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Implement metadata end-points #130

Merged
merged 50 commits into from Oct 27, 2023
Merged

Implement metadata end-points #130

merged 50 commits into from Oct 27, 2023

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BonfaceKilz
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This PR creates/reworks endpoints for fetching RDF metadata.

@BonfaceKilz BonfaceKilz force-pushed the feature/display-rdf branch 3 times, most recently from 671c7c7 to 64a3c0c Compare October 24, 2023 12:52
@BonfaceKilz
Update RDF prefixes.
8584422 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Simplify CONSTRUCT query when fetching a dataset's metadata.
d471589 
* gn3/api/metadata.py (dataset): Update docstring.
* gn3/db/rdf.py (get_dataset_metadata): Simplify CONSTRUCT query.
Also, now you can fetch metadata using either an accession_id or the
dataset's name.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Remove get_url_local_name when processing result keys.
8b0ca96 
* gn3/db/rdf.py (sparql_query): Delete "get_url_local_name".

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Derive RDF_PREFIXES string from PREFIXES.
c2629d3 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Add missing dcat: prefix.
787bc35
@BonfaceKilz
Implement "GET /metadata/datasets/:name".
9e69d38 
* gn3/api/metadata.py: Import json, SPARQLWrapper.{JSON, JSONLD}.
(dataset): Rename this to ...
(datasets): ... this.  Return a well formatted JSONLD result from a
dataset.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/datasets/search/:term".
3f4ccee 
* gn3/api/metadata.py (search_datasets): New search endpoint with
pagination.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Add fabio: and prism: to PREFIXES.
672f543 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/publications/:name".
e6376da 
* gn3/api/metadata.py: Delete gn3.db.rdf.get_publication_metadata.
(publication): Rename this ...
(publications): ... to this.  Return a json-ld result.
* gn3/db/rdf.py (get_publication_metadata): Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/publications/search/:term".
56a72e4 
* gn3/api/metadata.py (search_publications): New function.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/genotypes/:name".
78fa147 
* gn3/api/metadata.py: Delete gn3.db.rdf.get_genotype_metadata.
(genotype): Rename this to ...
(genotypes): ... this.  Construct a query for fetching genotypes and
return a response as json-ld.
@BonfaceKilz
Delete get_dataset_metadata.
9563cbd 
* gn3/db/rdf.py (get_dataset_metadata): Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Remove un-used get_dataset_metadata import.
f16ed8c 
* gn3/api/metadata.py: Delete gn3.db.rdf.get_dataset_metadata.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/phenotypes/:name".
43e7c97 
* gn3/api/metadata.py: Delete gn3.db.rdf.get_phenotype_metadata.
(phenotype): Rename this to ...
(phenotypes): ...  this and implement update logic.
* gn3/db/rdf.py (get_phenotype_metadata): Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Delete db.rdf.get_url_local_name.
4fe4244 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /genewikis/gn/:symbol".
c1d0c51 
* gn3/api/metadata.py (get_genewiki_entries): Rename this to ...
(get_gn_genewiki_entries): ... this.  Create an end-point for querying
GN GeneRIF entries.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Delete gn3.db.rdf.sparql_query.
bfcdf89 
* gn3/api/metadata.py: Remove sparql_query import.
* gn3/db/rdf.py: Remove unused imports.
(sparql_query): Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /genewikis/ncbi/:symbol".
084cc70 
* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point.
@BonfaceKilz
Implement "GET /species".
8363a54 
* gn3/api/metadata.py (list_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /species/:name".
cb4fb8c 
* gn3/api/metadata.py (fetch_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET metadata/groups".
c3f567a 
* gn3/api/metadata.py (fetch_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /group/:name".
728795e 
* gn3/api/metadata.py (fetch_group_by_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Add extra prefixes to the context.
356e87f 
* gn3/api/metadata.py (groups): Update the json-ld's context.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Remove PREFIXES when querying datasets.
47c5d77 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Support using AccessionId to fetch datasets.
ba2f2ee 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/datasets/:group/list".
96eb019 
* gn3/api/metadata.py (list_datasets_by_group): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
REmove un-necessary prefixes when searching datasets.
ca17329 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Use virtuoso's full text search when searching datasets.
e3a7c2a 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Remove un-necessary prefixes when searching publications.
0d10aee 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Remove un-necessary prefixes when fetching a phenotype.
c72f60e 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /phenotype/:group/:name".
6f0deb3 
* gn3/api/metadata.py (fetch_phenotype_by_group): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Remove un-necessary prefixes when fetching gn genewiki entries.
0429ca3 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Remove un-necessary prefixes when fetching NCBI genewiki entries.
f089f8c 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Rename "limit" query paramater to "per-page".
47501c2 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Add missing prefixes.
7e0abe8 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/genotypes/:name".
af5a45d 
* gn3/api/metadata.py (fetch_group_by_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/genewikis/gn/:symbol".
aeef385 
* gn3/api/metadata.py (get_gn_genewiki_entries): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/genewikis/ncbi/:symbol".
744ed06 
* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/species".
3d00662 
* gn3/api/metadata.py (list_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/species/:name".
cb2c14f 
* gn3/api/metadata.py (fetch_group_by_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/group".
6e5d8a5 
* gn3/api/metadata.py (groups): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/groups/:name".
0b49346 
* gn3/api/metadata.py (fetch_group_by_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Delete duplicate function.
88b3b9f 
* gn3/api/metadata.py (genotypes): Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Implement "GET /metadata/probesets/:name".
1ddf70b 
* gn3/api/metadata.py (fetch_group_by_species): New end-point.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Remove duplicate key in dictionary.
0309c86 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Delete unused imports.
eb1dd1b 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Abstract out (sparql) CONSTRUCT into a function.
bd13ff1 
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz
Make implicit optional type hints PEP 484 compliant.
e9dcf12 
Ran the command:

    pipx run no_implicit_optional ./

in the root directory.
@BonfaceKilz
Ignore construct result for mypy compliance
aa292c0 
This commit addresses the mypy issue below by ignoring the construct
result.

```
error: Item "None" of "bytes | str | dict[Any, Any] | Graph | Document | None" has no attribute "serialize" [union-attr]
```
@BonfaceKilz
Make scripts/ a module since it referenced in argparse_actions.py.
972320b 
* scripts/__init__.py: New file.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
@BonfaceKilz BonfaceKilz changed the title Feature/display rdf Implement metadata end-points Oct 27, 2023
@BonfaceKilz BonfaceKilz merged commit 036240a into genenetwork:main Oct 27, 2023
@BonfaceKilz BonfaceKilz deleted the feature/display-rdf branch October 27, 2023 10:45
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@BonfaceKilz