Use public oncokb instance for portal without token #7457

zhx828 · 2020-04-29T23:55:40Z

This is a part of fix for oncokb/oncokb#1975

Update the oncokb message when deploying the instance without configuring the oncokb token
Update the oncokb data documentation to include the instructions on how to configure portal to use oncokb.org

zhx828 · 2020-04-29T23:56:13Z

docs/OncoKB-Data-Access.md

@@ -1,13 +1,23 @@
 # Introduction


@jjgao could you take a look these instructions? Thank you.

zhx828 · 2020-04-29T23:57:01Z

web/src/main/java/org/cbioportal/web/config/WebServletContextListener.java

@@ -41,12 +44,11 @@ public void afterPropertiesSet() throws Exception {
    }

    private void checkOncokbInfo() {


@jjgao I still remained the message. But let me know if you think it's no longer needed.

docs/OncoKB-Data-Access.md

onursumer · 2020-05-04T17:37:26Z

docs/FAQ.md

@@ -132,7 +132,7 @@ The Network tab was retired on November 1, 2019. We will soon release a new feat
 #### Does the portal contain cancer study X?
 Check out the [Data Sets Page](https://www.cbioportal.org/data_sets.jsp) for the complete set of cancer studies currently stored in the portal. If you do not see your specific cancer study of interest, please [contact us](mailto:cbioportal@googlegroups.com), and we will let you know if it's in the queue.
 #### Which resources are integrated for variant annotation?
-cBioPortal supports the annotation of variants from several different databases. These databases provide information about the recurrence of, or prior knowledge about, specific amino acid changes. For each variant, the number of occurrences of mutations at the same amino acid position present in the COSMIC database are reported. Furthermore, variants are annotated as “hotspots” if the amino acid positions were found to be recurrent linear hotspots, as defined by the Cancer Hotspots method ([cancerhotspots.org](http://www.cancerhotspots.org/)), or three-dimensional hotspots, as defined by 3D Hotspots ([3dhotspots.org](https://www.3dhotspots.org/)). Prior knowledge about variants, including clinical actionability information, is provided from three different sources: OncoKB ([oncokb.org](http://oncokb.org/)), CIViC ([civicdb.org](https://civicdb.org/)), as well as My Cancer Genome ([mycancergenome.org](https://www.mycancergenome.org/)). For OncoKB, exact levels of clinical actionability are displayed in cBioPortal, as defined by [the OncoKB paper](http://ascopubs.org/doi/full/10.1200/PO.17.00011).
+cBioPortal supports the annotation of variants from several different databases. These databases provide information about the recurrence of, or prior knowledge about, specific amino acid changes. For each variant, the number of occurrences of mutations at the same amino acid position present in the COSMIC database are reported. Furthermore, variants are annotated as “hotspots” if the amino acid positions were found to be recurrent linear hotspots, as defined by the Cancer Hotspots method ([cancerhotspots.org](http://www.cancerhotspots.org/)), or three-dimensional hotspots, as defined by 3D Hotspots ([3dhotspots.org](https://www.3dhotspots.org/)). Prior knowledge about variants, including clinical actionability information, is provided from three different sources: OncoKB ([www.oncokb.org](https://www.oncokb.org/)), CIViC ([civicdb.org](https://civicdb.org/)), as well as My Cancer Genome ([mycancergenome.org](https://www.mycancergenome.org/)). For OncoKB, exact levels of clinical actionability are displayed in cBioPortal, as defined by [the OncoKB paper](http://ascopubs.org/doi/full/10.1200/PO.17.00011).


I couldn't spot the change in this line, am I missing something?

@onursumer only changing http:oncokb.org to https://www.oncokb.org

jjgao

@zhx828 Could you list all the configuration parameters in portal.properties for OncoKB? Maybe we can make some changes, e.g. reduce or consolidate some of them.

jjgao · 2020-05-04T18:10:52Z

src/main/resources/portal.properties.EXAMPLE

@@ -165,7 +165,7 @@ segfile.url=http://cbio.mskcc.org/cancergenomics/gdac-portal/seg/
 show.oncokb=true


Is it possible to specify the API URL?

Please see below. oncokb.public_api.url can be used

jjgao · 2020-05-04T18:13:31Z

docs/OncoKB-Data-Access.md

+Following properties can be edited in the `portal.properties` file or set in system variables if you are using docker. 
+- `show.oncokb` should be set to `true`
+- `oncokb.token` should be set to a valid OncoKB access token value
+- `oncokb.public_api.url` should be set to `https://www.oncokb.org`


Is there a different parameter for authenticated API?

@jjgao no, there are only three parameters for oncokb and all listed here. As long as they supply the token, we will attach that to the authentication header.

leexgh · 2020-05-04T18:30:55Z

docs/OncoKB-Data-Access.md

+- `show.oncokb` should be set to `true`
+- `oncokb.token` should be set to a valid OncoKB access token value
+- `oncokb.public_api.url` should be set to `https://www.oncokb.org`


I think we have a default value: DEFAULT_ONCOKB_URL = "https://public.api.oncokb.org/api/v1", any difference between public.api.oncokb.org/api/v1 and www.oncokb.org?

@leexgh we actually changed the default to public.api.oncokb.org which does not require authentication. But good catch! Here should be www.oncokb.org/api/v1

leexgh · 2020-05-04T20:18:44Z

web/src/main/java/org/cbioportal/web/config/WebServletContextListener.java

@@ -30,6 +32,7 @@ public void contextInitialized(ServletContextEvent arg0) {

        this.showOncokb = Boolean.parseBoolean(getProperty("show.oncokb", "true"));
        this.oncokbToken = getProperty("oncokb.token", "");
+        this.oncokbURL = getProperty("oncokb.public_api.url", "");


@zhx828 do you think we need to set a default url for this one?

@leexgh I don't think so. We use its empty status for later printing out the warning message.

Update documentation for using oncokb token to access therapeutic info Update all oncokb url to https Co-authored-by: Onur Sumer <s.onur.sumer@gmail.com> Signed-off-by: Hongxin Zhang <hongxin@cbio.mskcc.org>

inodb

LGTM!

zhx828 requested review from jjgao, onursumer and leexgh April 29, 2020 23:55

zhx828 commented Apr 29, 2020

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docs/OncoKB-Data-Access.md

@@ -1,13 +1,23 @@

# Introduction

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@jjgao could you take a look these instructions? Thank you.

zhx828 commented Apr 29, 2020

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zhx828 added do not merge ready to review and removed do not merge labels Apr 29, 2020

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zhx828 added the do not merge label May 5, 2020

zhx828 force-pushed the use-public-oncokb-instance branch from 5313ddf to d0db996 Compare May 5, 2020 21:59

zhx828 requested a review from jjgao May 5, 2020 21:59

zhx828 removed the do not merge label May 5, 2020

zhx828 requested review from leexgh and onursumer May 5, 2020 21:59

onursumer approved these changes May 5, 2020

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alisman approved these changes May 7, 2020

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Give warning when the instance is connecting to a public oncokb instance

b06888b

Update documentation for using oncokb token to access therapeutic info Update all oncokb url to https Co-authored-by: Onur Sumer <s.onur.sumer@gmail.com> Signed-off-by: Hongxin Zhang <hongxin@cbio.mskcc.org>

zhx828 force-pushed the use-public-oncokb-instance branch from 8bce47f to b06888b Compare May 7, 2020 21:19

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inodb approved these changes May 7, 2020

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inodb added the cl-external-api label May 7, 2020

zhx828 merged commit b81ec59 into cBioPortal:master May 7, 2020

zhx828 deleted the use-public-oncokb-instance branch May 7, 2020 21:59

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Use public oncokb instance for portal without token #7457

Use public oncokb instance for portal without token #7457

zhx828 commented Apr 29, 2020

zhx828 Apr 29, 2020

zhx828 Apr 29, 2020

onursumer May 4, 2020

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zhx828 May 4, 2020

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leexgh May 4, 2020 •

edited

zhx828 May 4, 2020

leexgh May 4, 2020

zhx828 May 4, 2020

inodb left a comment

		@@ -41,12 +44,11 @@ public void afterPropertiesSet() throws Exception {
		}

		private void checkOncokbInfo() {

		@@ -165,7 +165,7 @@ segfile.url=http://cbio.mskcc.org/cancergenomics/gdac-portal/seg/
		show.oncokb=true

Use public oncokb instance for portal without token #7457

Use public oncokb instance for portal without token #7457

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zhx828 commented Apr 29, 2020

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leexgh May 4, 2020 • edited

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leexgh May 4, 2020 •

edited