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authorMunyoki Kilyungi2024-02-15 11:31:34 +0300
committerBonfaceKilz2024-02-15 11:35:00 +0300
commit1a14fe968149908ecedb71500314f666985dfa27 (patch)
tree6aeea3608fe4ea7052ecc5a1f6046f4152ba99c7 /gn3
parentdba5dbd6b43ea088f62426cc2ce6df4787cd9f78 (diff)
downloadgenenetwork3-1a14fe968149908ecedb71500314f666985dfa27.tar.gz
Use correct names for dataset entries in json result.
Since we are appending to an already flattened json-ld file, we don't need to add the prefixes. * gn3/api/metadata.py (DATASET_CONTEXT): Add missing "experimentType" key. * gn3/db/datasets.py (retrieve_dataset_metadata): Match the __subject dict with entries from DATASET_CONTEXT. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'gn3')
-rw-r--r--gn3/api/metadata.py1
-rw-r--r--gn3/db/datasets.py24
2 files changed, 13 insertions, 12 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index fbdc8f5..7334abb 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -38,6 +38,7 @@ DATASET_CONTEXT = {
"description": "dct:description",
"ex": "http://example.org/stuff/1.0/",
"experimentDesignInfo": "gnt:hasExperimentDesignInfo",
+ "experimentType": "gnt:hasExperimentType",
"foaf": "http://xmlns.com/foaf/0.1/",
"geoSeriesId": "gnt:hasGeoSeriesId",
"gnt": "http://genenetwork.org/term/",
diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py
index 6ec2126..043be4c 100644
--- a/gn3/db/datasets.py
+++ b/gn3/db/datasets.py
@@ -337,18 +337,18 @@ def retrieve_dataset_metadata(name: str) -> dict:
"""Return the full data given a path, NAME"""
result = {}
__subject = {
- "summary": "dct:description",
- "tissue": "gnt:hasTissueInfo",
- "specifics": "gnt:hasTissueInfo",
- "cases": "gnt:hasCaseInfo",
- "platform": "gnt:hasPlatformInfo",
- "processing": "gnt:hasDataProcessingInfo",
- "notes": "gnt:hasNotes",
- "experiment-design": "gnt:hasExperimentDesignInfo",
- "acknowledgment": "gnt:hasAcknowledgement",
- "citation": "dct:isReferencedBy",
- "experiment-type": "gnt:hasExperimentType",
- "contributors": "dct:creator",
+ "summary": "description",
+ "tissue": "tissueInfo",
+ "specifics": "specifics",
+ "cases": "caseInfo",
+ "platform": "platformInfo",
+ "processing": "processingInfo",
+ "notes": "notes",
+ "experiment-design": "experimentDesignInfo",
+ "acknowledgment": "acknowledgement",
+ "citation": "citation",
+ "experiment-type": "experimentType",
+ "contributors": "contributors",
}
for __file in Path(name).glob("*rtf"):
with __file.open() as _f: