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* gn3/api/metadata.py: Remove duplicate imports.
* gn3/db/constants.py: Add docstring.
* gn3/db/rdf.py (get_wiki_entries_by_symbol): Remove duplicate
dictionary key.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/errors.py (handle_sparql_errors): Use the exception's class name
to fetch the status code.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (get_wiki_entries): Return an empty {} when
there's no data.
* gn3/db/rdf.py (query_frame_and_compact): Delete check for empty
results. Instead just return the context as is.
(query_and_compact): Ditto.
(query_and_frame): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py: Import jsonify, make_response.
(get_wiki_entries): Set a 404 status code when a response is empty.
Set correct Content-Type header for ld+json.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf.py (get_wiki_entries_by_symbol): Use list comprehensions.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py: Import "get_wiki_entries_by_symbol".
(get_gn_genewiki_entries): Rename this to...
(get_wiki_entries): this; and update the URL endpoint.
* gn3/db/rdf.py: Import constants.BASE_CONTEXT.
(get_wiki_entries_by_symbol): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py: Move constants from here...
* gn3/db/rdf.py: ... and here, to...
* gn3/db/constants.py: ... here.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* Add better error messages
* Create more modular functions
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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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Add the `gn3.oauth2` which will handle the authorisations.
It is intended to eventually replace the `gn3.auth` module which is a
left over from when the authorisation server was part of GN3.
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* gn3/api/search.py (parse_boolean_prefixed_field): New function.
(parse_query): Use parse_boolean_prefixed_field for the group field.
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With the STEM_SOME, xapian does not stem query words that start with a
capital letter. Hence, we switch to the STEM_ALL strategy.
* gn3/api/search.py (parse_query): Set stemming strategy to STEM_ALL.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* scripts/index-genenetwork (is_data_modified): Provide directory
instead of specific ttl file.
(create_xapian_index): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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original: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/maintainance/addRif.py
Included some changes to make it python3 compatible
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environment
Also fixes issue where the control marker keyword was wrong
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* scripts/index-genenetwork (hash_rdf_graph): Remove check for the
turtle directory.
(is_data_modified): Ditto.
(create_xapian_index): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* scripts/index-genenetwork (hash_generif_graph): Rename to
hash_rdf_graph. Generate a checksum of all the turtle files inside
the ttl directory that's the basis for the GN virtuoso graph.
(create_xapian_index): Rename hash_generif_graph -> hash_rdf_graph.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* scripts/index-genenetwork (hash_generif_graph): Add proper type
hints.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* scripts/index-genenetwork (hash_generif_graph): Build the generif
checksum by directly building it from the file.
(is_data_modified): Update how generif-checksums are verified.
(create_xapian_index): Update how generif-checksums are stored in
XAPIAN.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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