Google Summer of Code Open Health GDC exploration (NCI's Genomic Data Commons)
Live at https://mathbiol.github.io/gdcfun !
Current version: v0.1.0
gdcfun is designed to make the query of GDC simple. It enables users to quickly search data or files with a little effort through the GDC REST API.
gdcfun library supports three methods to use:
- Install the gdcfun library with
npm i gdcfunornpm install gdcfun. - Run
http-server -i <port number>in command line and edit the contents inlocalhost:<port number>
- Include the gdcfun library script in the html contents.
<script src="https://mathbiol.github.io/gdcfun/ray.js"></script>- Open a new notebook in Observable Notebook
- Specify the
requirestatement in the code block.
gf = require('https://mathbiol.github.io/gdcfun/ray.js')The correct method to require ray.js is use await to resolve the promise and .method() to retrieve the functions. A common wrong method to require ray.js only with require() would not be resolved with complete functions.
ray = new(await require('https://mathbiol.github.io/gdcfun/ray.js')).method() // correct method
r = require('https://mathbiol.github.io/gdcfun/ray.js') // wrong methodray.getObj() is an asynchronous function that reads in an object that specifies the requirement of search/retrieval and returns the corresponding results of API fetch. It is a new feature in v0.0.2, and it enables users to fetch API easily without the knowledge of the functions in the Examples section.
The basic format of the object is
{
"method": "projects",
"from": 0,
"size": 8,
"sort": "project.project_id:asc",
"pretty": true
}Supported methods are ["status", "projects", "project", "files", "file", "cases", "case", "annotations", "_mapping"].
With the method specified, ray.getObj() calls the function ray.getProjects(). The whole process returns the following message if succeeded.
method found: projects
success: getting projects?from=0&size=8&sort=project.project_id:asc&pretty=true
And the response is
{
"data": {
"hits": [
{
"dbgap_accession_number": null,
"disease_type": [
"Brain Lower Grade Glioma"
],
"released": true,
"state": "legacy",
"primary_site": [
"Brain"
],
"project_id": "TCGA-LGG",
"id": "TCGA-LGG",
"name": "Brain Lower Grade Glioma"
},
...
],
"pagination": {
"count": 2,
"sort": "project.project_id:asc",
"from": 0,
"page": 1,
"total": 39,
"pages": 20,
"size": 2
}
},
"warnings": {}
}If method is not specified in the object, ray.getObj() would return the following message and calls ray.getStatus() instead.
missing method, return status instead
If method is not supported (listed above) or invalid, ray.getObj() would return the following message and calls ray.getStatus() as well.
invalid method, return status instead
The main fetch function in the gdcfun library to conduct the ray.get() function.
ray.get=async(cmd, callback)This will return an object promise and a status message. By default the ray.get() would return the promise result of ray.get('status') if no parameters are specified. The detailed promise description from chrome is:
Promise {<pending>}
__proto__:Promise
[[PromiseStatus]]:"resolved"
[[PromiseValue]]:Object
success: getting status
All the methods mentioned in the Examples section would call ray.get() eventually with different parameters specified.
ray.getProjects() returns the list of project records and pagination data. The function is called by ray.getProjects(cmd, from, size, sort, pretty), or directly by ray.getObj({"method": "projects", ...}). By default, the object of query and settings is
projectsJson = {
"method": "projects",
"from": 0,
"size": 2,
"sort": "project.project_id:asc",
"pretty": true
}The status message and the result returned are:
success: getting projects?from=0&size=2&sort=project.project_id:asc&pretty=true
{
"data": {
"hits": [
{
"dbgap_accession_number": null,
"disease_type": [
"Brain Lower Grade Glioma"
],
"released": true,
"state": "legacy",
"primary_site": [
"Brain"
],
"project_id": "TCGA-LGG",
"id": "TCGA-LGG",
"name": "Brain Lower Grade Glioma"
},
...
],
"pagination": {
"count": 2,
"sort": "project.project_id:asc",
"from": 0,
"page": 1,
"total": 39,
"pages": 20,
"size": 2
}
},
"warnings": {}
}ray.getProject() returns the metadata of a single project by project_id. The function is called by ray.getProject(cmd, project_id, expand, pretty), or directly by ray.getObj({"method": "project", ...}). By default, the object of query and settings is (If a valid project_id is fed, for example TARGET-NBL )
projectJson = {
"method" : "project",
"project_id": "TARGET-NBL",
"expand": "summary,summary.experimental_strategies,summary.data_categories",
"pretty": true
}The status message and the result returned are:
success: getting projects/TARGET-NBL?expand=summary,summary.experimental_strategies,summary.data_categories&pretty=true
{
"data": {
"dbgap_accession_number": "phs000467",
"disease_type": [
"Neuroblastoma"
],
"summary": {
"data_categories": [
{
"case_count": 7,
"file_count": 1,
"data_category": "Clinical"
},
...
],
"case_count": 1127,
"file_count": 2806,
"experimental_strategies": [
{
"case_count": 221,
"file_count": 2174,
"experimental_strategy": "WXS"
},
...
],
"file_size": 8157614402888
},
"released": true,
"state": "legacy",
"primary_site": [
"Nervous System"
],
"project_id": "TARGET-NBL",
"name": "Neuroblastoma"
},
"warnings": {}
}If project_id is missing, .getProject() would return an empty object and the status message would be
failure: missing project_id
ray.getCases() returns the list of hits of cases by the specific query. The function is called by ray.getCases(cmd, query, pretty), or directly by ray.getObj({"method": "cases", ...}). By default, the object of query and settings is
casesJson = {
"method": "cases",
"query": {"op":"and","content":[{"op":"in","content":{"field":"submitter_id","value":["TCGA-BH-A0EA"]}}]},
"pretty": true
}The status message and the result returned are:
method found: cases
success: getting cases?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22submitter_id%22%2C%22value%22%3A%5B%22TCGA-BH-A0EA%22%5D%7D%7D%5D%7D%0A%0A&pretty=true
{
"data": {
"hits": [
{
"updated_datetime": "2018-05-21T16:07:40.645885-05:00",
"submitter_analyte_ids": [
"TCGA-BH-A0EA-01A-11R",
"TCGA-BH-A0EA-10A-01W",
"TCGA-BH-A0EA-01A-11W",
"TCGA-BH-A0EA-01A-11D",
"TCGA-BH-A0EA-10A-01D"
],
"analyte_ids": [
"f19f408a-815f-43d9-8032-e9482b796371",
"fe678556-acf4-4bde-a95e-860bb0150a95",
"66ed0f86-5ca5-4dec-ba76-7ee4dcf31831",
"69ddc092-88a0-4839-a2bb-9f1c9e760409",
"30cb470f-66d4-4085-8c30-83a42e8453d4"
],
"submitter_id": "TCGA-BH-A0EA",
"case_id": "1f601832-eee3-48fb-acf5-80c4a454f26e",
"id": "1f601832-eee3-48fb-acf5-80c4a454f26e",
"disease_type": "Breast Invasive Carcinoma",
"sample_ids": [
"9a6c71a6-82cd-42b1-a93f-f569370848d6",
"7f791228-dd77-4ab0-8227-d784a4c7fea1",
"55864d86-dab8-47bb-a3e3-8cfb198b06c1"
],
"portion_ids": [
"cb6086d1-3416-4310-b109-e8fa6e8b72d4",
"8629bf5a-cdaf-4f6a-90bb-27dd4a7565c5",
"ae4f5816-f97a-4605-9b05-9ab820467dee"
],
"submitter_portion_ids": [
"TCGA-BH-A0EA-01A-21-A13C-20",
"TCGA-BH-A0EA-01A-11",
"TCGA-BH-A0EA-10A-01"
],
"created_datetime": null,
"slide_ids": [
"90154ea1-6b76-4445-870e-d531d6fa1239",
"a0826f0d-986a-491b-8c6f-b34f8929f3ee",
"1dd1cab5-5a81-428a-8153-91e8c4cf9905"
],
"state": "live",
"aliquot_ids": [
"eef9dce1-6ba6-432b-bbe2-53c7dbe64fe7",
"cde982b7-3b0a-49eb-8710-a599cb0e44c1",
...
],
"primary_site": "Breast",
"submitter_aliquot_ids": [
"TCGA-BH-A0EA-10A-01D-A113-01",
"TCGA-BH-A0EA-01A-11R-A115-07",
...
],
"submitter_sample_ids": [
"TCGA-BH-A0EA-10A",
"TCGA-BH-A0EA-01Z",
"TCGA-BH-A0EA-01A"
],
"submitter_slide_ids": [
"TCGA-BH-A0EA-01Z-00-DX1",
"TCGA-BH-A0EA-01A-01-MSA",
"TCGA-BH-A0EA-01A-01-TSA"
]
}
],
"pagination": {
"count": 1,
"sort": "",
"from": 0,
"page": 1,
"total": 1,
"pages": 1,
"size": 10
}
},
"warnings": {}
}If query is missing, .getCases() would return an empty object and the status message would be
failure: missing queryray.getCase() returns the metadata of a single project by UUID. The function is called by getCase= (cmd, uuid, pretty, expand), or directly by ray.getObj({"method": "case", ...}). By default, the object of query and settings is (If a valid uuid is fed, for example 1f601832-eee3-48fb-acf5-80c4a454f26e )
method found: case
success: getting cases/1f601832-eee3-48fb-acf5-80c4a454f26e?pretty=true&expand=diagnoses
{
"data": {
"diagnoses": [
{
"classification_of_tumor": "not reported",
"last_known_disease_status": "not reported",
"updated_datetime": "2016-05-16T10:59:16.740358-05:00",
"primary_diagnosis": "c50.9",
"submitter_id": "TCGA-BH-A0EA_diagnosis",
"tumor_stage": "stage iia",
"age_at_diagnosis": 26548.0,
"vital_status": "dead",
"morphology": "8500/3",
"days_to_death": 991.0,
"days_to_last_known_disease_status": null,
"days_to_last_follow_up": null,
"state": null,
"days_to_recurrence": null,
"diagnosis_id": "84654ad5-2a2c-5c3b-8340-ecac6a5550fe",
"tumor_grade": "not reported",
"tissue_or_organ_of_origin": "c50.9",
"days_to_birth": -26548.0,
"progression_or_recurrence": "not reported",
"prior_malignancy": "not reported",
"site_of_resection_or_biopsy": "c50.9",
"created_datetime": null
}
],
"sample_ids": [
"7f791228-dd77-4ab0-8227-d784a4c7fea1",
"9a6c71a6-82cd-42b1-a93f-f569370848d6"
],
"portion_ids": [
"cb6086d1-3416-4310-b109-e8fa6e8b72d4",
"8629bf5a-cdaf-4f6a-90bb-27dd4a7565c5",
"ae4f5816-f97a-4605-9b05-9ab820467dee"
],
"submitter_portion_ids": [
"TCGA-BH-A0EA-01A-11",
"TCGA-BH-A0EA-01A-21-A13C-20",
"TCGA-BH-A0EA-10A-01"
],
"created_datetime": null,
"submitter_aliquot_ids": [
"TCGA-BH-A0EA-01A-11R-A114-13",
"TCGA-BH-A0EA-01A-11D-A111-01",
...
],
"updated_datetime": "2016-05-02T14:37:43.619198-05:00",
"submitter_analyte_ids": [
"TCGA-BH-A0EA-01A-11R",
"TCGA-BH-A0EA-01A-11D",
"TCGA-BH-A0EA-01A-11W",
"TCGA-BH-A0EA-10A-01W",
"TCGA-BH-A0EA-10A-01D"
],
"analyte_ids": [
"30cb470f-66d4-4085-8c30-83a42e8453d4",
"66ed0f86-5ca5-4dec-ba76-7ee4dcf31831",
"f19f408a-815f-43d9-8032-e9482b796371",
"69ddc092-88a0-4839-a2bb-9f1c9e760409",
"fe678556-acf4-4bde-a95e-860bb0150a95"
],
"submitter_id": "TCGA-BH-A0EA",
"case_id": "1f601832-eee3-48fb-acf5-80c4a454f26e",
"state": null,
"aliquot_ids": [
"bcb7fc6d-60a0-48b7-aa81-14c0dda72d76",
"97c64d6a-7dce-4d0f-9cb3-b3e4eb4719c5",
...
],
"slide_ids": [
"90154ea1-6b76-4445-870e-d531d6fa1239",
"a0826f0d-986a-491b-8c6f-b34f8929f3ee"
],
"submitter_sample_ids": [
"TCGA-BH-A0EA-01A",
"TCGA-BH-A0EA-10A"
]
},
"warnings": {}
}If uuid is missing, .getProject() would return an empty object and the status message would be
failure: missing uuid
ray.getFiles() returns the metadata of a single project by project_id. The function is called by ray.getProjects(cmd, from, size, sort, pretty), or directly by ray.getObj({"method": "project", ...}). By default, the object of query and settings is
filesJson = {
"method": "files",
"from": 0,
"size": 3,
"sort": "file_size:asc",
"pretty": true
}The status message and the result returned are:
method found: files
success: getting files?from=0&size=3&sort=file_size:asc&pretty=true
{
"data": {
"hits": [
{
"data_type": "Raw Simple Somatic Mutation",
"updated_datetime": "2017-03-04T16:45:40.925270-06:00",
"file_name": "9f78a291-2d50-472c-8f56-5f8fbd09ab2a.snp.Somatic.hc.vcf.gz",
"submitter_id": "TCGA-13-0757-01A-01W-0371-08_TCGA-13-0757-10A-01W-0371-08_varscan",
"file_id": "9f78a291-2d50-472c-8f56-5f8fbd09ab2a",
"file_size": 1120,
"id": "9f78a291-2d50-472c-8f56-5f8fbd09ab2a",
"created_datetime": "2016-05-04T14:50:54.560567-05:00",
"md5sum": "13c1ceb3519615e2c67128b350365fbf",
"data_format": "VCF",
"acl": [
"phs000178"
],
"access": "controlled",
"state": "live",
"data_category": "Simple Nucleotide Variation",
"type": "simple_somatic_mutation",
"file_state": "submitted",
"experimental_strategy": "WXS"
},
{
"data_type": "Raw Simple Somatic Mutation",
"updated_datetime": "2017-03-04T16:45:40.925270-06:00",
"file_name": "7780009b-abb6-460b-903d-accdac626c2e.snp.Somatic.hc.vcf.gz",
"submitter_id": "TCGA-HC-8261-01A-11D-2260-08_TCGA-HC-8261-10A-01D-2260-08_varscan",
"file_id": "7780009b-abb6-460b-903d-accdac626c2e",
"file_size": 1237,
"id": "7780009b-abb6-460b-903d-accdac626c2e",
"created_datetime": "2016-05-08T13:54:38.369393-05:00",
"md5sum": "fd9bb46c8022b96af730c48dc00e2c41",
"data_format": "VCF",
"acl": [
"phs000178"
],
"access": "controlled",
"state": "live",
"data_category": "Simple Nucleotide Variation",
"type": "simple_somatic_mutation",
"file_state": "submitted",
"experimental_strategy": "WXS"
}
],
"pagination": {
"count": 2,
"sort": "file_size:asc",
"from": 0,
"page": 1,
"total": 274724,
"pages": 137362,
"size": 2
}
},
"warnings": {}
}ray.getFile() returns the metadata of a single case using its uuid. The function is called by ray.getFile(cmd, uuid, pretty), or directly by ray.getObj({"method": "file", ...}). By default, the object of query and settings is (If a valid uuid is fed (for example 6680627c-f70b-45fd-854b-208be561a9e8))
fileJson = {
"method": "file",
"uuid": "6680627c-f70b-45fd-854b-208be561a9e8",
"pretty": true
}The status message and the result returned are:
method found: file
success: getting files/6680627c-f70b-45fd-854b-208be561a9e8?pretty=true
{
"data": {
"data_type": "Annotated Somatic Mutation",
"updated_datetime": "2017-10-24T10:21:24.570405-05:00",
"created_datetime": "2017-09-10T13:52:40.396812-05:00",
"file_name": "6680627c-f70b-45fd-854b-208be561a9e8.vep.vcf.gz",
"md5sum": "9af5e6d636771e245605243eb9f36505",
"data_format": "VCF",
"acl": [
"phs001179"
],
"access": "controlled",
"state": "submitted",
"file_id": "6680627c-f70b-45fd-854b-208be561a9e8",
"data_category": "Simple Nucleotide Variation",
"file_size": 7982,
"submitter_id": "AD8753_AnnotatedSomaticMutation",
"type": "annotated_somatic_mutation",
"file_state": "submitted",
"experimental_strategy": "Targeted Sequencing"
},
"warnings": {}
}If uuid is missing, .getFile() would return an empty object and the status message would be
failure: missing uuid
ray.getAnnotations() returns the query result in search and retrieval of annotations stored. The function is called by ray.getAnnotations(cmd, query, pretty), or directly by ray.getObj({"method": "annotations", ...}). By default, the object of query and settings is
annotationsJson = {
"method": "annotations",
"query": {
"op":"in",
"content":{
"field":"entity_id",
"value":[
"e0d36cc0-652c-4224-bb10-09d15c7bd8f1",
"25ebc29a-7598-4ae4-ba7f-618d448882cc",
"fe660d7c-2746-4b50-ab93-b2ed99960553"
]
}
},
"pretty": true
}The status message and the result returned are:
method found: annotations
success: getting annotations?filter=%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22entity_id%22%2C%22value%22%3A%5B%22e0d36cc0-652c-4224-bb10-09d15c7bd8f1%22%2C%2225ebc29a-7598-4ae4-ba7f-618d448882cc%22%2C%22fe660d7c-2746-4b50-ab93-b2ed99960553%22%5D%7D%7D
{
"data": {
"hits": [
{
"category": "Item flagged DNU",
"status": "Approved",
"entity_id": "fe660d7c-2746-4b50-ab93-b2ed99960553",
"classification": "CenterNotification",
"entity_type": "aliquot",
"created_datetime": "2015-09-28T00:00:00",
"annotation_id": "5ddadefe-8b57-5ce2-b8b2-918d63d99a59",
"notes": "The aliquot failed Broad pipeline QC and not all files are suitable for use. Consult the SDRF file to determine which files are usable.",
"updated_datetime": "2017-03-09T13:20:38.962182-06:00",
"submitter_id": "29087",
"state": "submitted",
"case_id": "41b59716-116f-4942-8b63-409870a87e26",
"case_submitter_id": "TCGA-DK-A3IM",
"entity_submitter_id": "TCGA-DK-A3IM-10A-01D-A20B-01",
"id": "5ddadefe-8b57-5ce2-b8b2-918d63d99a59"
},
{
"category": "Item is noncanonical",
"status": "Approved",
"entity_id": "25ebc29a-7598-4ae4-ba7f-618d448882cc",
"classification": "Notification",
"entity_type": "sample",
"created_datetime": "2012-07-12T00:00:00",
"annotation_id": "d6500f94-618f-5334-a810-ade76b887ec9",
"notes": "No Matching Normal",
"updated_datetime": "2017-03-09T13:47:18.182075-06:00",
"submitter_id": "8009",
"state": "submitted",
"case_id": "bd114e05-5a97-41e2-a0d5-5d39a1e9d461",
"case_submitter_id": "TCGA-08-0514",
"entity_submitter_id": "TCGA-08-0514-01A",
"id": "d6500f94-618f-5334-a810-ade76b887ec9"
},
{
"category": "Prior malignancy",
"status": "Approved",
"entity_id": "e0d36cc0-652c-4224-bb10-09d15c7bd8f1",
"classification": "Notification",
"entity_type": "case",
"created_datetime": "2013-03-12T00:00:00",
"annotation_id": "33336cdf-2cf0-5af2-bb52-fecd3427f180",
"notes": "Patient had a prior lymphoma. Unknown radiation or systemic chemotherapy.",
"updated_datetime": "2017-03-09T12:11:31.786013-06:00",
"submitter_id": "15630",
"state": "submitted",
"case_id": "e0d36cc0-652c-4224-bb10-09d15c7bd8f1",
"case_submitter_id": "TCGA-FS-A1ZF",
"entity_submitter_id": "TCGA-FS-A1ZF",
"id": "33336cdf-2cf0-5af2-bb52-fecd3427f180"
}
],
"pagination": {
"count": 3,
"sort": "",
"from": 0,
"page": 1,
"total": 3,
"pages": 1,
"size": 10
}
},
"warnings": {}
}If query is missing, .getAnnotations() would return default results and the status message would be
success: getting annotations?filter=&pretty=trueray.convertQuery() returns the encoded string of the query object by obj input. The function is called by ray.convertQuery(parms) . The input object obj would be first stringfied and then be encoded with Percent-(URL)-encoding method. A sample input is
queryObj = {
"method": "case",
"op": "and",
"content": [
{
"op": "in",
"content": {
"field": "cases.submitter_id",
"value": [
"TCGA-CK-4948",
"TCGA-D1-A17N",
"TCGA-4V-A9QX",
"TCGA-4V-A9QM"
]
}
},
{
"op": "=",
"content": {
"field": "files.data_type",
"value": "Gene Expression Quantification"
}
}
]
}The result of calling ray.converQuery(queryObj) is
resultConvertQuery = "%7B%22method%22%3A%22case%22%2C%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.submitter_id%22%2C%22value%22%3A%5B%22TCGA-CK-4948%22%2C%22TCGA-D1-A17N%22%2C%22TCGA-4V-A9QX%22%2C%22TCGA-4V-A9QM%22%5D%7D%7D%2C%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%22Gene%20Expression%20Quantification%22%7D%7D%5D%7D"ray.parseQuery() returns the decoded object of the encoded query string by query input. The function is called by ray.parseQuery(query) . The input object query would be first split by & and then be separated into key-value pairs. A sample input is
sampleStr = "filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.submitter_id%22%2C%22value%22%3A%5B%22TCGA-CK-4948%22%2C%22TCGA-D1-A17N%22%2C%22TCGA-4V-A9QX%22%2C%22TCGA-4V-A9QM%22%5D%7D%7D%2C%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%22Gene%20Expression%20Quantification%22%7D%7D%5D%7D&format=tsv&fields=file_id,file_name,cases.submitter_id,cases.case_id,data_category,data_type,cases.samples.tumor_descriptor,cases.samples.tissue_type,cases.samples.sample_type,cases.samples.submitter_id,cases.samples.sample_id,analysis.workflow_type,cases.project.project_id,cases.samples.portions.analytes.aliquots.aliquot_id,cases.samples.portions.analytes.aliquots.submitter_id&size=1000"The result of calling ray.parseQuery(sampleObj) is
resultParseQuery = {
"fields": "file_id,file_name,cases.submitter_id,cases.case_id,data_category,data_type,cases.samples.tumor_descriptor,cases.samples.tissue_type,cases.samples.sample_type,cases.samples.submitter_id,cases.samples.sample_id,analysis.workflow_type,cases.project.project_id,cases.samples.portions.analytes.aliquots.aliquot_id,cases.samples.portions.analytes.aliquots.submitter_id",
"filters": "%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.submitter_id%22%2C%22value%22%3A%5B%22TCGA-CK-4948%22%2C%22TCGA-D1-A17N%22%2C%22TCGA-4V-A9QX%22%2C%22TCGA-4V-A9QM%22%5D%7D%7D%2C%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%22Gene%20Expression%20Quantification%22%7D%7D%5D%7D",
"format": "tsv",
"size": "1000"
}ray.tryParseJSON() returns the parsed object of the object-format string or the stringfied object by jsonString input. The function is called by ray.tryParseJSON(query) . The input string jsonString would directly return itself if jsonString is already an object. A sample input is
sampleJsonStr = "{"method":"cases","query":{"op":"and","content":[{"op":"in","content":{"field":"submitter_id","value":["TCGA-BH-A0EA"]}}]},"pretty":true}"The result of calling ray.parseJSON(sampleJsonStr) is
resultParseJSON = {
"method": "cases",
"query": {
"op": "and",
"content": [
{
"op": "in",
"content": {
"field": "submitter_id",
"value": [
"TCGA-BH-A0EA"
]
}
}
]
},
"pretty": true
}