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🚧 Map Concepts between KF and FHIR #78

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🚧 Map Concepts between KF and FHIR #78

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cac3148
:sparkles: ignore vscode cache
liberaliscomputing Feb 13, 2020
9eaa241
::construction: map concepts
liberaliscomputing Feb 13, 2020
81638f9
:construction: update profiles against updated ig
liberaliscomputing Feb 17, 2020
16c882c
:construction: fix typo
liberaliscomputing Feb 17, 2020
bab1841
Fix syntax
fiendish Feb 17, 2020
2d18c42
Merge pull request #79 from kids-first/fixes
liberaliscomputing Feb 17, 2020
86f6cc6
:construction: import constants and concepts
liberaliscomputing Feb 17, 2020
0cae8fb
:construction: deprecate dict update
liberaliscomputing Feb 17, 2020
06d21ff
:construction: convert individual template to prototype
fiendish Feb 17, 2020
ddbcbb3
:construction: wip
fiendish Feb 18, 2020
89dbdc2
:construction: wip
fiendish Feb 19, 2020
554f71c
:construction: individuals load now
fiendish Feb 19, 2020
dee356d
:construction: samples load now
fiendish Feb 19, 2020
f4b1a0b
:construction: abort without waiting
fiendish Feb 20, 2020
90c8f41
:construction: updates + phenotype wip
fiendish Feb 21, 2020
efe586e
🚧 update readme
liberaliscomputing Feb 21, 2020
707652e
🚧 fix indentation
liberaliscomputing Feb 21, 2020
890cc8b
🚧 update readme
liberaliscomputing Feb 21, 2020
3d6f29c
🚧 fix indentation
liberaliscomputing Feb 21, 2020
a3f204c
Merge pull request #82 from kids-first/functified
liberaliscomputing Feb 25, 2020
c01eda9
:construction: change style
liberaliscomputing Feb 28, 2020
e55247c
:construction: change style and add kfid assignment
liberaliscomputing Feb 28, 2020
29b8490
:construction: functify disease
liberaliscomputing Feb 28, 2020
2252e76
:construction: add .DS_Store
liberaliscomputing Mar 4, 2020
8327509
:construction: add mappers
liberaliscomputing Mar 4, 2020
90c936e
:construction: add id max char restriction
liberaliscomputing Mar 4, 2020
38b3a1c
:construction: add resource caches
liberaliscomputing Mar 4, 2020
02e6574
:construction: add HPO ontology and code system
liberaliscomputing Mar 4, 2020
3ad4fd1
:construction: add disease terminology
liberaliscomputing Mar 6, 2020
6bba1f3
:construction: update packer
liberaliscomputing Mar 6, 2020
0098372
:construction: add loading disease and phenotypic feature
liberaliscomputing Mar 6, 2020
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42 changes: 29 additions & 13 deletions docs/no_peeking/mappings/biosample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,15 +39,19 @@

def yield_biosamples(eng, table, study_id, individuals):
for row in make_select(
eng, table, CONCEPT.BIOSPECIMEN.ID, CONCEPT.PARTICIPANT.ID,
CONCEPT.BIOSPECIMEN.TARGET_SERVICE_ID, CONCEPT.BIOSPECIMEN.VOLUME_UL,
CONCEPT.BIOSPECIMEN.COMPOSITION, CONCEPT.BIOSPECIMEN.VISIBLE
):
eng, table,
CONCEPT.BIOSPECIMEN.ID,
CONCEPT.BIOSPECIMEN.TARGET_SERVICE_ID,
CONCEPT.PARTICIPANT.ID,
CONCEPT.BIOSPECIMEN.COMPOSITION,
CONCEPT.BIOSPECIMEN.VOLUME_UL,
CONCEPT.BIOSPECIMEN.VISIBLE
):
id = get(row, CONCEPT.BIOSPECIMEN.ID)
subject_id = get(row, CONCEPT.PARTICIPANT.ID)
kfid = get(row, CONCEPT.BIOSPECIMEN.TARGET_SERVICE_ID)
volume_ul = get(row, CONCEPT.BIOSPECIMEN.VOLUME_UL)
subject_id = get(row, CONCEPT.PARTICIPANT.ID)
composition = get(row, CONCEPT.BIOSPECIMEN.COMPOSITION)
volume_ul = get(row, CONCEPT.BIOSPECIMEN.VOLUME_UL)
visible = get(row, CONCEPT.BIOSPECIMEN.VISIBLE)

if not id:
Expand All @@ -63,24 +67,36 @@ def yield_biosamples(eng, table, study_id, individuals):
"meta": {
"profile": ["http://ga4gh.org/fhir/phenopackets/StructureDefinition/Biosample"]
},
"identifier": [{"system": f"http://kf-api-dataservice.kidsfirstdrc.org/biospecimens?study_id={study_id}", "value": id}],
"identifier": [
{
"system": f"http://kf-api-dataservice.kidsfirstdrc.org/biospecimens?study_id={study_id}", "value": id
}
],
"status": biosample_status[visible or constants.COMMON.TRUE],
}

if kfid:
retval["identifier"].append(
{
"system": "http://kf-api-dataservice.kidsfirstdrc.org/biospecimens", "value": kfid
}
)

if subject_id:
retval["subject"] = {
"reference": f"Patient/{individuals[subject_id]['id']}"
"reference": f"Patient/{individuals[subject_id]['id']}",
"type": iRType
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@fiendish fiendish Feb 28, 2020 •
edited
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what is this type field for? "Patient" is already part of the reference url component. I think if anything the reference field should be f"{iRType}/{individuals[subject_id]['id']}". .

}

if composition:
retval["type"] = codeable_concept(
composition, [v2_0487_compositions], "Biosample Composition"
)

if volume_ul:
retval.setdefault("collection", {})["quantity"] = {
"unit": "uL",
"value": float(volume_ul),
}

if composition:
retval["type"] = codeable_concept(
composition, [v2_0487_compositions], "Biosample Composition"
)

yield retval, id