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Installation with Docker solution - problem with “migrate_db.py” #71

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KingAlex1985 opened this issue Dec 20, 2024 · 0 comments
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@KingAlex1985
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Hello everyone.
I am trying to get cBioPortal running with Docker (https://docs.cbioportal.org/deployment/docker/#quick-start).
When I run “./init.sh” with Git Bash (on Windows 11) a lot of things happen, which runs without errors so far.
However, at some point I get the following error message and it doesn't really continue but gets stuck in an endless loop.

2024-12-19 23:01:23 /core/scripts/migrate_db.py:270: SyntaxWarning: invalid escape sequence '\s'
2024-12-19 23:01:23 line_parts = re.split("--\s", line)
2024-12-19 23:01:23 (1146, "Table 'cbioportal.patient_list' doesn't exist")
2024-12-19 23:02:10 mysqladmin: [Warning] Using a password on the command line interface can be insecure.
2024-12-19 23:02:10 /core/scripts/migrate_db.py:270: SyntaxWarning: invalid escape sequence '\s'
2024-12-19 23:02:10 line_parts = re.split("--\s", line)
2024-12-19 23:02:10 (1146, "Table 'cbioportal.patient_list' doesn't exist")

grafik

I don't know if this line is the actual problem and if it won't continue.
According to Github Copilot the fix is something small.

Path / file: ...\cbioportal-core\scripts\migrate_db.py

Old:
line_parts = re.split("--\s", line)

New:
line_parts = re.split(**r**"--\s", line)

Or am I misunderstanding this and the actual error lies somewhere else?

Thanks in advance.
Regards
Alex

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