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The Name is generally used as the identifier, while the FullName can container spaces which can cause problems
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This reverts commit b21102bc4ad3678173e7c94d3e66333ec7c1d40a.
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Without this check, there will always be an error when this script is
run with the "is-data-modified" flag should there be no database in
the XAPIAN_DIRECTORY.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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In the CI build, the actual build is run in the
xapian_directory/build, which is seen as the xapian_directory in this
script. The CI handles clean up WRT removing files related to the
build process.
* scripts/index-genenetwork (create_xapian_index): Create the xapian
directory if it doesn't exist. If the xapian directory has files,
exit. Create the temporary directory inside the xapian_directory.
Remove "build_directory.rmdir()"
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* scripts/index-genenetwork (is_data_modified): Replace click.echo
with the respective sys.exit call.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Right now, the checks are done in Guix's build expression. This moves
that work to the index-genenetwork script.
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* scripts/index-genenetwork (verify_checksums): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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This global caches has 3,528 entries and there's no expectation for it
to grow significantly. Since child processes inherit the parent’s
memory, we can pass the global cache to them, reducing fetch times
from 0.001s to 0.00001s, significantly boosting performance when
indexing the entire database and enriching results with RDF metadata.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* scripts/index-genenetwork: Import Template, lru_cache,
SPARQLWrapper, JSON
(get_rif_metadata): New function.
(index_rif_comments): New function.
(index_genes): Add rif comments to probeset index.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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The script is not used in GN3.
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* scripts/__init__.py: New file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Authentication should be handled by the auth server (gn-auth) and thus, this
commit removes code handling user authentication from the GN3 system.
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After copying the calls to assign appropriate roles to the admin in the
script, I forgot to update the variable name. This commit fixes that.
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Add delays to avoid overwhelming the DB server.
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* scripts/index-genenetwork (main): Write table checksums into index.
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* scripts/index-genenetwork (SQLTableClause): New variable.
(genes_query, phenotypes_query): Express tables using SQLTableClause.
(serialize_sql): Serialize SQLTableClause.
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* scripts/index-genenetwork (write_document, index_query): Fold long lines.
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* scripts/index-genenetwork (main): Ensure no other indexing job is running.
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* scripts/register_sys_admin.py: fix linting error
* tests/unit/auth/fixtures/oauth2_client_fixtures.py: hash client secret in
database. The code expects it hashed in the database.
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To ease registration of system-admin user, provide a CLI script to register
the user and mark them as sys admin in one go.
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Document some CLI utility commands useful for development and for supporting
the operation of the GN3 app.
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A script to assign existing data not assigned to any group to publicly-visible
resources.
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