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Endpoints description fixes #148

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merged 2 commits into from
Oct 8, 2024
Merged

Endpoints description fixes #148

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a6fe8ad
Cleanup of descriptions in endpoints files
mbaudis Jul 17, 2024
7443dd2
Merge branch 'schema-urgent-fixes' into endpoints-description-fixes
costero-e Oct 8, 2024
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15 changes: 0 additions & 15 deletions bin/yamlerRunner.sh
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Original file line number Diff line number Diff line change
@@ -1,28 +1,13 @@
BASEDIR=$(dirname $0)
UNITYPATH=$BASEDIR/..

# initial conversion from separate schemas
# DEPRECATED
# BEACONMODELPATH=$BASEDIR/../../beacon-v2-Models/BEACON-V2-Model
# BEACONFRAMEWORKPATH=$BASEDIR/../../beacon-framework-v2

BEACONMODELNAME=beacon-v2-default-model

# for UPSTREAM in $BEACONMODELPATH $BEACONFRAMEWORKPATH
# do
# echo "pulling $UPSTREAM"
# git -C $UPSTREAM pull
# done

for KIND in src json
do
mkdir -p $UNITYPATH/models/$KIND/$BEACONMODELNAME
mkdir -p $UNITYPATH/framework/$KIND
done

# $BASEDIR/beaconYamler.py -i $BEACONMODELPATH -t json -x yaml -o $UNITYPATH/models/src/$BEACONMODELNAME
# $BASEDIR/beaconYamler.py -i $BEACONFRAMEWORKPATH -t json -x yaml -o $UNITYPATH/framework/src

# recurring conversion from the source files to the exported versions
$BASEDIR/beaconYamler.py -i $UNITYPATH/models/src/$BEACONMODELNAME -t yaml -x json -o $UNITYPATH/models/json/$BEACONMODELNAME
$BASEDIR/beaconYamler.py -i $UNITYPATH/framework/src -t yaml -x json -o $UNITYPATH/framework/json
12 changes: 6 additions & 6 deletions models/json/beacon-v2-default-model/analyses/endpoints.json
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Expand Up @@ -91,7 +91,7 @@
"paths": {
"/analyses": {
"get": {
"description": "Get a list of bioinformatics analysis",
"description": "Get a Beacon response for bioinformatics analyses",
"operationId": "getAnalyses",
"parameters": [
{
Expand Down Expand Up @@ -123,7 +123,7 @@
]
},
"post": {
"description": "Get a list of bioinformatics analysis",
"description": "Get a Beacon response for bioinformatics analyses",
"operationId": "postAnalysesRequest",
"requestBody": {
"content": {
Expand Down Expand Up @@ -207,8 +207,8 @@
},
"/analyses/{id}/g_variants": {
"get": {
"description": "Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id'",
"operationId": "getOneAnalysisVariants",
"description": "Get a *genomic variations* response for one bioinformatics analysis, identified by its (unique) 'id'",
"operationId": "getOneAnalysisVariationsRequest",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
Expand Down Expand Up @@ -239,8 +239,8 @@
}
],
"post": {
"description": "Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id'",
"operationId": "postOneAnalysisVariantsRequest",
"description": "Get a *genomic variations* response for one bioinformatics analysis, identified by its (unique) 'id'",
"operationId": "postOneAnalysisVariationsRequest",
"requestBody": {
"content": {
"application/json": {
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24 changes: 12 additions & 12 deletions models/json/beacon-v2-default-model/biosamples/endpoints.json
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Expand Up @@ -95,7 +95,7 @@
"paths": {
"/biosamples": {
"get": {
"description": "Get a list of biosamples",
"description": "Get a Beacon response for biosamples",
"operationId": "getBiosamples",
"parameters": [
{
Expand Down Expand Up @@ -127,7 +127,7 @@
]
},
"post": {
"description": "Get a list of biosamples",
"description": "Get a Beacon response for biosamples",
"operationId": "postBiosamplesRequest",
"requestBody": {
"content": {
Expand Down Expand Up @@ -204,8 +204,8 @@
},
"/biosamples/{id}/analyses": {
"get": {
"description": "Get the analysis list from one biosample, identified by its (unique) 'id'",
"operationId": "getOneBiosampleAnalysis",
"description": "Get an *analyses* response from one biosample, identified by its (unique) 'id'",
"operationId": "getOneBiosampleAnalyses",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
Expand Down Expand Up @@ -236,8 +236,8 @@
}
],
"post": {
"description": "Get the analysis list from one biosample, identified by its (unique) 'id'",
"operationId": "postOneBiosampleAnalysis",
"description": "Get an *analyses* response from one biosample, identified by its (unique) 'id'",
"operationId": "postOneBiosampleAnalyses",
"requestBody": {
"content": {
"application/json": {
Expand All @@ -264,8 +264,8 @@
},
"/biosamples/{id}/g_variants": {
"get": {
"description": "Get the genomic variants list from one biosample, identified by its (unique) 'id'",
"operationId": "getOneBiosampleGenomicVariants",
"description": "Get a *genomic variations* response from one biosample, identified by its (unique) 'id'",
"operationId": "getOneBiosampleGenomicVariations",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
Expand Down Expand Up @@ -296,8 +296,8 @@
}
],
"post": {
"description": "Get the genomic variants list from one biosample, identified by its (unique) 'id'",
"operationId": "postOneBiosampleGenomicVariants",
"description": "Get a *genomic variations* response from one biosample, identified by its (unique) 'id'",
"operationId": "postOneBiosampleGenomicVariations",
"requestBody": {
"content": {
"application/json": {
Expand All @@ -324,7 +324,7 @@
},
"/biosamples/{id}/runs": {
"get": {
"description": "Get the runs list from one biosample, identified by its (unique) 'id'",
"description": "Get a *runs* response from one biosample, identified by its (unique) 'id'",
"operationId": "getOneBiosampleRuns",
"parameters": [
{
Expand Down Expand Up @@ -363,7 +363,7 @@
}
],
"post": {
"description": "Get the runs list from one biosample, identified by its (unique) 'id'",
"description": "Get a *runs* response from one biosample, identified by its (unique) 'id'",
"operationId": "postOneBiosampleRuns",
"requestBody": {
"content": {
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12 changes: 6 additions & 6 deletions models/json/beacon-v2-default-model/cohorts/endpoints.json
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Expand Up @@ -108,7 +108,7 @@
"paths": {
"/cohorts": {
"get": {
"description": "Get a list of cohorts",
"description": "Get a Beacon *cohorts* response",
"operationId": "getCohorts",
"parameters": [
{
Expand Down Expand Up @@ -137,7 +137,7 @@
]
},
"post": {
"description": "Get a list of cohorts",
"description": "Get a Beacon *cohorts* response",
"operationId": "postCohortsRequest",
"requestBody": {
"content": {
Expand Down Expand Up @@ -219,7 +219,7 @@
},
"/cohorts/{id}/filtering_terms": {
"get": {
"description": "Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'",
"description": "Get a response about the *filtering terms* that could be used with a given cohort, identified by its (unique) 'id'",
"operationId": "getOneCohortFilteringTerms",
"parameters": [
{
Expand Down Expand Up @@ -255,7 +255,7 @@
}
],
"post": {
"description": "Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'",
"description": "Get a response about the *filtering terms* that could be used with a given cohort, identified by its (unique) 'id'",
"operationId": "postOneCohortFilteringTerms",
"requestBody": {
"content": {
Expand Down Expand Up @@ -290,7 +290,7 @@
},
"/cohorts/{id}/individuals": {
"get": {
"description": "Get the individuals from one cohort, identified by its (unique) 'id'",
"description": "Get an *individuals* response for one cohort, identified by its (unique) 'id'",
"operationId": "getOneCohortIndividuals",
"parameters": [
{
Expand Down Expand Up @@ -322,7 +322,7 @@
}
],
"post": {
"description": "Get the individuals from one cohort, identified by its (unique) 'id'",
"description": "Get an *individuals* response for one cohort, identified by its (unique) 'id'",
"operationId": "postOneCohortEntries",
"requestBody": {
"content": {
Expand Down
18 changes: 9 additions & 9 deletions models/json/beacon-v2-default-model/datasets/endpoints.json
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Expand Up @@ -135,7 +135,7 @@
]
},
"post": {
"description": "Get a list of datasets",
"description": "Get a Beacon *datasets* response",
"operationId": "postDatasetsRequest",
"requestBody": {
"content": {
Expand Down Expand Up @@ -217,7 +217,7 @@
},
"/datasets/{id}/biosamples": {
"get": {
"description": "Get the biosamples list from one dataset, identified by its (unique) 'id'",
"description": "Get a *biosamples* response for one dataset, identified by its (unique) 'id'",
"operationId": "getOneDatasetBiosamples",
"parameters": [
{
Expand Down Expand Up @@ -249,7 +249,7 @@
}
],
"post": {
"description": "Get the biosamples list from one dataset, identified by its (unique) 'id'",
"description": "Get a *biosamples* response for one dataset, identified by its (unique) 'id'",
"operationId": "postOneDatasetBiosamples",
"requestBody": {
"content": {
Expand Down Expand Up @@ -277,7 +277,7 @@
},
"/datasets/{id}/filtering_terms": {
"get": {
"description": "Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id'",
"description": "Get a response about the *filtering terms* that could be used with a given dataset, identified by its (unique) 'id'",
"operationId": "getOneDatasetFilteringTerms",
"parameters": [
{
Expand Down Expand Up @@ -313,7 +313,7 @@
}
],
"post": {
"description": "Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id'",
"description": "Get a response about the *filtering terms* that could be used with a given dataset, identified by its (unique) 'id'",
"operationId": "postOneDatasetFilteringTerms",
"requestBody": {
"content": {
Expand Down Expand Up @@ -348,7 +348,7 @@
},
"/datasets/{id}/g_variants": {
"get": {
"description": "Get the genomic variants list from one dataset, identified by its (unique) 'id'",
"description": "Get a *genomic variations* response for one dataset, identified by its (unique) 'id'",
"operationId": "getOneDatasetEntries",
"parameters": [
{
Expand Down Expand Up @@ -380,7 +380,7 @@
}
],
"post": {
"description": "Get the genomic variants list from one dataset, identified by its (unique) 'id'",
"description": "Get a *genomic variations* response for one dataset, identified by its (unique) 'id'",
"operationId": "postOneDatasetEntries",
"requestBody": {
"content": {
Expand Down Expand Up @@ -408,7 +408,7 @@
},
"/datasets/{id}/individuals": {
"get": {
"description": "Get the individuals list from one dataset, identified by its (unique) 'id'",
"description": "Get an *individuals* response for one dataset, identified by its (unique) 'id'",
"operationId": "getOneDatasetIndividuals",
"parameters": [
{
Expand Down Expand Up @@ -440,7 +440,7 @@
}
],
"post": {
"description": "Get the biosamples list from one dataset, identified by its (unique) 'id'",
"description": "Get an *individuals* response for one dataset, identified by its (unique) 'id'",
"operationId": "postOneDatasetIndividuals",
"requestBody": {
"content": {
Expand Down
24 changes: 12 additions & 12 deletions models/json/beacon-v2-default-model/genomicVariations/endpoints.json
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Expand Up @@ -193,8 +193,8 @@
"paths": {
"/g_variants": {
"get": {
"description": "Get a list of example entries",
"operationId": "getExampleEntries",
"description": "Get a Beacon response for genomic variations",
"operationId": "getGenomicVariations",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
Expand Down Expand Up @@ -258,8 +258,8 @@
]
},
"post": {
"description": "Get a list of example entries",
"operationId": "postExampleEntriesRequest",
"description": "Get a Beacon response for genomic variations",
"operationId": "postGenomicVariationsRequest",
"requestBody": {
"content": {
"application/json": {
Expand Down Expand Up @@ -335,8 +335,8 @@
},
"/g_variants/{id}/biosamples": {
"get": {
"description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'",
"operationId": "getOneGenomicVariantBiosamples",
"description": "Get a *biosamples* response from one genomic variant, identified by its (unique) 'id'",
"operationId": "getOneGenomicVariationBiosamples",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
Expand Down Expand Up @@ -367,8 +367,8 @@
}
],
"post": {
"description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'",
"operationId": "postOneGenomicVariantBiosamples",
"description": "Get a *biosamples* response from one genomic variant, identified by its (unique) 'id'",
"operationId": "postOneGenomicVariationBiosamples",
"requestBody": {
"content": {
"application/json": {
Expand All @@ -395,8 +395,8 @@
},
"/g_variants/{id}/individuals": {
"get": {
"description": "Get the individuals list from one genomic variant, identified by its (unique) 'id'",
"operationId": "getOneGenomicVariantIndividuals",
"description": "Get an *individuals* response from one genomic variant, identified by its (unique) 'id'",
"operationId": "getOneGenomicVariationIndividuals",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
Expand Down Expand Up @@ -427,8 +427,8 @@
}
],
"post": {
"description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'",
"operationId": "postOneGenomicVariantIndividuals",
"description": "Get an *individuals* response from one genomic variant, identified by its (unique) 'id'",
"operationId": "postOneGenomicVariationIndividuals",
"requestBody": {
"content": {
"application/json": {
Expand Down
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