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Prior to this commit, an assumption is made that the application is
invoked with the root of the repository being the current working
directory. If this assumption is not met, then the system will not
find the appropriate path.
This commit forces the use of an absolute path, which should help
avoid issues with misplaced relative paths.
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This reverts commit 0d15840913c9cc401d1e74295aa5e17e34f2987b.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf/wiki.py (__sanitize_result): When fetching pubmed_ids and
categories, default to [] if the key misses, and remove the subsequent
one-line if/else statement.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf/wiki.py (update_wiki_comment) [query]: Replace
"rdf:label" with "rdfs:label".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf/wiki.py (get_comment_history) [query]: Replace
?symbolName with ?symbolName.
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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* gn3/api/metadata_api/wiki.py (edit_wiki): Remove comment_id from
args---it's already in the insert_dict.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata_api/wiki.py (edit_wiki) [insert_dict]: Add species,
categories fields.
[update_wiki_comment]: Pass in insert_dict, and get rid of redundant
keys. Directly pass in sparql_auth's conf params instead of a dict.
* gn3/db/rdf/wiki.py (get_next_comment_version): Get rid of redundant
params. Use fields directly from insert_dict. Directly pass in
sparql_auth's conf params instead of a dict.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata_api/wiki.py (edit_wiki): Pass in the createtime as
an arg.
* gn3/db/rdf/wiki.py: Remove un-used imports.
(update_wiki_comment): Use passed in "created" arg in the createtime
field. This makes sure that the SQL/RDF timestamps match.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata_api/wiki.py (edit_wiki): Get the next version Id
from SQL
* gn3/db/rdf/wiki.py (get_next_comment_version): Delete.
(update_wiki_comment): Provide the next_version id as an extra arg.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata_api/wiki.py: Import update_wiki_comment.
(edit_wiki): Update wiki in RDF.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf/wiki.py: Import datetime, update_rdf.
(update_wiki_comment): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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The RDF ttl files were updated to have:
comment gnt:symbol "name" .
instead of:
comment gnt:symbol symbolQname .
* gn3/db/rdf/wiki.py (get_wiki_entries_by_symbol): Fetch symbol using
it's string literal name.
(get_comment_history): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf/wiki.py (get_next_comment_version): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf/__init__.py (sparql_construct_query): Rename to...
(sparql_query): ... this. Extend function to be able to return JSQN
for SELECT queries.
(query_frame_and_compact): Ditto.
(query_and_compact): Ditto.
(query_and_frame): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf/__init__.py: Import POST, DIGEST, JSON.
(update_rdf): 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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* gn3/api/metadata_api/wiki.py: Re-order imports to fix pylint errors.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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The flask.current_app object depends on the application context
existing. In the case that no such context existing, then we still log
out information, gracefully with this commit.
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