AllenInstitute / AllenInstitute/microns_tutorial
Server Error When Following Tutorial: Database Connection Failed
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Description
I'm working through the tutorial at https://tutorial.microns-explorer.org/quickstart_notebooks/07-cave-download-skeleton.html and encountered a server error when running this example code.
from pcg_skel import get_meshwork_from_client
sk_mesh = get_meshwork_from_client(example_cell_id,
client=client,
synapses=True,
restore_graph=True,
restore_properties=True,
skeleton_version=4,
)
sk_mesh
I'm using CAVEclient version 1412 of minne65_public
Output:
HTTPError: 500 Server Error: Cannot connect to database 'minnie65_public__mat1300'. Please check if the database exists and is accessible. Connection URI: postgres://postgres:welcometothematrix@127.0.0.1:3306/minnie65_public__mat1300. Error: (psycopg2.OperationalError) connection to server at "127.0.0.1", port 3306 failed: FATAL: database "minnie65_public__mat1300" does not exist
Is this a known issue with the database server, or am I missing a setup step? Any guidance would be appreciated.
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Research direction
Start with the quickstart notebook at tutorial.microns-explorer.org/quickstart_notebooks/07-cave-download-skeleton.html and reproduce the get_meshwork_from_client example using CAVEclient version 1412 of minne65_public. Investigate the reported PostgreSQL connection to minnie65_public__mat1300 and determine whether the tutorial is missing a setup step or references an unavailable database. Done means the example runs successfully or the tutorial clearly documents the required setup.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- postgresql, python
- Domain
- databases, documentation
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100