The Cytobank API is a RESTful JSON web API that extends use of basic and advanced functionality of the Cytobank Cloud to any software application. Learn more about the Cytobank API.
\nThis v1 API endpoint reference documentation provides information and low-level instructions for access to each API endpoint via HTTP request. Higher level wrappers in programming languages such as R are available here.
\nIf an endpoint can't be found on this page it doesn't exist yet. The Cytobank API is under continuous development. Look for exciting releases in the near future. Get in contact with Cytobank Support to request additional endpoints or get beta access to new API functionality.
\nCytobank API endpoints are divided into different groups in this reference guide. These groups logically separate the different functionalities of Cytobank and the API endpoints that serve them. In order to find a functionality of interest, first consult the groups on the left for relevance. Click to expand a group in order to see the API endpoints inside it. Make sure to start with the Authentication section.
\nView an endpoint in this documentation for directions on how to access it via HTTP request and to read useful supporting information. The HTTP method (e.g. POST, GET, etc.), headers, example body, and example responses are shown where relevant.
\nCode snippets in a variety of programming languages are shown for each request. The language shown can be adjusted at the top right of this page. Copy the snippets and execute them in the desired language in order to try the API in a simple context. Please note that code snippets are automatically generated and it's possible that not every snippet will work in every language. The exception to this are requests in cURL, which are all expected to work.
\nCapitalized variables in double brackets, {{LIKE_THIS}}, should be replaced with actual values if examples from this documentation are being used directly. These bracketed variables appear throughout the documentation. For example:
\nhttps://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/authenticate
...would become...
https://YourCytobank.cytobank.org/cytobank/api/v1/authenticate
\"username\": \"{{user_name}}\", \"password\": \"{{userpassword}}\"
...would become...
\"username\": \"YourUsername\", \"password\": \"YourPassword\"
Currently the Cytobank API has a default rate limit of 100 requests per 1 minute. If this rate is exceeded the server will respond with a 429 status code and an error message about the rate limits. Requests are binned per minute according to the clock on the server.
\nThe Cytobank API will respond to requests with a HTTP status code and return content via JSON. In the case of an error, a status code will be accompanied by a useful message where possible. A variety of status codes are used and not all will be listed here. However, at a high level, anything in the 200 range indicates success, 400 range indicates a client-side error such as a malformatted request or disallowed operation, and 500 range indicates a server-side error. Keep in mind that Cytobank has a permissions framework that the API adheres to. If an error message of Not Authorized To Access Resource is encountered, double check the accessing account has proper access levels for the desired operation, or clone the experiment in question to make an accessible copy.
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Show a specific automatic gating analysis in an experiment.
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Update settings of an automatic gating analysis.
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\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","advanced_analyses","auto_gate_inference","{{ANALYSIS_ID}}"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[],"_postman_id":"a1c6196c-7d08-46fb-bbf5-38d4d4508f1f"},{"name":"Delete autogating analysis","id":"fac471ce-97dc-4f15-8b3d-d6ae4008e78f","protocolProfileBehavior":{"disableBodyPruning":true},"request":{"method":"DELETE","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"formdata","formdata":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/advanced_analyses/{{ANALYSIS_ID}}","description":"Delete an automatic gating analysis.
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List all dimensionality reduction analyses in an experiment of the specified type (tSNE-CUDA, opt-SNE, UMAP, or viSNE).
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The integers in the fileGrouping attribute reference the respective {{FILE_GROUP}} from the fileGroupNames attribute in the order in which they appear starting from 0.
POPULATION.GATE_SET_ID parameter in the gateSetId attribute is the gateSetId attribute value of the population on which to run CITRUS. Note that this argument is the gateSetId attribute of a population object and not the ID of the object itself. This secondary ID is experiment-specific and will be a smaller number. An argument of 0 corresponds to the ungated population, i.e., the raw data with no filtering applied. Another term for a population is a \"gate set\" because it's a set of gates (learn more).
The clusteringCharacterization attribute can have a value of \"medians\" or \"abundances\".
The plotTheme attribute can have a value of \"white\" or \"black\". This corresponds to the values of \"light\" and \"dark\" in the Cytobank web interface.
Delete a CITRUS analysis permanently.
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CHANNEL_ID parameters are the normalizedShortNameId attribute of the channels to run SPADE on. This information can be retrieved from the Panels endpoints.
downSampledEventsTarget attribute can have a value of either \"percent\" or \"absoluteNumber\" with a corollary numeric argument.
For analyses using fold change, all files in the experiment must be represented within a fold change group, and only within one group. Learn more about fold change setup.
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\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","attachments","{{ATTACHMENT_ID}}"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[],"_postman_id":"d2581fe7-b231-4c25-a928-54fe35db72c6"},{"name":"Delete Attachment","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 204\"] = responseCode.code === 204;",""]}}],"id":"37d23a74-ebdf-406d-9628-e62c3a37f3e9","request":{"method":"DELETE","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/attachments/{{ATTACHMENT_ID}}","description":"Delete an attachment from an Experiment.
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\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","logout"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[],"_postman_id":"6819b49f-6125-422a-9650-20ad5094c051"},{"name":"Revoke All Tokens","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;","","tests[\"Body contains successful revoked all tokens message\"] = responseBody.has(\"All issued tokens has been successfully revoked.\");"]}}],"id":"7f4dcada-36aa-4c8e-8fa8-ea1dc5107f12","request":{"method":"POST","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/revoke_tokens","description":"Invalidate all existing tokens for the user making this call.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","revoke_tokens"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[],"_postman_id":"7f4dcada-36aa-4c8e-8fa8-ea1dc5107f12"},{"name":"Revoke all Tokens for any User (Admin only)","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;","","tests[\"Body contains successful revoked user's all tokens message\"] = responseBody.has(\"All issued tokens forEvery call to the Cytobank API must be accompanied by an authentication token. Tokens are generated from the Authenticate API endpoint with a username and password, or on a user profile page within Cytobank. Tokens should be kept secure as they confer access to the data and analyses of an account.
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\n","_postman_id":"560dc130-9be2-43e5-8c9c-25b12ff633bc"},{"name":"Compensations","item":[{"name":"List Compensations for Experiment","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"]}}],"id":"e3d92ccd-3e86-4a8e-80e3-dff30d6aacb8","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/compensations","description":"List compensations in an Experiment.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","compensations"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[{"id":"f3d47b43-8cc7-44af-b01e-78790ad6c237","name":"List Compensations for Experiment","originalRequest":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/compensations"},"status":"OK","code":200,"_postman_previewlanguage":"","header":[],"cookie":[],"responseTime":null,"body":"{\n \"compensations\": [\n {\n \"id\": 151,\n \"name\": \"Example Comp\",\n \"sources\": [\n {\n \"name\": \"Ax488-A\",\n \"id\": 36,\n \"shortName\": \"Ax488-A\"\n },\n {\n \"name\": \"PE-A\",\n \"id\": 7,\n \"shortName\": \"PE-A\"\n },\n {\n \"name\": \"PerCP-Cy55-A\",\n \"id\": 38,\n \"shortName\": \"PerCP-Cy55-A\"\n },\n {\n \"name\": \"PE-Cy7-A\",\n \"id\": 9,\n \"shortName\": \"PE-Cy7-A\"\n },\n {\n \"name\": \"Ax647-A\",\n \"id\": 39,\n \"shortName\": \"Ax647-A\"\n },\n {\n \"name\": \"PacBlu-A\",\n \"id\": 42,\n \"shortName\": \"PacBlu-A\"\n }\n ],\n \"detectors\": [\n {\n \"name\": \"Ax488-A\",\n \"id\": 36,\n \"shortName\": \"Ax488-A\"\n },\n {\n \"name\": \"PE-A\",\n \"id\": 7,\n \"shortName\": \"PE-A\"\n },\n {\n \"name\": \"PerCP-Cy55-A\",\n \"id\": 38,\n \"shortName\": \"PerCP-Cy55-A\"\n },\n {\n \"name\": \"PE-Cy7-A\",\n \"id\": 9,\n \"shortName\": \"PE-Cy7-A\"\n },\n {\n \"name\": \"Ax647-A\",\n \"id\": 39,\n \"shortName\": \"Ax647-A\"\n },\n {\n \"name\": \"PacBlu-A\",\n \"id\": 42,\n \"shortName\": \"PacBlu-A\"\n }\n ],\n \"compensationMatrix\": [\n [\n 1,\n 0.2986,\n 0.0165,\n 0,\n 0,\n 0\n ],\n [\n 0.007,\n 1,\n 0.0726,\n 0.0055,\n 0,\n 0.0017\n ],\n [\n 0,\n 0.0006,\n 1,\n 0.134,\n 0.0495,\n 0.012\n ],\n [\n 0.0023,\n 0.0703,\n 0.015,\n 1,\n 0,\n 0.0034\n ],\n [\n 0,\n 0.0005,\n 0.0039,\n 0.0004,\n 1,\n 0\n ],\n [\n 0.0026,\n 0.002,\n 0,\n 0,\n 0,\n 1\n ]\n ],\n \"experimentId\": 10559,\n \"createdAt\": \"2016-07-26T22:02:09Z\",\n \"updatedAt\": \"2016-07-26T22:02:46Z\",\n \"creationMethodType\": 0\n },\n {\n \"id\": 152,\n \"name\": \"Example Comp 2\",\n \"sources\": [\n {\n \"name\": \"Ax488-A\",\n \"id\": 36,\n \"shortName\": \"Ax488-A\"\n },\n {\n \"name\": \"PE-A\",\n \"id\": 7,\n \"shortName\": \"PE-A\"\n },\n {\n \"name\": \"PerCP-Cy55-A\",\n \"id\": 38,\n \"shortName\": \"PerCP-Cy55-A\"\n },\n {\n \"name\": \"PE-Cy7-A\",\n \"id\": 9,\n \"shortName\": \"PE-Cy7-A\"\n },\n {\n \"name\": \"Ax647-A\",\n \"id\": 39,\n \"shortName\": \"Ax647-A\"\n },\n {\n \"name\": \"PacBlu-A\",\n \"id\": 42,\n \"shortName\": \"PacBlu-A\"\n }\n ],\n \"detectors\": [\n {\n \"name\": \"Ax488-A\",\n \"id\": 36,\n \"shortName\": \"Ax488-A\"\n },\n {\n \"name\": \"PE-A\",\n \"id\": 7,\n \"shortName\": \"PE-A\"\n },\n {\n \"name\": \"PerCP-Cy55-A\",\n \"id\": 38,\n \"shortName\": \"PerCP-Cy55-A\"\n },\n {\n \"name\": \"PE-Cy7-A\",\n \"id\": 9,\n \"shortName\": \"PE-Cy7-A\"\n },\n {\n \"name\": \"Ax647-A\",\n \"id\": 39,\n \"shortName\": \"Ax647-A\"\n },\n {\n \"name\": \"PacBlu-A\",\n \"id\": 42,\n \"shortName\": \"PacBlu-A\"\n }\n ],\n \"compensationMatrix\": [\n [\n 1,\n 0.2986,\n 0.0165,\n 0,\n 0,\n 0\n ],\n [\n 0.007,\n 1,\n 0.0726,\n 0.0055,\n 0,\n 0.0017\n ],\n [\n 0,\n 0.0006,\n 1,\n 0.134,\n 0.0495,\n 0.012\n ],\n [\n 0.0023,\n 0.0703,\n 0.015,\n 1,\n 0,\n 0.0034\n ],\n [\n 0,\n 0.0005,\n 0.0039,\n 0.0004,\n 1,\n 0\n ],\n [\n 0.0026,\n 0.002,\n 0,\n 0,\n 0,\n 1\n ]\n ],\n \"experimentId\": 10559,\n \"createdAt\": \"2016-07-26T22:02:48Z\",\n \"updatedAt\": \"2016-07-26T22:02:53Z\",\n \"creationMethodType\": 0\n }\n ]\n}"}],"_postman_id":"e3d92ccd-3e86-4a8e-80e3-dff30d6aacb8"},{"name":"Show Compensation Details","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"]}}],"id":"b60d3257-150d-426e-867f-b43d5e7f7c6b","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/compensations/{{COMP_ID}}","description":"Show details for a compensation.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","compensations","{{COMP_ID}}"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[{"id":"2956c751-390a-4811-a18d-19f7f55f2e4e","name":"Show Compensation Details","originalRequest":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/compensations/151"},"status":"OK","code":200,"_postman_previewlanguage":"javascript","header":[{"name":"Cache-Control","key":"Cache-Control","value":"max-age=0, private, must-revalidate","description":"","enabled":true},{"name":"Connection","key":"Connection","value":"keep-alive","description":"","enabled":true},{"name":"Content-Length","key":"Content-Length","value":"1020","description":"","enabled":true},{"name":"Content-Type","key":"Content-Type","value":"application/json;charset=utf-8","description":"","enabled":true},{"name":"Date","key":"Date","value":"Fri, 29 Jul 2016 06:41:05 GMT","description":"","enabled":true},{"name":"ETag","key":"ETag","value":"\"fb9f35ee7579235a68b06c711ecefbec\"","description":"","enabled":true},{"name":"Server","key":"Server","value":"Apache-Coyote/1.1","description":"","enabled":true},{"name":"Strict-Transport-Security","key":"Strict-Transport-Security","value":"max-age=31622400; includeSubDomains","description":"","enabled":true},{"name":"X-Runtime","key":"X-Runtime","value":"0.611000","description":"","enabled":true},{"name":"X-UA-Compatible","key":"X-UA-Compatible","value":"IE=Edge,chrome=1","description":"","enabled":true}],"cookie":[{"expires":"Invalid Date","hostOnly":true,"httpOnly":true,"domain":"ucsf.cytobank.org","path":"/","secure":true,"session":true,"value":"7a59662ea89b04bd926eb9a5c1322b87"}],"responseTime":null,"body":"{\n \"compensation\": {\n \"id\": 151,\n \"name\": \"Example Comp\",\n \"sources\": [\n {\n \"name\": \"Ax488-A\",\n \"id\": 36,\n \"shortName\": \"Ax488-A\"\n },\n {\n \"name\": \"PE-A\",\n \"id\": 7,\n \"shortName\": \"PE-A\"\n },\n {\n \"name\": \"PerCP-Cy55-A\",\n \"id\": 38,\n \"shortName\": \"PerCP-Cy55-A\"\n },\n {\n \"name\": \"PE-Cy7-A\",\n \"id\": 9,\n \"shortName\": \"PE-Cy7-A\"\n },\n {\n \"name\": \"Ax647-A\",\n \"id\": 39,\n \"shortName\": \"Ax647-A\"\n },\n {\n \"name\": \"PacBlu-A\",\n \"id\": 42,\n \"shortName\": \"PacBlu-A\"\n }\n ],\n \"detectors\": [\n {\n \"name\": \"Ax488-A\",\n \"id\": 36,\n \"shortName\": \"Ax488-A\"\n },\n {\n \"name\": \"PE-A\",\n \"id\": 7,\n \"shortName\": \"PE-A\"\n },\n {\n \"name\": \"PerCP-Cy55-A\",\n \"id\": 38,\n \"shortName\": \"PerCP-Cy55-A\"\n },\n {\n \"name\": \"PE-Cy7-A\",\n \"id\": 9,\n \"shortName\": \"PE-Cy7-A\"\n },\n {\n \"name\": \"Ax647-A\",\n \"id\": 39,\n \"shortName\": \"Ax647-A\"\n },\n {\n \"name\": \"PacBlu-A\",\n \"id\": 42,\n \"shortName\": \"PacBlu-A\"\n }\n ],\n \"compensationMatrix\": [\n [\n 1,\n 0.2986,\n 0.0165,\n 0,\n 0,\n 0\n ],\n [\n 0.007,\n 1,\n 0.0726,\n 0.0055,\n 0,\n 0.0017\n ],\n [\n 0,\n 0.0006,\n 1,\n 0.134,\n 0.0495,\n 0.012\n ],\n [\n 0.0023,\n 0.0703,\n 0.015,\n 1,\n 0,\n 0.0034\n ],\n [\n 0,\n 0.0005,\n 0.0039,\n 0.0004,\n 1,\n 0\n ],\n [\n 0.0026,\n 0.002,\n 0,\n 0,\n 0,\n 1\n ]\n ],\n \"experimentId\": 10559,\n \"createdAt\": \"2016-07-26T22:02:09Z\",\n \"updatedAt\": \"2016-07-26T22:02:46Z\",\n \"creationMethodType\": 0\n }\n}"}],"_postman_id":"b60d3257-150d-426e-867f-b43d5e7f7c6b"},{"name":"Upload Compensation CSV","id":"2225eac3-ab5f-4ca1-b106-167c9370ca46","request":{"method":"POST","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"formdata","formdata":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/upload_compensation_matrix","description":"Upload a compensation CSV to an Experiment.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","upload_compensation_matrix"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[{"id":"628cbc47-0e1d-4853-87eb-3b9e4e180518","name":"Upload Compensation CSV","originalRequest":{"method":"POST","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"formdata","formdata":[{"key":"file","value":"@{{FILE_NAME}}","type":"text"}]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/upload_compensation_matrix"},"status":"OK","code":200,"_postman_previewlanguage":"","header":[],"cookie":[],"responseTime":null,"body":"{\n \"message\": \"Successfully imported compensation from uploaded file test_comp.csv\"\n}"}],"_postman_id":"2225eac3-ab5f-4ca1-b106-167c9370ca46"}],"id":"a6096811-d655-44e5-8cf3-8c0ca9957ea1","description":"Get information about compensations stored in Cytobank with these endpoints. For information about file-internal compensation for an individual FCS file, consult the FCS Files endpoints. Learn more about compensation in Cytobank.
\n","_postman_id":"a6096811-d655-44e5-8cf3-8c0ca9957ea1"},{"name":"DROP","item":[{"name":"[Deprecated] Upload FCS File (CSV to FCS) - Refer to Files Upload & Download/Upload","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;","tests[\"HSTS header is present\"] = postman.getResponseHeader(\"Strict-Transport-Security\") === \"max-age=31622400; includeSubDomains\";","var data = JSON.parse(responseBody);","tests[\"Successfully uploaded fcs file\"] = data.fcsFiles.length >= 1 && responseBody !== \"\";","if (data.fcsFiles[0].filename === \"comp_percp_cy55.fcs\"){"," for (var i = 0; i < data.fcsFiles.length; i++){"," data.fcsFiles[i].id = null;"," data.fcsFiles[i].experimentId = null;"," data.fcsFiles[i].createdAt = null;"," data.fcsFiles[i].updatedAt = null;"," data.fcsFiles[i].experimentName = null;"," }"," var respBody = JSON.stringify(data);"," if (typeof environment.gold_std_pbmc_fcsFile_cy55_upload === 'undefined' || environment.gold_std_pbmc_fcsFile_cy55_upload === \"\"){"," postman.setEnvironmentVariable(\"gold_std_pbmc_fcsFile_cy55_upload\", respBody);"," }"," tests[\"Body matches gold standard data\"] = respBody === environment.gold_std_pbmc_fcsFile_cy55_upload;","}"]}}],"id":"4ed7663b-c654-4a44-aa35-e53a098602ba","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{user_jwt}}"}],"body":{"mode":"formdata","formdata":[{"key":"file","type":"file","value":null,"warning":"","description":"Can upload CSV/TSV/TXT/FCS
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151,\n \"gateId\": 17,\n \"fcsFileId\": null,\n \"createdAt\": \"2016-07-27T02:31:57Z\",\n \"updatedAt\": \"2016-07-27T02:31:57Z\",\n \"definition\": {\n \"scale\": {\n \"flag\": 4,\n \"argument\": \"150\",\n \"min\": -200,\n \"max\": 262144,\n \"bins\": 256,\n \"size\": 256\n },\n \"positive\": false,\n \"negative\": false,\n \"label\": [\n 1.943562680744588,\n 0.48888888888888893\n ],\n \"range\": {\n \"x1\": 0.9069780023473097,\n \"x2\": 3.051635957652019,\n \"y\": 0.4571428571428572\n }\n },\n \"xShortName\": \"ax488-a\"\n }\n ]\n}"}],"_postman_id":"08a8bde4-69a1-4a85-a74d-09d2c47b6457"},{"name":"Show Gate Details","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"]}}],"id":"bb48bd11-e6e1-4802-89c3-95f200d80064","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/gates/{{GATE_ID}}","description":"Show details for a gate in an Experiment. The gate ID passed in the request is the value of the id attribute of the gate and not the gate_id attribute.
List populations (aka gate sets) for an Experiment. Currently only the Scratch Populations from the gating interface are returned. These have a version of -1. This is to be contrasted with Experiment Populations, which will have a version number that is a positive integer equal to the number of times the version has been incremented in the gating interface. Learn more about gate versioning in Cytobank. The same principle applies to populations.
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Pass the value for the id attribute of the population and not the gateSetId attribute.
Download gates via Gating-ML for an Experiment. Learn more about Gating-ML.
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\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","upload_gatingml"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[],"_postman_id":"18b8b6d0-0bb4-4678-b2f1-3f1fb701da7e"},{"name":"Apply Gates","id":"eebe3381-53ae-435e-a69a-cd703f4eba73","protocolProfileBehavior":{"disableBodyPruning":true},"request":{"method":"POST","header":[],"body":{"mode":"raw","raw":"{\n \"experiment\": \n { \n \"gateVersion\": 0\n }\n}","options":{"raw":{"language":"json"}}},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/apply_gates","description":"\"Apply gates\", by saving current scratch gates. See details on this concept here.
\nRequest body must specify the current gate version, to prevent multiple simultaneous users from interfering with each other's changes. Current gate version can be found via 'Show experiment details' endpoint.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","apply_gates"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[{"id":"961d3dca-3e29-4877-abdf-1011c606f808","name":"Apply Gates","originalRequest":{"method":"POST","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}","type":"text"},{"key":"Content-Type","name":"Content-Type","value":"application/json","type":"text"}],"body":{"mode":"raw","raw":"{\n \"experiment\":\n {\n \"gateVersion\": 1\n }\n}","options":{"raw":{"language":"json"}}},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/apply_gates"},"status":"OK","code":200,"_postman_previewlanguage":"json","header":null,"cookie":[],"responseTime":null,"body":"{\n \"gateVersion\": 1\n}"}],"_postman_id":"eebe3381-53ae-435e-a69a-cd703f4eba73"}],"id":"64e000fd-8813-4be5-b2f3-da74894f6a31","description":"In Cytobank there is a distinction between gates and populations. A gate is simply a shape drawn on a plot. A population is a set of gates and can have parents and children. Learn more about gates and populations.
\nCurrently gate and population information can only be read and not written to Cytobank via the JSON API. To write gates and populations to Cytobank via the API, the Upload Gating-ML endpoint should be used.
\n","_postman_id":"64e000fd-8813-4be5-b2f3-da74894f6a31"},{"name":"Panels","item":[{"name":"List Panels for Experiment","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;",""]}}],"id":"2973439c-3ac5-4f34-8061-bec554326bea","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/panels","description":"List panels in an Experiment and associated details.
\nThe object returned is an array of panels. Each panel has an id, name, array of channels, array of files that are in the panel, and a panelChannelMappings object. Each file will only appear in one (or zero) panels. The panelChannelMappings object gives information about the order that the channels appear within files within panels, because groups of files within the same panel could have channels in different orders. While potentially critical for index-based operations on features within FCS files on a local computer, no operations via the Cytobank API will rely on this ordering information and thus this nested object can be ignored.
Various functions of the Cytobank API will require a mastery of using the list of panels and nested arrays of channels and files. Many Cytobank API endpoints take an argument of normalizedShortNameId (a numeric proxy for the shortName), which is an attribute of a channel, and describes unambiguously which column of data to operate on for a given file. The longName of the channel is not guaranteed to be unique within a panel, although it usually is. Typically the longName is the starting point for analysis. Consider fetching statistics, for example. The objective might be to fetch median intensity of CD8+ T cells on the pSTAT3 channel in a particular named file. The Statistics endpoint requires id attributes for all these components to return statistics. The Gates and Populations and FCS Files endpoints would be used to get the id and gateSetId attribute for their respective components. Next, the normalizedShortNameId is needed for pSTAT3. This is obtained by first fetching panel information from this endpoint. Next, the arrays of file ids are searched to establish which panel the file is in. When the panel is found, its list of channels is searched by longName for pSTAT3. This gives a normalizedShortNameId and the key to submitting the statistics request.
Show details for a panel in an Experiment.
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\"Ax488-A\",\n \"longName\": \"pStat3\",\n \"normalizedShortNameId\": 36,\n \"fcsFileChannelIndex\": 3\n },\n {\n \"shortName\": \"Ax647-A\",\n \"longName\": \"pp38\",\n \"normalizedShortNameId\": 39,\n \"fcsFileChannelIndex\": 8\n },\n {\n \"shortName\": \"Ax700-A\",\n \"longName\": \"Ax700-A\",\n \"normalizedShortNameId\": 40,\n \"fcsFileChannelIndex\": 9\n },\n {\n \"shortName\": \"Ax750-A\",\n \"longName\": \"Ax750-A\",\n \"normalizedShortNameId\": 41,\n \"fcsFileChannelIndex\": 10\n },\n {\n \"shortName\": \"FSC-A\",\n \"longName\": \"FSC-A\",\n \"normalizedShortNameId\": 1,\n \"fcsFileChannelIndex\": 0\n },\n {\n \"shortName\": \"FSC-W\",\n \"longName\": \"FSC-W\",\n \"normalizedShortNameId\": 2,\n \"fcsFileChannelIndex\": 1\n },\n {\n \"shortName\": \"PacBlu-A\",\n \"longName\": \"CD4\",\n \"normalizedShortNameId\": 42,\n \"fcsFileChannelIndex\": 11\n },\n {\n \"shortName\": \"PacOrange-A\",\n \"longName\": \"PacOrange-A\",\n \"normalizedShortNameId\": 44,\n \"fcsFileChannelIndex\": 13\n },\n {\n \"shortName\": \"PE-A\",\n \"longName\": \"CD33\",\n \"normalizedShortNameId\": 7,\n \"fcsFileChannelIndex\": 4\n },\n {\n \"shortName\": \"PE-Cy7-A\",\n \"longName\": \"CD3\",\n \"normalizedShortNameId\": 9,\n \"fcsFileChannelIndex\": 7\n },\n {\n \"shortName\": \"PE-TR-A\",\n \"longName\": \"PE-TR-A\",\n \"normalizedShortNameId\": 37,\n \"fcsFileChannelIndex\": 5\n },\n {\n \"shortName\": \"PerCP-Cy55-A\",\n \"longName\": \"CD20\",\n \"normalizedShortNameId\": 38,\n \"fcsFileChannelIndex\": 6\n },\n {\n \"shortName\": \"Qdot525-A\",\n \"longName\": \"Qdot525-A\",\n \"normalizedShortNameId\": 43,\n \"fcsFileChannelIndex\": 12\n },\n {\n \"shortName\": \"Qdot605-A\",\n \"longName\": \"Qdot605-A\",\n \"normalizedShortNameId\": 45,\n \"fcsFileChannelIndex\": 14\n },\n {\n \"shortName\": \"Qdot655-A\",\n \"longName\": \"Qdot655-A\",\n \"normalizedShortNameId\": 46,\n \"fcsFileChannelIndex\": 15\n },\n {\n \"shortName\": \"Qdot705-A\",\n \"longName\": \"Qdot705-A\",\n \"normalizedShortNameId\": 47,\n \"fcsFileChannelIndex\": 16\n },\n {\n \"shortName\": \"SSC-A\",\n \"longName\": \"SSC-A\",\n \"normalizedShortNameId\": 4,\n \"fcsFileChannelIndex\": 2\n },\n {\n \"shortName\": \"Time\",\n \"longName\": \"Time\",\n \"normalizedShortNameId\": 12,\n \"fcsFileChannelIndex\": 17\n }\n ],\n \"fcsFiles\": [\n 209014,\n 209015,\n 209016,\n 209017\n ],\n \"panelChannelMappings\": {\n \"uniqueChannelOrders\": [\n [\n {\n \"id\": 1770310,\n \"shortName\": \"FSC-A\",\n \"longName\": \"FSC-A\",\n \"normalizedShortNameId\": 1,\n \"fcsFileChannelIndex\": 0\n },\n {\n \"id\": 1770311,\n \"shortName\": \"FSC-W\",\n \"longName\": \"FSC-W\",\n \"normalizedShortNameId\": 2,\n \"fcsFileChannelIndex\": 1\n },\n {\n \"id\": 1770312,\n \"shortName\": \"SSC-A\",\n \"longName\": \"SSC-A\",\n \"normalizedShortNameId\": 4,\n \"fcsFileChannelIndex\": 2\n },\n {\n \"id\": 1770313,\n \"shortName\": \"Ax488-A\",\n \"longName\": \"pStat3\",\n \"normalizedShortNameId\": 36,\n \"fcsFileChannelIndex\": 3\n },\n {\n \"id\": 1770314,\n \"shortName\": \"PE-A\",\n \"longName\": \"CD33\",\n \"normalizedShortNameId\": 7,\n \"fcsFileChannelIndex\": 4\n },\n {\n \"id\": 1770315,\n \"shortName\": \"PE-TR-A\",\n \"longName\": \"PE-TR-A\",\n \"normalizedShortNameId\": 37,\n \"fcsFileChannelIndex\": 5\n },\n {\n \"id\": 1770316,\n \"shortName\": \"PerCP-Cy55-A\",\n \"longName\": \"CD20\",\n \"normalizedShortNameId\": 38,\n \"fcsFileChannelIndex\": 6\n },\n {\n \"id\": 1770317,\n \"shortName\": \"PE-Cy7-A\",\n \"longName\": \"CD3\",\n \"normalizedShortNameId\": 9,\n \"fcsFileChannelIndex\": 7\n },\n {\n \"id\": 1770318,\n \"shortName\": \"Ax647-A\",\n \"longName\": \"pp38\",\n \"normalizedShortNameId\": 39,\n \"fcsFileChannelIndex\": 8\n },\n {\n \"id\": 1770319,\n \"shortName\": \"Ax700-A\",\n \"longName\": \"Ax700-A\",\n \"normalizedShortNameId\": 40,\n \"fcsFileChannelIndex\": 9\n },\n {\n \"id\": 1770320,\n \"shortName\": 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Learn more about panels in Cytobank.
\n","_postman_id":"1237a672-1286-4d20-9b95-e804fa82ed64"},{"name":"Sample Tags","item":[{"name":"Download Sample Tags","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"]}}],"id":"0436949e-f809-4b6d-856f-3a28cecd24ea","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/download_sample_tags","description":"Download sample tags from an Experiment as a TSV (tab separated values) table file. Learn more about exporting and importing sample tags.
\nCurrently there is no JSON support for Sample Tags and the information can only be exchanged via file.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","download_sample_tags"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[],"_postman_id":"0436949e-f809-4b6d-856f-3a28cecd24ea"},{"name":"Upload sample tags to an Experiment","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"]}}],"id":"ecec1ea5-7633-462e-9db3-172f7b6044bb","request":{"method":"POST","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"formdata","formdata":[{"key":"file","type":"text","value":"@{{FILE_NAME}}"}]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/upload_sample_tags","description":"Upload sample tags to an Experiment. Sample tags should be in the form of a TSV (tab separated values) table file, which can be sourced from the Download Sample Tags endpoint. Learn more about importing and exporting sample tags.
\nCurrently there is no JSON support for Sample Tags and the information can only be exchanged via file.
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\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","scales"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[{"id":"044ca2b4-2999-4aed-a428-88f845d848e8","name":"List Scales for Experiment","originalRequest":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/10559/scales"},"status":"OK","code":200,"_postman_previewlanguage":"javascript","header":[{"name":"Cache-Control","key":"Cache-Control","value":"max-age=0, private, must-revalidate","description":"","enabled":true},{"name":"Connection","key":"Connection","value":"keep-alive","description":"","enabled":true},{"name":"Content-Type","key":"Content-Type","value":"application/json;charset=utf-8","description":"","enabled":true},{"name":"Date","key":"Date","value":"Wed, 27 Jul 2016 02:50:06 GMT","description":"","enabled":true},{"name":"ETag","key":"ETag","value":"\"02153475f0bd49a74592fd6d9173ca65\"","description":"","enabled":true},{"name":"Server","key":"Server","value":"Apache-Coyote/1.1","description":"","enabled":true},{"name":"Strict-Transport-Security","key":"Strict-Transport-Security","value":"max-age=31622400; 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\nA scale type of 1 is linear. 2 is log. 4 is arcsinh.
\n","_postman_id":"81d2476c-a77c-4f98-9f17-a961f29457ee"},{"name":"Sharing","item":[{"name":"List Full Access Users for Experiment","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;",""]}}],"id":"09bc0111-2a4b-4282-ac61-a65b671481be","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/full_access_users","description":"List all full access users in an experiment.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","full_access_users"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[{"id":"8cd03c94-6321-4643-90cf-03569ce28227","name":"List Full Access Users for Experiment","originalRequest":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/full_access_users"},"status":"OK","code":200,"_postman_previewlanguage":"","header":[],"cookie":[],"responseTime":null,"body":"{\n \"experiment\": {\n \"full_access_users\": [\n {\n \"id\": 43,\n \"name\": \"Cytobank Support\",\n \"email\": \"redacted@cytobank.org\"\n },\n {\n \"id\": 102,\n \"name\": \"Cyril Cytometry\",\n \"email\": \"redacted@cytobank.org\"\n }\n ]\n }\n}"}],"_postman_id":"09bc0111-2a4b-4282-ac61-a65b671481be"},{"name":"Add Full Access User to Experiment","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"]}}],"id":"6ce79301-bf24-4370-b3e1-761766a0c239","request":{"method":"POST","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"},{"key":"Content-Type","value":"application/json"}],"body":{"mode":"raw","raw":"{\n \"experiment\":\n {\n \"userId\": {{FULL_ACCESS_USER_ID}}\n }\n}"},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/add_full_access_user","description":"Add a full access user to an experiment.
\nUsers can be added by using one of the following fields:
\nuserIduserNameuserEmailRemove a full access user from an experiment.
\nUsers can be removed by using one of the following fields:
\nuserIduserNameuserEmailOne should never analyze alone... Learn more about sharing and collaboration in Cytobank.
\n","_postman_id":"01c29dfb-4350-4f30-bed1-885c3aa3e78a"},{"name":"Statistics","item":[{"name":"Show General Statistics","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;",""]}}],"id":"637c2d98-e513-4f9c-bb23-de2a8aeb7caa","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/statistics?experimentId={{EXPT_ID}}&gateVersion={{GATE_VERSION}}&experimentVersion={{EXPT_VERSION}}&compensationId={{COMP_ID}}&fcsFileIds={{FCS_FILE_ID_1}}&fcsFileIds={{FCS_FILE_ID_2}}&channelIds={{CHANNEL_ID_1}}&channelIds={{CHANNEL_ID_2}}&gateSetIds={{POPULATION_ID_1}}&gateSetIds={{POPULATION_ID_2}}","description":"Retrieve a batch of common statistics for an Experiment.
\nParameter Details:
\nEXPT_VERSION must be set to the current version of the Experiment, which can be seen as the version attribute returned from a call to the Show Experiment Details endpoint.GATE_VERSION of -1 corresponds to the state of gates and populations in the gating interface. Faster performance can be achieved by using the maximum gate version from the experiment (learn more about gate versions). Maximum gate version can be seen as the gateVersion attribute returned from a call to the Show Experiment Details endpoint.COMP_ID is the ID of the compensation to apply to the statistics. Use -2 for file-internal compensation. Use -1 for uncompensated.FCS_FILE_ID parameters are the IDs of FCS files to calculate statistics on. Multiple are permitted.CHANNEL_ID parameters are the normalizedShortNameId attribute of the channels to calculate statistics on. This information can be retrieved from the Panels endpoints.POPULATION.GATE_SET_ID parameters are the gateSetId attribute values of the populations to calculate statistics for. Multiple are permitted. Note that this argument is the gateSetId attribute of a population object and not the ID of the object itself. This secondary ID is experiment-specific and will be a smaller number. An argument of 0 corresponds to the ungated population, i.e., the raw data with no filtering applied. Another term for a population is a \"gate set\" because it's a set of gates (learn more).The minimum parameters to receive a response are EXPT_VERSION, GATE_VERSION, COMP_ID, EXPT_ID, and FCS_FILE_ID. Without POPULATION.GATE_SET_ID then statistics will be returned for all populations. Without CHANNEL_ID then only event counts will be returned.
When submitting a single request with multiple files and channels, make sure that all the channels appear within all the files. An error will result otherwise.
\nReturned data:
\nStatistics returned include event count, minimum, maximum, mean, median, variance, standard deviation, and 2nd/98th percentile.
\nResults objects will be returned for each file by each population in the Experiment. Within each results object, results for multiple channels are keyed on the normalizedShortNameId attribute within each statistic type. The short name and long name that correspond to this ID can be deciphered using panel information from the Panels API endoints.
\nPerformance note:
\nWhile this endpoint accepts multiple parameters at once, for large datasets it may be necessary to send multiple requests to avoid client timeouts. Also note that if only event counts are being fetched then optimizations can be made for a faster request (see Show Event Count Statistics endpoint below).
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","statistics"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[{"key":"experimentId","value":"{{EXPT_ID}}"},{"key":"gateVersion","value":"{{GATE_VERSION}}"},{"key":"experimentVersion","value":"{{EXPT_VERSION}}"},{"key":"compensationId","value":"{{COMP_ID}}"},{"key":"fcsFileIds","value":"{{FCS_FILE_ID_1}}"},{"key":"fcsFileIds","value":"{{FCS_FILE_ID_2}}"},{"key":"channelIds","value":"{{CHANNEL_ID_1}}"},{"key":"channelIds","value":"{{CHANNEL_ID_2}}"},{"key":"gateSetIds","value":"{{POPULATION_ID_1}}"},{"key":"gateSetIds","value":"{{POPULATION_ID_2}}"}],"variable":[]}},"response":[{"id":"34d8c512-a33a-401c-859b-8c071e37acd5","name":"Show General Statistics","originalRequest":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":{"raw":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/statistics?experimentId={{EXPT_ID}}&gateVersion={{GATE_VERSION}}&experimentVersion={{EXPT_VERSION}}&compensationId={{COMP_ID}}&fcsFileIds={{FCS_FILE_ID_1}}&fcsFileIds={{FCS_FILE_ID_2}}&channelIds={{CHANNEL_ID_1}}&channelIds={{CHANNEL_ID_2}}&gateSetIds={{POPULATION.GATE_SET_ID_1}}&gateSetIds={{POPULATION.GATE_SET_ID_2}}","protocol":"https","host":["{{CYTOBANK}}","cytobank","org"],"path":["cytobank","api","v1","statistics"],"query":[{"key":"experimentId","value":"{{EXPT_ID}}"},{"key":"gateVersion","value":"{{GATE_VERSION}}"},{"key":"experimentVersion","value":"{{EXPT_VERSION}}"},{"key":"compensationId","value":"{{COMP_ID}}"},{"key":"fcsFileIds","value":"{{FCS_FILE_ID_1}}"},{"key":"fcsFileIds","value":"{{FCS_FILE_ID_2}}"},{"key":"channelIds","value":"{{CHANNEL_ID_1}}"},{"key":"channelIds","value":"{{CHANNEL_ID_2}}"},{"key":"gateSetIds","value":"{{POPULATION.GATE_SET_ID_1}}"},{"key":"gateSetIds","value":"{{POPULATION.GATE_SET_ID_2}}"}]}},"status":"OK","code":200,"_postman_previewlanguage":"javascript","header":[{"name":"Cache-Control","key":"Cache-Control","value":"nocache","description":"","enabled":true},{"name":"Connection","key":"Connection","value":"keep-alive","description":"","enabled":true},{"name":"Content-Length","key":"Content-Length","value":"2610","description":"","enabled":true},{"name":"Content-Type","key":"Content-Type","value":"application/json;charset=utf-8","description":"","enabled":true},{"name":"Date","key":"Date","value":"Wed, 27 Jul 2016 05:07:04 GMT","description":"","enabled":true},{"name":"Server","key":"Server","value":"Apache-Coyote/1.1","description":"","enabled":true},{"name":"Strict-Transport-Security","key":"Strict-Transport-Security","value":"max-age=31622400; includeSubDomains","description":"","enabled":true},{"name":"X-Content-Type-Options","key":"X-Content-Type-Options","value":"nosniff","description":"","enabled":true},{"name":"X-Frame-Options","key":"X-Frame-Options","value":"DENY","description":"","enabled":true},{"name":"X-XSS-Protection","key":"X-XSS-Protection","value":"1; mode=block","description":"","enabled":true}],"cookie":[{"expires":"Invalid Date","hostOnly":true,"httpOnly":true,"domain":"ucsf.cytobank.org","path":"/","secure":true,"session":true,"value":"106fc2868543ffd5979d985305fb6dec"}],"responseTime":null,"body":"[\n {\n \"populationIdentifierKey\": \"209014,10559,32,[3],-1,-1,,30,popid\",\n \"experimentId\": 10559,\n \"gateVersion\": -1,\n \"compensationId\": -1,\n \"fcsFileId\": 209014,\n \"gateSetId\": 3,\n \"eventCount\": 38420,\n \"minimums\": {},\n \"maximums\": {},\n \"means\": {},\n \"medians\": {},\n \"variances\": {},\n \"standardDeviations\": {},\n \"secondPercentiles\": {},\n \"ninetyEighthPercentiles\": {},\n \"channelShortNameIds\": []\n },\n {\n \"populationIdentifierKey\": \"209014,10559,32,[4],-1,-1,,30,popid\",\n \"experimentId\": 10559,\n \"gateVersion\": -1,\n \"compensationId\": -1,\n \"fcsFileId\": 209014,\n \"gateSetId\": 4,\n \"eventCount\": 43643,\n \"minimums\": {},\n \"maximums\": {},\n \"means\": {},\n \"medians\": {},\n \"variances\": {},\n \"standardDeviations\": {},\n \"secondPercentiles\": {},\n \"ninetyEighthPercentiles\": {},\n \"channelShortNameIds\": []\n },\n {\n \"populationIdentifierKey\": \"209015,10559,32,[3],-1,-1,,30,popid\",\n \"experimentId\": 10559,\n \"gateVersion\": -1,\n \"compensationId\": -1,\n \"fcsFileId\": 209015,\n \"gateSetId\": 3,\n \"eventCount\": 36455,\n \"minimums\": {},\n \"maximums\": {},\n \"means\": {},\n \"medians\": {},\n \"variances\": {},\n \"standardDeviations\": {},\n \"secondPercentiles\": {},\n \"ninetyEighthPercentiles\": {},\n \"channelShortNameIds\": []\n },\n {\n \"populationIdentifierKey\": \"209015,10559,32,[4],-1,-1,,30,popid\",\n \"experimentId\": 10559,\n \"gateVersion\": -1,\n \"compensationId\": -1,\n \"fcsFileId\": 209015,\n \"gateSetId\": 4,\n \"eventCount\": 43622,\n \"minimums\": {},\n \"maximums\": {},\n \"means\": {},\n \"medians\": {},\n \"variances\": {},\n \"standardDeviations\": {},\n \"secondPercentiles\": {},\n \"ninetyEighthPercentiles\": {},\n \"channelShortNameIds\": []\n }\n]"}],"_postman_id":"637c2d98-e513-4f9c-bb23-de2a8aeb7caa"},{"name":"Show Event Count Statistics","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;",""]}}],"id":"bb27af4f-d26d-4bf5-990f-b52daaac89e3","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/statistics?experimentId={{EXPT_ID}}&gateVersion={{GATE_VERSION}}&experimentVersion={{EXPT_VERSION}}&compensationId={{COMP_ID}}&fcsFileIds={{FCS_FILE_ID_1}}&fcsFileIds={{FCS_FILE_ID_2}}&gateSetIds={{POPULATION_ID_1}}&gateSetIds={{POPULATION_ID_2}}","description":"This is just another take on the general statistics endpoint. It works the same but excludes channel parameters. In the absence of channel information only event count data are returned. If only event count data are needed, this approach can be faster than retrieving all statistics by avoiding unnecessary computation.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","statistics"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[{"key":"experimentId","value":"{{EXPT_ID}}"},{"key":"gateVersion","value":"{{GATE_VERSION}}"},{"key":"experimentVersion","value":"{{EXPT_VERSION}}"},{"key":"compensationId","value":"{{COMP_ID}}"},{"key":"fcsFileIds","value":"{{FCS_FILE_ID_1}}"},{"key":"fcsFileIds","value":"{{FCS_FILE_ID_2}}"},{"key":"gateSetIds","value":"{{POPULATION_ID_1}}"},{"key":"gateSetIds","value":"{{POPULATION_ID_2}}"}],"variable":[]}},"response":[{"id":"bc1793e2-4ffb-4508-bd41-fb8a407ba8ba","name":"Show Event Count Statistics","originalRequest":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"urlencoded","urlencoded":[]},"url":{"raw":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/statistics?experimentId={{EXPT_ID}}&gateVersion={{GATE_VERSION}}&experimentVersion={{EXPT_VERSION}}&compensationId={{COMP_ID}}&fcsFileIds={{FCS_FILE_ID_1}}&fcsFileIds={{FCS_FILE_ID_2}}&gateSetIds={{POPULATION_ID_1}}&gateSetIds={{POPULATION_ID_2}}","protocol":"https","host":["{{CYTOBANK}}","cytobank","org"],"path":["cytobank","api","v1","statistics"],"query":[{"key":"experimentId","value":"{{EXPT_ID}}"},{"key":"gateVersion","value":"{{GATE_VERSION}}"},{"key":"experimentVersion","value":"{{EXPT_VERSION}}"},{"key":"compensationId","value":"{{COMP_ID}}"},{"key":"fcsFileIds","value":"{{FCS_FILE_ID_1}}"},{"key":"fcsFileIds","value":"{{FCS_FILE_ID_2}}"},{"key":"gateSetIds","value":"{{POPULATION_ID_1}}"},{"key":"gateSetIds","value":"{{POPULATION_ID_2}}"}]}},"status":"OK","code":200,"_postman_previewlanguage":"javascript","header":[{"name":"Cache-Control","key":"Cache-Control","value":"nocache","description":"","enabled":true},{"name":"Connection","key":"Connection","value":"keep-alive","description":"","enabled":true},{"name":"Content-Length","key":"Content-Length","value":"1378","description":"","enabled":true},{"name":"Content-Type","key":"Content-Type","value":"application/json;charset=utf-8","description":"","enabled":true},{"name":"Date","key":"Date","value":"Wed, 27 Jul 2016 05:08:47 GMT","description":"","enabled":true},{"name":"Server","key":"Server","value":"Apache-Coyote/1.1","description":"","enabled":true},{"name":"Strict-Transport-Security","key":"Strict-Transport-Security","value":"max-age=31622400; includeSubDomains","description":"","enabled":true},{"name":"X-Content-Type-Options","key":"X-Content-Type-Options","value":"nosniff","description":"","enabled":true},{"name":"X-Frame-Options","key":"X-Frame-Options","value":"DENY","description":"","enabled":true},{"name":"X-XSS-Protection","key":"X-XSS-Protection","value":"1; mode=block","description":"","enabled":true}],"cookie":[{"expires":"Invalid Date","hostOnly":true,"httpOnly":true,"domain":"ucsf.cytobank.org","path":"/","secure":true,"session":true,"value":"106fc2868543ffd5979d985305fb6dec"}],"responseTime":null,"body":"[\n {\n \"populationIdentifierKey\": \"209014,10559,32,[3],-1,-1,,30,popid\",\n \"experimentId\": 10559,\n \"gateVersion\": -1,\n \"compensationId\": -1,\n \"fcsFileId\": 209014,\n \"gateSetId\": 3,\n \"eventCount\": 38420,\n \"minimums\": {},\n \"maximums\": {},\n \"means\": {},\n \"medians\": {},\n \"variances\": {},\n \"standardDeviations\": {},\n \"secondPercentiles\": {},\n \"ninetyEighthPercentiles\": {},\n \"channelShortNameIds\": []\n },\n {\n \"populationIdentifierKey\": \"209014,10559,32,[4],-1,-1,,30,popid\",\n \"experimentId\": 10559,\n \"gateVersion\": -1,\n \"compensationId\": -1,\n \"fcsFileId\": 209014,\n \"gateSetId\": 4,\n \"eventCount\": 43643,\n \"minimums\": {},\n \"maximums\": {},\n \"means\": {},\n \"medians\": {},\n \"variances\": {},\n \"standardDeviations\": {},\n \"secondPercentiles\": {},\n \"ninetyEighthPercentiles\": {},\n \"channelShortNameIds\": []\n },\n {\n \"populationIdentifierKey\": \"209015,10559,32,[3],-1,-1,,30,popid\",\n \"experimentId\": 10559,\n \"gateVersion\": -1,\n \"compensationId\": -1,\n \"fcsFileId\": 209015,\n \"gateSetId\": 3,\n \"eventCount\": 36455,\n \"minimums\": {},\n \"maximums\": {},\n \"means\": {},\n \"medians\": {},\n \"variances\": {},\n \"standardDeviations\": {},\n \"secondPercentiles\": {},\n \"ninetyEighthPercentiles\": {},\n \"channelShortNameIds\": []\n },\n {\n \"populationIdentifierKey\": \"209015,10559,32,[4],-1,-1,,30,popid\",\n \"experimentId\": 10559,\n \"gateVersion\": -1,\n \"compensationId\": -1,\n \"fcsFileId\": 209015,\n \"gateSetId\": 4,\n \"eventCount\": 43622,\n \"minimums\": {},\n \"maximums\": {},\n \"means\": {},\n \"medians\": {},\n \"variances\": {},\n \"standardDeviations\": {},\n \"secondPercentiles\": {},\n \"ninetyEighthPercentiles\": {},\n \"channelShortNameIds\": []\n }\n]"}],"_postman_id":"bb27af4f-d26d-4bf5-990f-b52daaac89e3"}],"id":"3f255ad7-a464-414b-9092-26485c98c81d","_postman_id":"3f255ad7-a464-414b-9092-26485c98c81d","description":""},{"name":"Users","item":[{"name":"List Users","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"]}}],"id":"13453f15-7b8a-47e5-9835-82c46b197181","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"formdata","formdata":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/users","description":"List all users on this Cytobank. This endpoint is for admins only and will respond with an authorization error if accessed by a non-admin.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","users"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[],"_postman_id":"13453f15-7b8a-47e5-9835-82c46b197181"},{"name":"Show User Details","event":[{"listen":"test","script":{"type":"text/javascript","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"]}}],"id":"c5688f02-cb90-4255-bc8c-78f16b27ae76","request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"body":{"mode":"formdata","formdata":[]},"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/users/{{USER_ID}}","description":"Show details for a user. This endpoint is for admins only and will respond with an authorization error if accessed by a non-admin.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","users","{{USER_ID}}"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[],"_postman_id":"c5688f02-cb90-4255-bc8c-78f16b27ae76"}],"id":"23c3a71a-ff18-402c-8b55-20942879dbb0","description":"One should never analyze alone...
\n","_postman_id":"23c3a71a-ff18-402c-8b55-20942879dbb0"},{"name":"Files Upload & Download","item":[{"name":"Upload","item":[{"name":"[New] Get upload file token","event":[{"listen":"test","script":{"id":"432d419a-d8e5-4406-a016-1b27d66b5b79","exec":["var data = JSON.parse(responseBody);","postman.setEnvironmentVariable(\"UPLOAD_SESSION_TOKEN\", data.sessionToken);","if(data.input.queryStringParameters.acs == \"false\") {"," postman.setEnvironmentVariable(\"UPLOAD_PATH\", data.uploadBucketName + \"/experiments/\" + data.experimentId + \"/{{filename}}\");","} else {"," postman.setEnvironmentVariable(\"UPLOAD_PATH\", data.uploadBucketName + \"/acs/\" + data.userId + \"/{{filename}}\");","}","tests[\"Status code is 200\"] = responseCode.code === 200;"],"type":"text/javascript"}}],"id":"a489ae54-81b5-4923-8a5b-91ad79e34a0f","protocolProfileBehavior":{"disableBodyPruning":true},"request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}","type":"text"}],"url":"https://{{CYTOBANK}}-api.cytobank.org/api/v1/upload/token?userId={{USER_ID}}&experimentId={{EXPT_ID}}&acs={{ACS}}","description":"Request an AWS STS token granting temporary write access to this site's S3 file upload bucket. Using the AWS SDK (or Cytobank R package) for the language of your choice is the easiest way to use this token to upload your files to the site.
\n","urlObject":{"protocol":"https","path":["api","v1","upload","token"],"host":["{{CYTOBANK}}-api","cytobank","org"],"query":[{"description":{"content":"(Required) researcher id
\n","type":"text/plain"},"key":"userId","value":"{{USER_ID}}"},{"description":{"content":"(Required) experiment id
\n","type":"text/plain"},"key":"experimentId","value":"{{EXPT_ID}}"},{"description":{"content":"(Required) if try to upload an ACS file
\n","type":"text/plain"},"key":"acs","value":"{{ACS}}"}],"variable":[]}},"response":[{"id":"808fb6c4-fcfc-4969-806f-9771f3af3f4d","name":"200 response","originalRequest":{"method":"GET","header":[{"description":{"content":"Added as a part of security scheme: apikey","type":"text/plain"},"key":"Authorization","value":"Request the processing/ingestion status of all the files for the provided experimentId.
\n","urlObject":{"protocol":"https","path":["api","v1","experiments","{{EXPT_ID}}","upload_status"],"host":["{{CYTOBANK}}-api","cytobank","org"],"query":[],"variable":[{"type":"any","value":"1997","key":"id"}]}},"response":[{"id":"e9444a3b-f4e3-40a8-8040-225b682d1fcd","name":"200 response","originalRequest":{"method":"GET","header":[{"description":{"content":"Added as a part of security scheme: apikey","type":"text/plain"},"key":"Authorization","value":"Cytobank API for uploading and downloading files.
\n1). Get Cytobank JWT token thought endpoint https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/authenticate
\nHere is a response format. The last attribute is cytobank token
\n{\n \"user\": {\n \"id\": 5,\n \"username\": \"demo_user\",\n \"location\": \"United States (US)\",\n \"organization\": \"Beckman\",\n \"bio\": \"\",\n \"firstName\": \"demo_user\",\n \"lastName\": \"demo_user\",\n \"email\": \"demo_user@beckman.com\",\n \"principalInvestigatorId\": null,\n \"hideEmail\": true,\n \"createdAt\": \"2021-09-06T01:51:15Z\",\n \"updatedAt\": \"2021-11-17T08:55:10Z\",\n \"lastLoginAt\": \"2021-11-17T06:02:14Z\",\n \"lastLoginIp\": \"134.217.237.30\",\n \"admin\": true,\n \"invisible\": false,\n \"validated\": true,\n \"inactive\": false,\n \"emailVerified\": true,\n \"billingAdmin\": false,\n \"authToken\": \"eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJqdGkiOiJiOTJjODMzOGU5ZjE1YzQ5MTQ0OWYyZDNmNDM0YmJkYyIsImlhdCI6MTYzNzEzOTMxMCwiZXhwIjoxNjM3MTY4MTEwLCJ1c2VyX2lkIjozNywibmJmIjoxNjM3MTM5MzEwLCJhdWQiOiJjeXRvYmFua19hcGlfdjFfdXNlcnMiLCJpc3MiOiJodHRwczovL3BlcmYtc2VkbmEuY3l0b2Jhbmsub3JnLyIsInN1YiI6ImN5dG9iYW5rX2FwaV92MSJ9.WgWur-FKPXJlKm0-_etausxiEgNLAgkDAxrn-Q6SW1s\"\n }\n}\n2). Call the /upload/token endpoint with the Cytobank JWT token. This endpoint will return an AWS STS token and S3 bucket destination for uploading.
\nHere is a response sample. And the 'accessKeyId' and 'secretAccessKey' can be found in the response.
\n{\n \"accessKeyId\": \"ASIAWBZY36WXU5YDH2ZC\",\n \"secretAccessKey\": \"GOMOnXtcgqo9aO42L5nafUrxwY6RSMRJEZxwJcb0\",\n \"sessionToken\": \"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\",\n \"uploadBucketName\": \"demo-dev-us-west-1-upload\",\n \"awsRegion\": \"us-west-1\",\n \"userId\": \"37\",\n \"experimentId\": \"1233\",\n \"writable\": true,\n \"input\": {\n \"resource\": \"/v1/upload/token\",\n \"path\": \"/v1/upload/token\",\n \"httpMethod\": \"GET\",\n \"headers\": {\n \"Accept\": \"*/*\",\n \"Accept-Encoding\": \"gzip, deflate, br\",\n \"Authorization\": \"Bearer eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJqdGkiOiJiOTJjODMzOGU5ZjE1YzQ5MTQ0OWYyZDNmNDM0YmJkYyIsImlhdCI6MTYzNzEzOTMxMCwiZXhwIjoxNjM3MTY4MTEwLCJ1c2VyX2lkIjozNywibmJmIjoxNjM3MTM5MzEwLCJhdWQiOiJjeXRvYmFua19hcGlfdjFfdXNlcnMiLCJpc3MiOiJodHRwczovL3BlcmYtc2VkbmEuY3l0b2Jhbmsub3JnLyIsInN1YiI6ImN5dG9iYW5rX2FwaV92MSJ9.WgWur-FKPXJlKm0-_etausxiEgNLAgkDAxrn-Q6SW1s\",\n \"Host\": \"u80k85q6u7.execute-api.us-west-1.amazonaws.com\",\n \"Postman-Token\": \"9dc443fa-cd08-47aa-8ad4-14ee891a05f9\",\n \"User-Agent\": \"PostmanRuntime/7.28.4\",\n \"X-Amzn-Trace-Id\": \"Root=1-6194c8c8-60ae18a8096f4b36191181cb\",\n \"X-Forwarded-For\": \"134.217.237.30\",\n \"X-Forwarded-Port\": \"443\",\n \"X-Forwarded-Proto\": \"https\"\n },\n \"multiValueHeaders\": {\n \"Accept\": [\n \"*/*\"\n ],\n \"Accept-Encoding\": [\n \"gzip, deflate, br\"\n ],\n \"Authorization\": [\n \"Bearer eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJqdGkiOiJiOTJjODMzOGU5ZjE1YzQ5MTQ0OWYyZDNmNDM0YmJkYyIsImlhdCI6MTYzNzEzOTMxMCwiZXhwIjoxNjM3MTY4MTEwLCJ1c2VyX2lkIjozNywibmJmIjoxNjM3MTM5MzEwLCJhdWQiOiJjeXRvYmFua19hcGlfdjFfdXNlcnMiLCJpc3MiOiJodHRwczovL3BlcmYtc2VkbmEuY3l0b2Jhbmsub3JnLyIsInN1YiI6ImN5dG9iYW5rX2FwaV92MSJ9.WgWur-FKPXJlKm0-_etausxiEgNLAgkDAxrn-Q6SW1s\"\n ],\n \"Host\": [\n \"u80k85q6u7.execute-api.us-west-1.amazonaws.com\"\n ],\n \"Postman-Token\": [\n \"9dc443fa-cd08-47aa-8ad4-14ee891a05f9\"\n ],\n \"User-Agent\": [\n \"PostmanRuntime/7.28.4\"\n ],\n \"X-Amzn-Trace-Id\": [\n \"Root=1-6194c8c8-60ae18a8096f4b36191181cb\"\n ],\n \"X-Forwarded-For\": [\n \"134.217.237.30\"\n ],\n \"X-Forwarded-Port\": [\n \"443\"\n ],\n \"X-Forwarded-Proto\": [\n \"https\"\n ]\n },\n \"queryStringParameters\": {\n \"experimentId\": \"1233\"\n },\n \"multiValueQueryStringParameters\": {\n \"experimentId\": [\n \"1233\"\n ]\n },\n \"pathParameters\": null,\n \"stageVariables\": null,\n \"requestContext\": {\n \"resourceId\": \"poyh1m\",\n \"authorizer\": {\n \"principalId\": \"37\",\n \"integrationLatency\": 471,\n \"userId\": \"37\"\n },\n \"resourcePath\": \"/v1/upload/token\",\n \"httpMethod\": \"GET\",\n \"extendedRequestId\": \"I8RPWE36SK4FueQ=\",\n \"requestTime\": \"17/Nov/2021:09:18:00 +0000\",\n \"path\": \"/public-dev/v1/upload/token\",\n \"accountId\": \"416194229679\",\n \"protocol\": \"HTTP/1.1\",\n \"stage\": \"public-dev\",\n \"domainPrefix\": \"u80k85q6u7\",\n \"requestTimeEpoch\": 1637140680454,\n \"requestId\": \"9afc4a0a-0610-46a1-83a6-5dc57058ad8b\",\n \"identity\": {\n \"cognitoIdentityPoolId\": null,\n \"accountId\": null,\n \"cognitoIdentityId\": null,\n \"caller\": null,\n \"sourceIp\": \"134.217.237.30\",\n \"principalOrgId\": null,\n \"accessKey\": null,\n \"cognitoAuthenticationType\": null,\n \"cognitoAuthenticationProvider\": null,\n \"userArn\": null,\n \"userAgent\": \"PostmanRuntime/7.28.4\",\n \"user\": null\n },\n \"domainName\": \"u80k85q6u7.execute-api.us-west-1.amazonaws.com\",\n \"apiId\": \"u80k85q6u7\"\n },\n \"body\": null,\n \"isBase64Encoded\": false\n }\n}\n3). Use the AWS S3 SDK for your language of choice to upload a file with AWS token. You will need to include S3 object metadata as specified in the table below.
\nIf your programming language doesn't support the AWS S3 sdk, then please reference the AWS docs to upload the file using HTTP POST.
\n4). Upload destinations
\n5). Call the /experiments/{id}/upload_status endpoint with the Cytobank JWT token to get the status of all files as they're processed in the backend. It will show pending, processing, failed, or success for each file in the response. When all files are have succeeded the backend has finished processing them.
\nresponse = httpClient.get(\"{baseUrl}/upload/token?userId={userId}&experimentId={experimentId}&acs=false\").withToken({cytobank_token})\n\nsts_token = (response.accessKeyId, response.secretAccessKey, response.sessionToken)\n\nfile_destination = STS_TOKEN_RESPONSE.uploadBucketName + \"/experiments/{experimentId}/{filename}\"\n// ** if uploading an acs file\n// file_destination = STS_TOKEN_RESPONSE.uploadBucketName + \"/acs/{user_id}/{filename}\"\n\ntransaction_id = UUID.toString()\n\ns3_object_user_metadata = new metadata()\ns3_object_user_metadata.put(\"tid\", transaction_id)\n// ** if uploading an attachment\n// s3_object_user_metadata.put(\"attachment\", \"true\")\n// ** if uploading a drop file\n// s3_object_user_metadata.put(\"drop\", \"true\")\n\nupload(sts_token, file_destination, s3_object_user_metadata)\n\nfileItems = httpClient.get(\"{baseUrl}/upload/token?userId={userId}&experimentId={experimentId}&acs=false\").withToken({cytobank_token})\n\nfor(item : fileItems) {\n if(transaction_id.equals(item.getTransctionId())){\n // this file is being uploaded in this time.\n }\n}\nRequest a temprorary download URL for the specified file by the hashkey. The file is located using the hashkey and the filename will be what it's called when saved via the download link.
\nGet Cytobank JWT token thought endpoint https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/authenticate
\nMake a GET request to the /download/url endpoint with Cytobank JWT token. The endpoint will return an 8 hour temporary download URL for the file.
\nRequest to download the file via the returned URL.
\nFcsFile or Attachment
\n","type":"text/plain"},"key":"fileType","value":"{{fileType}}"},{"key":"fileName","value":"{{file_name}}"}],"variable":[]}},"response":[{"id":"4d3f54eb-5e04-4fec-adf6-19810922e2be","name":"200 response","originalRequest":{"method":"GET","header":[{"description":{"content":"Added as a part of security scheme: apikey","type":"text/plain"},"key":"Authorization","value":"To zip and download the selected files and cytobank will send an e-mail that contains a temporary download URL for the ZIP file.
\nUse the \"FCS files list\" API endpoint to get a list of all filenames and their associated hashkeys to use in composing the body of this POST request.
\nLogin to Cytobank and get a Cytobank JWT token.
\nMake a GET request to the /download/zip endpoint with the Cytobank JWT token. If success is returned then the backend will initiate a process to ZIP all the requested files and send an email to the user containing an 8 hour temporary download link to the generated ZIP file.
\nThe user is able to download the zipped file with the link in the email.
\njson = \"\n{\n \"zipFileName\": \"zipFileName.zip\",\n \"experimentId\": {experiment_id},\n \"userId\": {user_id},\n \"fileList\": [\n {\n \"fileName\": \"fcs1.fcs\",\n \"keyPrefix\": \"fcs_files\",\n \"hashKey\": \"{file hashkey}\"\n },\n {\n \"fileName\": \"attachment.png\",\n \"keyPrefix\": \"attachments\",\n \"hashKey\": \"{file haskey}\"\n }\n ]\n}\n\"\n\nhttpClient.post(json).withToken({cytobank_token})\n\n\nGeneral endpoint to check the detailed progress for a given background task.
\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","background_task","{{background_task_id}}","progress"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[{"id":"8311ab9f-351b-4c5b-9202-66a80087d88b","name":"Check progress of background task","originalRequest":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/background_task/{{background_task_id}}/progress"},"_postman_previewlanguage":"json","header":[{"key":"Content-Type","value":"application/json","description":""}],"cookie":[],"responseTime":null,"body":"{\n \"id\": 272,\n \"current_progress_message\": \"Compressing pbmc_lrs005_il10-_1__comp-pok_b.txt\",\n \"work_done\": 12,\n \"total_work\": 12,\n \"progress\": 100,\n \"complete\": true,\n \"failed\": false,\n \"defunct\": false,\n \"canceled\": false,\n \"return_value\": 1468,\n \"running\": false,\n \"start_time\": 1741165282,\n \"end_time\": \" 1:32 am PST, Mar 05 2025\",\n \"updated_at\": 1741167144\n}"}],"_postman_id":"6a2a737c-d472-4c8c-9bfa-f4f50114359e"}],"id":"75d115cb-02f7-4873-9a0a-94549006ec61","_postman_id":"75d115cb-02f7-4873-9a0a-94549006ec61","description":""},{"name":"Gating Versions","item":[{"name":"List Saved Gating Versions for Experiment","event":[{"listen":"test","script":{"id":"073a18e7-a318-42c6-b996-222153aa90c1","exec":["tests[\"Status code is 200\"] = responseCode.code === 200;"],"type":"text/javascript","packages":{}}}],"id":"5cfab8fc-d15b-49d6-aad0-47a28dfa2102","protocolProfileBehavior":{"disableBodyPruning":true},"request":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/saved_gating_versions","description":"List all saved gating version for the given experiment.
\n\n","urlObject":{"protocol":"https","path":["cytobank","api","v1","experiments","{{EXPT_ID}}","saved_gating_versions"],"host":["{{CYTOBANK}}","cytobank","org"],"query":[],"variable":[]}},"response":[{"id":"a2fc27b0-7dbd-430c-84a7-d8061cae819a","name":"List Saved Gating Versions for Experiment","originalRequest":{"method":"GET","header":[{"key":"Authorization","value":"Bearer {{AUTH_TOKEN}}"}],"url":"https://{{CYTOBANK}}.cytobank.org/cytobank/api/v1/experiments/{{EXPT_ID}}/saved_gating_versions"},"_postman_previewlanguage":"json","header":[{"key":"Content-Type","value":"application/json","description":""}],"cookie":[],"responseTime":null,"body":"[\n {\n \"id\": 137,\n \"version\": 5,\n \"name\": \"demo1\",\n \"experimentId\": 453,\n \"createdAt\": \"Thu Mar 6 00:11:14 2025\",\n \"localOffsetCreatedAt\": \"Thu Mar 6 00:11:14 2025 -0800\"\n },\n {\n \"id\": 136,\n \"version\": 4,\n \"name\": \"test2\",\n \"experimentId\": 453,\n \"createdAt\": \"Wed Mar 5 23:14:03 2025\",\n \"localOffsetCreatedAt\": \"Wed Mar 5 23:14:03 2025 -0800\"\n }\n]"}],"_postman_id":"5cfab8fc-d15b-49d6-aad0-47a28dfa2102"}],"id":"07c8d07d-4ccd-42ac-9ccb-30f41e1162f0","_postman_id":"07c8d07d-4ccd-42ac-9ccb-30f41e1162f0","description":""}]}