nf-osi / jobs

0 stars 0 forks source link

Fix typo in README.md #92

Closed changtotheintothemoon closed 4 days ago

changtotheintothemoon commented 4 days ago

Corrected the snapshot's Docker run command in the README file by removing the unintended "run" keyword.

changtotheintothemoon commented 4 days ago

Also a comment that when running the example it seems to not recognize the synapseIDs: using #nf-test-logs (test channel) slack webhook's link for the envfile

(base) jmoon@w264 snapshot % docker run --env-file envfile ghcr.io/nf-osi/jobs-snapshot syn27242487 syn27242485

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Targets: ['syn27242487', 'syn27242485']
Welcome, james.moon!

UPGRADE AVAILABLE

A more recent version of the Synapse Client (4.6.0) is available. Your version (2.5.0) can be upgraded by typing:
    pip install --upgrade synapseclient

Python Synapse Client version 4.6.0 release notes

https://python-docs.synapse.org/news/

Traceback (most recent call last):
  File "/snapshot.py", line 38, in <module>
    version = syn.create_snapshot_version(table=target, comment=target_comment, label=target_label)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 3197, in create_snapshot_version
    ent = self.get(id_of(table), downloadFile=False)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 724, in get
    bundle = self._getEntityBundle(entity, version)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 1253, in _getEntityBundle
    bundle = self.restPOST(uri, body=json.dumps(requestedObjects))
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 3904, in restPOST
    response = self._rest_call('post', uri, body, endpoint, headers, retryPolicy, requests_session, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 3871, in _rest_call
    self._handle_synapse_http_error(response)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 3841, in _handle_synapse_http_error
    exceptions._raise_for_status(response, verbose=self.debug)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/core/exceptions.py", line 160, in _raise_for_status
    raise SynapseHTTPError(message, response=response)
synapseclient.core.exceptions.SynapseHTTPError: 404 Client Error: 
Resource: 'syn27242487' does not exist
Traceback (most recent call last):
  File "/snapshot.py", line 38, in <module>
    version = syn.create_snapshot_version(table=target, comment=target_comment, label=target_label)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 3197, in create_snapshot_version
    ent = self.get(id_of(table), downloadFile=False)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 724, in get
    bundle = self._getEntityBundle(entity, version)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 1253, in _getEntityBundle
    bundle = self.restPOST(uri, body=json.dumps(requestedObjects))
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 3904, in restPOST
    response = self._rest_call('post', uri, body, endpoint, headers, retryPolicy, requests_session, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 3871, in _rest_call
    self._handle_synapse_http_error(response)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/client.py", line 3841, in _handle_synapse_http_error
    exceptions._raise_for_status(response, verbose=self.debug)
  File "/usr/local/lib/python3.6/dist-packages/synapseclient-2.5.0-py3.6.egg/synapseclient/core/exceptions.py", line 160, in _raise_for_status
    raise SynapseHTTPError(message, response=response)
synapseclient.core.exceptions.SynapseHTTPError: 404 Client Error: 
Resource: 'syn27242485' does not exist
200
200
anngvu commented 4 days ago

Thanks. The example ids are out-of-date since the table doesn't exist anymore, so updated ids and added a note for future.