From 0e76707c4e813622af0a4e9513115c533c0dd5fe Mon Sep 17 00:00:00 2001 From: Retype GitHub Action Date: Fri, 15 Nov 2024 21:03:53 +0000 Subject: [PATCH] Refreshes Retype-generated documentation. Process triggered by inodb. --- 404.html | 8 ++++---- about-us/index.html | 8 ++++---- architecture-overview/index.html | 8 ++++---- backend-code-organization/index.html | 8 ++++---- backend-development-guidelines/index.html | 8 ++++---- create-and-publish-virtual-study/index.html | 10 +++++----- data-loading-for-developers/index.html | 8 ++++---- data-loading-maintaining-studies/index.html | 8 ++++---- .../index.html | 8 ++++---- data-loading/index.html | 10 +++++----- .../index.html | 10 +++++----- .../authenticating-users-via-ldap/index.html | 8 ++++---- .../authenticating-users-via-saml/index.html | 8 ++++---- .../index.html | 8 ++++---- .../user-authorization/index.html | 8 ++++---- .../index.html | 10 +++++----- deployment/customization/caching/index.html | 8 ++++---- .../index.html | 8 ++++---- .../index.html | 8 ++++---- .../portal.properties-reference/index.html | 8 ++++---- .../security.properties-reference/index.html | 10 +++++----- deployment/customization/studyview/index.html | 8 ++++---- .../build-from-source/index.html | 8 ++++---- .../deploying/index.html | 8 ++++---- .../import-the-seed-database/index.html | 8 ++++---- .../load-sample-cancer-study/index.html | 8 ++++---- .../pre-build-steps/index.html | 8 ++++---- .../software-requirements/index.html | 8 ++++---- deployment/docker/example_commands/index.html | 10 +++++----- deployment/docker/import_data/index.html | 10 +++++----- deployment/docker/index.html | 8 ++++---- .../docker/notes-for-non-linux/index.html | 8 ++++---- deployment/docker/using-keycloak/index.html | 10 +++++----- deployment/index.html | 8 ++++---- .../index.html | 8 ++++---- .../oncokb-data-access/index.html | 8 ++++---- .../build-different-frontend/index.html | 8 ++++---- development/cbioportal-er-diagram/index.html | 8 ++++---- development/database-versioning/index.html | 10 +++++----- development/deployment-procedure/index.html | 8 ++++---- development/documentation-site/index.html | 8 ++++---- .../feature-development-guide/index.html | 8 ++++---- development/index.html | 8 ++++---- development/manual-test-cases/index.html | 8 ++++---- development/release-procedure/index.html | 8 ++++---- .../session-service-working/index.html | 12 +++++------- downloads/index.html | 8 ++++---- file-formats/index.html | 10 +++++----- hardware-requirements/index.html | 8 ++++---- import-gene-panels/index.html | 8 ++++---- import-gene-sets/index.html | 8 ++++---- .../index.html | 8 ++++---- import-reference-genome/index.html | 8 ++++---- import-study-using-docker/index.html | 10 +++++----- imported-maf-columns/index.html | 8 ++++---- importer-tool/index.html | 8 ++++---- incremental-data-loading/index.html | 8 ++++---- index.html | 8 ++++---- inter-repository-dependencies/index.html | 8 ++++---- migration-guide/index.html | 8 ++++---- msk-maintenance/index.html | 8 ++++---- .../index.html | 8 ++++---- news-genie/index.html | 8 ++++---- news/index.html | 8 ++++---- resources/js/config.js | 2 +- rfc-list/index.html | 8 ++++---- session-service-management/index.html | 10 +++++----- sitemap.xml.gz | Bin 1353 -> 1354 bytes software-acknowledgments/index.html | 8 ++++---- study-curation-guide/index.html | 8 ++++---- testing/index.html | 10 +++++----- uninstall-docker-cbioportal/index.html | 10 +++++----- .../index.html | 10 +++++----- .../index.html | 10 +++++----- user-guide/by-page/index.html | 8 ++++---- user-guide/faq/index.html | 8 ++++---- user-guide/index.html | 8 ++++---- user-guide/new-users/index.html | 8 ++++---- user-guide/oql/index.html | 8 ++++---- user-guide/overview/index.html | 8 ++++---- using-the-dataset-validator/index.html | 10 +++++----- using-the-metaimport-script/index.html | 8 ++++---- web-api-and-clients/index.html | 10 +++++----- z-score-normalization-script/index.html | 8 ++++---- 84 files changed, 348 insertions(+), 350 deletions(-) diff --git a/404.html b/404.html index 0a86a8c76e0..51459d6e801 100644 --- a/404.html +++ b/404.html @@ -3,7 +3,7 @@ - + @@ -28,11 +28,11 @@ - + - + - + diff --git a/about-us/index.html b/about-us/index.html index 423024fb1b9..226b10f8989 100644 --- a/about-us/index.html +++ b/about-us/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/architecture-overview/index.html b/architecture-overview/index.html index 648319442dd..d5e3084e4c0 100644 --- a/architecture-overview/index.html +++ b/architecture-overview/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/backend-code-organization/index.html b/backend-code-organization/index.html index 0c735866203..4578e06454c 100644 --- a/backend-code-organization/index.html +++ b/backend-code-organization/index.html @@ -3,7 +3,7 @@ - + @@ -33,11 +33,11 @@ - + - + - + diff --git a/backend-development-guidelines/index.html b/backend-development-guidelines/index.html index 9d8c626b42a..49f21f90df2 100644 --- a/backend-development-guidelines/index.html +++ b/backend-development-guidelines/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/create-and-publish-virtual-study/index.html b/create-and-publish-virtual-study/index.html index ed9514f2fdb..270b029968c 100644 --- a/create-and-publish-virtual-study/index.html +++ b/create-and-publish-virtual-study/index.html @@ -3,7 +3,7 @@ - + @@ -31,12 +31,12 @@ - + - + - - + + diff --git a/data-loading-for-developers/index.html b/data-loading-for-developers/index.html index 15dab06f9ef..b8f4e11716c 100644 --- a/data-loading-for-developers/index.html +++ b/data-loading-for-developers/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/data-loading-maintaining-studies/index.html b/data-loading-maintaining-studies/index.html index faa005f0899..34ecf8a6af5 100644 --- a/data-loading-maintaining-studies/index.html +++ b/data-loading-maintaining-studies/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/data-loading-tips-and-best-practices/index.html b/data-loading-tips-and-best-practices/index.html index 967cb53436c..02220c2206f 100644 --- a/data-loading-tips-and-best-practices/index.html +++ b/data-loading-tips-and-best-practices/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/data-loading/index.html b/data-loading/index.html index d650c915d1f..7320859a0c7 100644 --- a/data-loading/index.html +++ b/data-loading/index.html @@ -3,7 +3,7 @@ - + @@ -31,12 +31,12 @@ - + - + - - + + diff --git a/deployment/authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak/index.html b/deployment/authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak/index.html index 424bc21acb5..15e952f9e6d 100644 --- a/deployment/authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak/index.html +++ b/deployment/authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak/index.html @@ -3,7 +3,7 @@ - + @@ -33,12 +33,12 @@ - + - + - - + + diff --git a/deployment/authorization-and-authentication/authenticating-users-via-ldap/index.html b/deployment/authorization-and-authentication/authenticating-users-via-ldap/index.html index 2cf7eec8430..02eff8d917f 100644 --- a/deployment/authorization-and-authentication/authenticating-users-via-ldap/index.html +++ b/deployment/authorization-and-authentication/authenticating-users-via-ldap/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/authorization-and-authentication/authenticating-users-via-saml/index.html b/deployment/authorization-and-authentication/authenticating-users-via-saml/index.html index a1bbf6fc903..721abacddc4 100644 --- a/deployment/authorization-and-authentication/authenticating-users-via-saml/index.html +++ b/deployment/authorization-and-authentication/authenticating-users-via-saml/index.html @@ -3,7 +3,7 @@ - + @@ -33,11 +33,11 @@ - + - + - + diff --git a/deployment/authorization-and-authentication/authenticating-users-via-tokens/index.html b/deployment/authorization-and-authentication/authenticating-users-via-tokens/index.html index d9febf8db6d..b3bb71667ec 100644 --- a/deployment/authorization-and-authentication/authenticating-users-via-tokens/index.html +++ b/deployment/authorization-and-authentication/authenticating-users-via-tokens/index.html @@ -3,7 +3,7 @@ - + @@ -33,11 +33,11 @@ - + - + - + diff --git a/deployment/authorization-and-authentication/user-authorization/index.html b/deployment/authorization-and-authentication/user-authorization/index.html index 42849f239e2..389c080a8a3 100644 --- a/deployment/authorization-and-authentication/user-authorization/index.html +++ b/deployment/authorization-and-authentication/user-authorization/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/customization/application.properties-reference/index.html b/deployment/customization/application.properties-reference/index.html index 611cf959071..c3d832e1f2d 100644 --- a/deployment/customization/application.properties-reference/index.html +++ b/deployment/customization/application.properties-reference/index.html @@ -3,7 +3,7 @@ - + @@ -33,12 +33,12 @@ - + - + - - + + diff --git a/deployment/customization/caching/index.html b/deployment/customization/caching/index.html index 60a04034e38..e4d7de16c42 100644 --- a/deployment/customization/caching/index.html +++ b/deployment/customization/caching/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/customization/customizing-your-instance-of-cbioportal/index.html b/deployment/customization/customizing-your-instance-of-cbioportal/index.html index 74c76c88bcb..883e47633ee 100644 --- a/deployment/customization/customizing-your-instance-of-cbioportal/index.html +++ b/deployment/customization/customizing-your-instance-of-cbioportal/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/customization/download_custom_buttons-reference/index.html b/deployment/customization/download_custom_buttons-reference/index.html index 5e5ba800af9..ec776b41bbc 100644 --- a/deployment/customization/download_custom_buttons-reference/index.html +++ b/deployment/customization/download_custom_buttons-reference/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/customization/portal.properties-reference/index.html b/deployment/customization/portal.properties-reference/index.html index fb86597b2f2..f1af24fd25e 100644 --- a/deployment/customization/portal.properties-reference/index.html +++ b/deployment/customization/portal.properties-reference/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/customization/security.properties-reference/index.html b/deployment/customization/security.properties-reference/index.html index c7fca8c5219..400e922ea9d 100644 --- a/deployment/customization/security.properties-reference/index.html +++ b/deployment/customization/security.properties-reference/index.html @@ -3,7 +3,7 @@ - + @@ -31,12 +31,12 @@ - + - + - - + + diff --git a/deployment/customization/studyview/index.html b/deployment/customization/studyview/index.html index 86b75efc6e1..9478fdb89fe 100644 --- a/deployment/customization/studyview/index.html +++ b/deployment/customization/studyview/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/deploy-without-docker/build-from-source/index.html b/deployment/deploy-without-docker/build-from-source/index.html index a4a6ac81ed6..60a781c5bef 100644 --- a/deployment/deploy-without-docker/build-from-source/index.html +++ b/deployment/deploy-without-docker/build-from-source/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/deploy-without-docker/deploying/index.html b/deployment/deploy-without-docker/deploying/index.html index b8e2b3ba911..61489083ab0 100644 --- a/deployment/deploy-without-docker/deploying/index.html +++ b/deployment/deploy-without-docker/deploying/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/deploy-without-docker/import-the-seed-database/index.html b/deployment/deploy-without-docker/import-the-seed-database/index.html index c88da56c53e..08050565952 100644 --- a/deployment/deploy-without-docker/import-the-seed-database/index.html +++ b/deployment/deploy-without-docker/import-the-seed-database/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/deploy-without-docker/load-sample-cancer-study/index.html b/deployment/deploy-without-docker/load-sample-cancer-study/index.html index d15e99bed31..a45b3e2ac05 100644 --- a/deployment/deploy-without-docker/load-sample-cancer-study/index.html +++ b/deployment/deploy-without-docker/load-sample-cancer-study/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/deploy-without-docker/pre-build-steps/index.html b/deployment/deploy-without-docker/pre-build-steps/index.html index 804fc550958..0259bb4a872 100644 --- a/deployment/deploy-without-docker/pre-build-steps/index.html +++ b/deployment/deploy-without-docker/pre-build-steps/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/deploy-without-docker/software-requirements/index.html b/deployment/deploy-without-docker/software-requirements/index.html index 75bc13d7469..104e0b6fe48 100644 --- a/deployment/deploy-without-docker/software-requirements/index.html +++ b/deployment/deploy-without-docker/software-requirements/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/docker/example_commands/index.html b/deployment/docker/example_commands/index.html index 550c2e85ba8..fd4345fd70b 100644 --- a/deployment/docker/example_commands/index.html +++ b/deployment/docker/example_commands/index.html @@ -3,7 +3,7 @@ - + @@ -31,12 +31,12 @@ - + - + - - + + diff --git a/deployment/docker/import_data/index.html b/deployment/docker/import_data/index.html index 3448b072b8d..e5c0d7abdd7 100644 --- a/deployment/docker/import_data/index.html +++ b/deployment/docker/import_data/index.html @@ -3,7 +3,7 @@ - + @@ -31,12 +31,12 @@ - + - + - - + + diff --git a/deployment/docker/index.html b/deployment/docker/index.html index a7a67691f25..989267ab39c 100644 --- a/deployment/docker/index.html +++ b/deployment/docker/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/docker/notes-for-non-linux/index.html b/deployment/docker/notes-for-non-linux/index.html index ee770148816..55504c19a86 100644 --- a/deployment/docker/notes-for-non-linux/index.html +++ b/deployment/docker/notes-for-non-linux/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/docker/using-keycloak/index.html b/deployment/docker/using-keycloak/index.html index 3fc6964007f..8b54b1cca23 100644 --- a/deployment/docker/using-keycloak/index.html +++ b/deployment/docker/using-keycloak/index.html @@ -3,7 +3,7 @@ - + @@ -31,12 +31,12 @@ - + - + - - + + diff --git a/deployment/index.html b/deployment/index.html index 144d80440b6..bbf775df6d8 100644 --- a/deployment/index.html +++ b/deployment/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/deployment/integration-with-other-webservices/index.html b/deployment/integration-with-other-webservices/index.html index 8b67cab38dc..ce34674e75c 100644 --- a/deployment/integration-with-other-webservices/index.html +++ b/deployment/integration-with-other-webservices/index.html @@ -3,7 +3,7 @@ - + @@ -28,11 +28,11 @@ - + - + - + diff --git a/deployment/integration-with-other-webservices/oncokb-data-access/index.html b/deployment/integration-with-other-webservices/oncokb-data-access/index.html index 6a76cd641b7..8fefb50c91a 100644 --- a/deployment/integration-with-other-webservices/oncokb-data-access/index.html +++ b/deployment/integration-with-other-webservices/oncokb-data-access/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/development/build-different-frontend/index.html b/development/build-different-frontend/index.html index b489c6eff7d..39cf23ba6b0 100644 --- a/development/build-different-frontend/index.html +++ b/development/build-different-frontend/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/development/cbioportal-er-diagram/index.html b/development/cbioportal-er-diagram/index.html index 814d5467891..ac412974d56 100644 --- a/development/cbioportal-er-diagram/index.html +++ b/development/cbioportal-er-diagram/index.html @@ -3,7 +3,7 @@ - + @@ -33,11 +33,11 @@ - + - + - + diff --git a/development/database-versioning/index.html b/development/database-versioning/index.html index 3bf7c50869f..0ca35541bcc 100644 --- a/development/database-versioning/index.html +++ b/development/database-versioning/index.html @@ -3,7 +3,7 @@ - + @@ -31,12 +31,12 @@ - + - + - - + + diff --git a/development/deployment-procedure/index.html b/development/deployment-procedure/index.html index 02772259dc7..d0ae9ed0e63 100644 --- a/development/deployment-procedure/index.html +++ b/development/deployment-procedure/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/development/documentation-site/index.html b/development/documentation-site/index.html index d7fe3260e3c..6387817c552 100644 --- a/development/documentation-site/index.html +++ b/development/documentation-site/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/development/feature-development-guide/index.html b/development/feature-development-guide/index.html index 9c783d7711a..6d8750cf43b 100644 --- a/development/feature-development-guide/index.html +++ b/development/feature-development-guide/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/development/index.html b/development/index.html index a3a0cff6ae4..506821ddbaa 100644 --- a/development/index.html +++ b/development/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/development/manual-test-cases/index.html b/development/manual-test-cases/index.html index b7b678a3c62..b568a71eccf 100644 --- a/development/manual-test-cases/index.html +++ b/development/manual-test-cases/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/development/release-procedure/index.html b/development/release-procedure/index.html index b769cb8a07b..a920ddf5e49 100644 --- a/development/release-procedure/index.html +++ b/development/release-procedure/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + diff --git a/development/session-service-working/index.html b/development/session-service-working/index.html index f7ac9644c69..f3d1aee529f 100644 --- a/development/session-service-working/index.html +++ b/development/session-service-working/index.html @@ -3,7 +3,7 @@ - + @@ -31,11 +31,11 @@ - + - + - + @@ -267,9 +267,7 @@

Here are the properties that needs to be set

-
WARNING: do not use session service with -Dauthenticate=false
- either use authentication or change to -Dauthenticate=noauthsessionservice
-session.service.url=
+
session.service.url=
 #if basic authentication is enabled on session service one should set:
 session.service.user=
 session.service.password=

diff --git a/downloads/index.html b/downloads/index.html
index 9e5e3db3265..1602ea5b66b 100644
--- a/downloads/index.html
+++ b/downloads/index.html
@@ -3,7 +3,7 @@
 
     
     
-    
+    
 
     
     
@@ -31,11 +31,11 @@
     
 
     
-    
+    
 
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diff --git a/file-formats/index.html b/file-formats/index.html
index 9e775e9a88e..91b979557d0 100644
--- a/file-formats/index.html
+++ b/file-formats/index.html
@@ -3,7 +3,7 @@
 
     
     
-    
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@@ -33,12 +33,12 @@
     
 
     
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diff --git a/hardware-requirements/index.html b/hardware-requirements/index.html
index dcbe2e2b09a..cb8ddb17dcc 100644
--- a/hardware-requirements/index.html
+++ b/hardware-requirements/index.html
@@ -3,7 +3,7 @@
 
     
     
-    
+    
 
     
     
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diff --git a/import-gene-panels/index.html b/import-gene-panels/index.html
index 319238604f5..caff16d1885 100644
--- a/import-gene-panels/index.html
+++ b/import-gene-panels/index.html
@@ -3,7 +3,7 @@
 
     
     
-    
+    
 
     
     
@@ -31,11 +31,11 @@
     
 
     
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diff --git a/import-gene-sets/index.html b/import-gene-sets/index.html
index 3e4aa34259b..45864fcb066 100644
--- a/import-gene-sets/index.html
+++ b/import-gene-sets/index.html
@@ -3,7 +3,7 @@
 
     
     
-    
+    
 
     
     
@@ -31,11 +31,11 @@
     
 
     
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diff --git a/import-oncokb-annotations-as-custom-driver-annotations/index.html b/import-oncokb-annotations-as-custom-driver-annotations/index.html
index e5136134441..e8befe0973e 100644
--- a/import-oncokb-annotations-as-custom-driver-annotations/index.html
+++ b/import-oncokb-annotations-as-custom-driver-annotations/index.html
@@ -3,7 +3,7 @@
 
     
     
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+    
 
     
     
@@ -31,11 +31,11 @@
     
 
     
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diff --git a/import-reference-genome/index.html b/import-reference-genome/index.html
index 410e054bf1b..57dae4cef8a 100644
--- a/import-reference-genome/index.html
+++ b/import-reference-genome/index.html
@@ -3,7 +3,7 @@
 
     
     
-    
+    
 
     
     
@@ -31,11 +31,11 @@
     
 
     
-    
+    
 
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diff --git a/import-study-using-docker/index.html b/import-study-using-docker/index.html
index 56be0dc293e..cd67a50cf57 100644
--- a/import-study-using-docker/index.html
+++ b/import-study-using-docker/index.html
@@ -3,7 +3,7 @@
 
     
     
-    
+    
 
     
     
@@ -31,12 +31,12 @@
     
 
     
-    
+    
 
-    
+    
     
-    
-    
+    
+    
 
     
 
diff --git a/imported-maf-columns/index.html b/imported-maf-columns/index.html
index 65708d5a720..634332c7eae 100644
--- a/imported-maf-columns/index.html
+++ b/imported-maf-columns/index.html
@@ -3,7 +3,7 @@
 
     
     
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