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Adding back in the test case Rabab created that i accidently removed …
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…via a force-push; updated initial seed fixtures to use calculated annotation versions; cleaned up the documentation for the create annotation manifest script for migration
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@SeriousHorncat
SeriousHorncat committed Sep 25, 2024
1 parent 986a247 commit db78839
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10 changes: 3 additions & 7 deletions etc/fixtures/create-annotation-manifest.js
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Expand Up @@ -2,17 +2,13 @@ const usage = `
mongosh /tmp/database/create-annotation-manifests.js
Script Options:
help: if true print this help message
overwrite: replace the existing analysis' annotation manifest
databaseName: different name of the database if needed
Generates an annotation manifest for each Rosalution analysis and updates
genomic unit annotations with matching dataset source and version.
Run mongosh help for mongosh connection and authentication usage.
Example:
docker exec -it rosalution-rosalution-db-1 mongosh --file /tmp/fixtures/create-annotation-manifest.js
mongosh --host localhost --port 27017 --file /tmp/fixtures/create-annotation-manifest.js --eval="databaseName='rosalution_db'"
docker exec -it <rosalution_db_container> mongosh --file /tmp/fixtures/create-annotation-manifest.js --eval="databaseName='rosalution_db'"
docker exec -it <rosalution_db_container> mongosh --file /tmp/fixtures/create-annotation-manifest.js help
`

help = process.argv.includes('help')
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209 changes: 209 additions & 0 deletions etc/fixtures/import/dev-test-analysis-C-PAM0084-duplicate.json
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@@ -0,0 +1,209 @@
{
"date": "2022-12-27T16:32:19.000Z",
"parental_names": {
"paternal_first_name": "",
"maternal_first_name": "",
"paternal_last_name": "",
"maternal_last_name": ""
},
"apgar": {},
"notes": {
"family_history": "",
"prenatal_development": "",
"indication_for_referral": "",
"genetic_notes": "",
"medical_history": "",
"diagnosis_notes": ""
},
"ethnicity": {
"maternal_ethnicity": [],
"paternal_ethnicity": []
},
"date_of_birth": {
"year": 2014
},
"solved": {
"status": "unsolved"
},
"external_id": "CPAM0084-duplicate",
"variants": [
{
"start_position": "7100249",
"evidence": [
"rare"
],
"gene": "ENSG00000132535",
"chromosome": "17",
"inheritance": "unknown",
"end_position": "7100249",
"transcript": "NM_001365.4",
"sanger": "NA",
"zygosity": "heterozygous",
"interpretation": "likely_pathogenic",
"reference_genome": "GRCh37",
"protein": "p.Glu347ArgTer12",
"effect": "deletion_frameshift",
"cdna": "c.1039del",
"segregation": "NA"
},
{
"evidence": [
"reported"
],
"gene": "ENSG00000160211",
"chromosome": "X",
"inheritance": "NA",
"transcript": "NM_001360016.2",
"sanger": "NA",
"zygosity": "heterozygous",
"interpretation": "pathogenic",
"reference_genome": "GRCh37",
"protein": "p.Ser188Phe",
"effect": "missense",
"dbsnp": "rs5030868",
"cdna": "c.563C>T",
"segregation": "NA"
}
],
"clinicalStatus": "affected",
"disorders": [],
"features": [
{
"id": "HP:0000739",
"label": "Anxiety",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0000750",
"label": "Delayed speech and language development",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0001249",
"label": "Intellectual disability",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0001260",
"label": "Dysarthria",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0001290",
"label": "Generalized hypotonia",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0001298",
"label": "Encephalopathy",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0002194",
"label": "Delayed gross motor development",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0002370",
"label": "Poor coordination",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0002425",
"label": "Anarthria",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0007018",
"label": "Attention deficit hyperactivity disorder",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0012758",
"label": "Neurodevelopmental delay",
"type": "phenotype",
"observed": "yes"
},
{
"id": "HP:0100702",
"label": "Arachnoid cyst",
"type": "phenotype",
"observed": "yes"
}
],
"date_of_death": {},
"contact": [
{
"name": "Aleksandra Foksinska",
"id": "xwiki:XWiki.affoksinska",
"email": "afoksin@uab.edu"
}
],
"last_modification_date": "2022-12-27T16:46:42.000Z",
"patient_name": {
"last_name": "",
"first_name": ""
},
"specificity": {
"date": "2022-12-27T16:47:27.068Z",
"score": 0.9144866681383053,
"server": "local-omim"
},
"nonstandard_features": [],
"id": "P0000055",
"prenatal_perinatal_history": {
"multipleGestation": null,
"icsi": null,
"ivf": null,
"assistedReproduction_donoregg": null,
"assistedReproduction_iui": null,
"twinNumber": null,
"assistedReproduction_fertilityMeds": null,
"gestation": null,
"assistedReproduction_surrogacy": null,
"assistedReproduction_donorsperm": null
},
"family_history": {
"miscarriages": null,
"consanguinity": null,
"affectedRelatives": null
},
"genes": [
{
"gene": "DLG4",
"id": "ENSG00000132535",
"strategy": [
"sequencing"
],
"status": "candidate"
},
{
"gene": "G6PD",
"id": "ENSG00000160211",
"status": "candidate"
}
],
"life_status": "alive",
"sex": "F",
"clinical-diagnosis": [],
"reporter": "affoksinska",
"last_modified_by": "affoksinska",
"report_id": "P0000055",
"meta": {
"hgnc_version": "2020-09-16T16:21:14.971Z",
"omim_version": "2018-10-03T17:01:45.970Z",
"ordo_version": "3.0",
"hpo_version": "hp/releases/2020-08-11",
"phenotips_version": "6.9.2.RELEASE"
}
}
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