/fixtures.py: headers={"Girder-Token": initial_api_key},
dandi/tests/fixtures.py: f"{GIRDER_URL}/api/v1/user/authentication", auth=("publish", "Z1lT4Fh7Kj")
dandi/tests/fixtures.py: # We can't refer to the Girder container as "girder" in
dandi/tests/fixtures.py: # DJANGO_DANDI_GIRDER_API_URL because Django doesn't recognize
dandi/tests/fixtures.py: # use the Girder container's in-network IP address.
dandi/tests/fixtures.py: about_girder = check_output(
dandi/tests/fixtures.py: ["docker", "inspect", f"{LOCAL_DOCKER_ENV}_girder_1"]
dandi/tests/fixtures.py: girder_ip = json.loads(about_girder)[0]["NetworkSettings"]["Networks"][
dandi/tests/fixtures.py: env["DJANGO_DANDI_GIRDER_API_URL"] = f"http://{girder_ip}:8080/api/v1"
dandi/tests/fixtures.py: env["DJANGO_DANDI_GIRDER_API_KEY"] = publish_api_key
dandi/tests/fixtures.py: f"{GIRDER_URL}/api/v1/system/setting",
dandi/tests/fixtures.py: headers={"Girder-Token": publish_api_key},
dandi/tests/fixtures.py: f"{GIRDER_URL}/api/v1/system/setting",
dandi/tests/fixtures.py: headers={"Girder-Token": publish_api_key},
dandi/tests/fixtures.py: yield {"girder_api_key": api_key, "django_api_key": django_api_key}
dandi/tests/test_dandiarchive.py: # ATM we point to drafts, so girder
dandi/tests/test_dandiarchive.py: # # And the hybrid for "drafts" where it still goes by girder ID
dandi/tests/test_dandiarchive.py: "girder": None,
dandi/tests/test_utils.py: "girder": None,
dandi/tests/test_utils.py: "girder": {"url": "https://girder.dandi"},
dandi/tests/test_utils.py: "girder": {"url": "https://girder.dandi"},
dandi/tests/test_utils.py: "girder": {"url": "https://girder.dandi"},
dandi/upload.py: # this is a path not a girder id
dandi/utils.py: ) # note: somehow was ending up with {"girder": None}
doc/demos/basic-workflow1.sh:# top url, would need to know girder id
setup.cfg: girder-client |
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@yarikoptic I meant, could you please specifically look through the |
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did another skim through diff (still see no coverage report overlay for some reason, but probably unrelated). Let's proceed -- thank you @jwodder ! and if no major issues we run into, let's release tomorrow or so. |
Closes #587.
TODOs
./dandi/tests/data/dandiarchive-docker/docker-compose.ymlto strip docker away - must not be needed.