interTwin Community
openEO EODC backend deployment via TOSCA #6
Replies: 7 comments 40 replies
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I report here the exampels I shared via email to test the deployed back-end:
import openeo
from openeo.metadata import CollectionMetadata
from openeo.processes import array_element
conn = openeo.connect('https://dev.openeo.eurac.edu').authenticate_basic("guest","changeme")
url = https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a
spatial_extent = {"east": 11.40, "north": 46.52, "south": 46.46, "west": 11.25}
temporal_extent = ["2022-06-01", "2022-06-30"]
bands = ["red", "nir"]
s2_datacube = conn.load_stac(
url=url,
spatial_extent=spatial_extent,
temporal_extent=temporal_extent,
bands=bands
)
s2_datacube.metadata = CollectionMetadata({"cube:dimensions":{"time":{"type":"temporal"},"band":{"type":"bands"}}})
def NDVI(data):
b04 = data.array_element(label="red")
b08 = data.array_element(label="nir")
return (b08 - b04) / (b08 + b04)
ndvi = s2_datacube.reduce_dimension(dimension="band",reducer=NDVI)
ndvi_median = ndvi.reduce_dimension(dimension="time", reducer="median")
result_ndvi = ndvi_median.download("ndvi_eurac.nc")
import openeo
import requests
from openeo.metadata import CollectionMetadata
from openeo.processes import array_element
s = requests.Session()
s.verify = False
conn = openeo.connect('https://openeo.62.217.83.68.nip.io/1.1.0/',session=s)
url = https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a
spatial_extent = {"east": 11.40, "north": 46.52, "south": 46.46, "west": 11.25}
temporal_extent = ["2022-06-01", "2022-06-30"]
bands = ["red", "nir"]
s2_datacube = conn.load_stac(
url=url,
spatial_extent=spatial_extent,
temporal_extent=temporal_extent,
bands=bands
)
s2_datacube.metadata = CollectionMetadata({"cube:dimensions":{"time":{"type":"temporal"},"band":{"type":"bands"}}})
def NDVI(data):
b04 = data.array_element(label="red")
b08 = data.array_element(label="nir")
return (b08 - b04) / (b08 + b04)
ndvi = s2_datacube.reduce_dimension(dimension="band",reducer=NDVI)
ndvi_median = ndvi.reduce_dimension(dimension="time", reducer="median")
result_ndvi = ndvi_median.download("ndvi_intertwin.nc")
It would be nice to have a working example using batch jobs and getting the result in STAC. @SerRichard where will the result be stored? Is there a linked object storage to this openEO back-end? @andrea-manzi I don't see Sean in the members, could you add him so that he can take part to the discussion? |
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I have invited Sean to the organization ! |
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@clausmichele Results currently would be stored in the volume claim used by the backend deployment, once we have these examples working it might be worth discussing making them available via S3 instead. At the minute I think the auth issue in the example above is related to the credentials/oidc endpoint not being available, this was an oversight on my side as I tested the urls VIA postman and not the client, so I just sent process graphs to the endpoint with the header provided. I will update the codebase and check this notebook will work on a deployment on myside before providing the next image update to @micafer |
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The initial issue here was the authorization. Following on I had some further issues with the result saving on the xarrays from stackstac and then a mistake I had made in the result return. I hadn't anticipated, but when you load items with stackstac, it seems to add all of the item properties to the xarray object, some properties go into the attributes ( in the form of a RasterSpec object which they define) , but then a lot of properties get dumped into the xarrays coordinates ( and not added to the dimensions? ). When trying to write these xarrays to netcdf, the majority of these additional values were unserializable. As a result I've dropped all coordinate values that are not also used in the dimensions of the xarray, and dropped the RasterSpec from the attributes. Additionally, I had made the mistake of only providing tar results via sync jobs, I've updated this to reflect the API documentation, that single files are returned directly, and only multiple files are returned as tar. The API has been updated to handle these different cases. Though currently STAC output is not included as part of the tar result, which is an openeo-api spec recommendation, @andrea-manzi we can add this quite easily if we want. |
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@SerRichard yea I am aware of the properties handled by stackstac, which are not so compatible with netCDF. For that and other reasons we are currently using/testing odc-stac, as described here: Open-EO/openeo-processes-dask#235 |
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If you change the line: conn = openeo.connect('https://openeo.62.217.83.68.nip.io/1.1.0/',session=s)With this, the authentication works (but I get another errors) token = "ey.........."
conn = openeo.connect('https://openeo.62.217.83.68.nip.io/1.1.0',session=s).authenticate_oidc_access_token(token)To get the value of the |
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Hi @SerRichard , I have a problem with the deployment, the openeo-openeo-argo pod is failing with this error: Traceback (most recent call last):
File "/usr/local/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/usr/local/lib/python3.11/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/openeo_argoworkflows_api/.venv/lib/python3.11/site-packages/uvicorn/_subprocess.py", line 78, in subprocess_started
target(sockets=sockets)
File "/opt/openeo_argoworkflows_api/.venv/lib/python3.11/site-packages/uvicorn/server.py", line 65, in run
return asyncio.run(self.serve(sockets=sockets))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/asyncio/runners.py", line 190, in run
return runner.run(main)
^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/asyncio/runners.py", line 118, in run
return self._loop.run_until_complete(task)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
return future.result()
^^^^^^^^^^^^^^^
File "/opt/openeo_argoworkflows_api/.venv/lib/python3.11/site-packages/uvicorn/server.py", line 69, in serve
await self._serve(sockets)
File "/opt/openeo_argoworkflows_api/.venv/lib/python3.11/site-packages/uvicorn/server.py", line 76, in _serve
config.load()
File "/opt/openeo_argoworkflows_api/.venv/lib/python3.11/site-packages/uvicorn/config.py", line 433, in load
self.loaded_app = import_from_string(self.app)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/openeo_argoworkflows_api/.venv/lib/python3.11/site-packages/uvicorn/importer.py", line 19, in import_from_string
module = importlib.import_module(module_str)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/opt/openeo_argoworkflows_api/app.py", line 10, in <module>
from openeo_argoworkflows_api.jobs import ArgoJobsRegister
File "/opt/openeo_argoworkflows_api/jobs.py", line 35, in <module>
from openeo_argoworkflows_api.tasks import queue_to_submit, submit_job
File "/opt/openeo_argoworkflows_api/tasks.py", line 13, in <module>
settings = ExtendedAppSettings()
^^^^^^^^^^^^^^^^^^^^^
File "pydantic/env_settings.py", line 40, in pydantic.env_settings.BaseSettings.__init__
File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for ExtendedAppSettings
OIDC_POLICIES
Policy '' contains too many comma seperated values. (type=value_error)
``
I tried several values of the variable and it is failing in all the cases. |
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@micafer is this blocking for the video for the Review? and in case shall we go back to the previous version? |
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I can record the deployment, but I cannot access the service because it is not running. |
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Tomorrow I can try to record it using the previous version. |
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I created an issue in the OpenEO API to track this problem: |
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@micafer The deployment can be updated, if you'd refer to the latest changes in the chart, the issues above should get resolved. The latest tags for the api and executor have also changed. Currently there's two points of open work that I'd like to address.
The first is pretty self explanatory, and I just need to allocate time to complete. The second, I'm still open for suggestions, but it would be good to implement some default tiling grid to control the output of the filesize, to limit possible pressure on the api on download, and on the dask workers when writing results. |
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@andrea-manzi could you give me access to the current one to update it? |
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i sent you the key to acccess |
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Hi all, After the last update of the API it seems that it is working now using this code to authenticate: import openeo
import requests
s = requests.Session()
token = "SOME_TOKEN"
conn = openeo.connect('https://openeo.intertwin.fedcloud.eu/1.1.0/', session=s)
conn.authenticate_oidc_access_token(token, "egi")
...I tied the computation suggested by @clausmichele, but it gets an error: Failed to parse API error response: [500] 'Internal Server Error' (headers: {'Date': 'Thu, 24 Oct 2024 14:41:23 GMT', 'Content-Type': 'text/plain; charset=utf-8', 'Content-Length': '21', 'Connection': 'keep-alive', 'Strict-Transport-Security': 'max-age=15724800; includeSubDomains'})And @SerRichard in the logs of the hera.exceptions.Forbidden: Server returned status code 403 with message: `workflows.argoproj.io is forbidden: User "system:serviceaccount:openeo:openeo-argo-access-sa" cannot create resource "workflows" in API group "argoproj.io" in the namespace "openeo"` |
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Now it seems to work, but I have another problem. |
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Ooooo, interesting So in the api I have the concept of a dask_profile, that gets parsed the executor, and the executor will make those requests. Ofc, as you can see those values are hard coded. An easy approach would be to make those values configurable via the application settings, and set defaults if values are not provided. That being said, the idea of the dask profile was to evolve with some idea of a user_profile, i.e if you had a free user vs some tiered user. Is that something that we want to be supported in this project? Regardless, I can make them immediately available as settings, and then we can move the profile idea forward if that is desired. |
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It will be great if you can make it available as settings. |
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A new api image has been released ( api-2024.10.2 ) and the helm chart has been updated, please refer to the read me for the new environment variables that can be set in the values.yaml. This should allow for smaller or larger dask cluster configurations. Any issues, give me another message. |
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Is there a minimum recommendable values to set? |
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In the current cluster I relaunched with a bigger WN and now the jobs fit in the size of the node and the example is completed successfully! |
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I also confirm that I was able to run successfully a sample graph in synchronous mode! |
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@micafer the openEO back-end is not reachable anymore, it returns 404: https://openeo.intertwin.fedcloud.eu/1.1.0/ |
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@micafer please update to image api-2024.11.5. After a few releases and some testing with the editor, I realised the issue was in the openeo-fastapi package. The endpoints on the top level of the application were not listed in the capabilities response, which the editor uses to infer the location of "/credentials/oidc". |
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updated to version 11.5 |
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Greaat, login is working! Seems to be an issue with the "/files" endpoints, will take a look at the logs on my side and see what the issue is, as that feature should be supported! |
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@micafer Was trickier to get enabled that I suspected, with the latest tag "api-2024.11.10", the files endpoints are now all functioning as expected and working with the editor |
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updated! |
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i guess now everything is working as expected, closing |
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Cluster deployed via IM at https://openeo.62.217.83.68.nip.io/1.1.0/
Need to clarify the EGI Check-in used. I have setup via IM to use the EGI Check-in demo instance, is that automatically configured ? or only the Production instance is there by default?
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