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Resolve issue #5242 #5245

Merged
merged 1 commit into from
Jan 11, 2019
Merged

Resolve issue #5242 #5245

merged 1 commit into from
Jan 11, 2019

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ao508
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@ao508 ao508 commented Nov 14, 2018

What? Why?

Fix #5242

Changes proposed in this pull request:

  • Resolve mismatch in cgds.sql and migration.sql varchar size for mutation_count_by_keyword.KEYWORD

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  • If this is a feature, the PR is to rc. If this is a bug fix, the PR is to master.

@ao508 ao508 mentioned this pull request Nov 14, 2018
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@ao508 ao508 requested review from sheridancbio and n1zea144 and removed request for n1zea144 November 14, 2018 15:38
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ao508 commented Dec 6, 2018

🔔 @pieterlukasse

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This corrects a divergence between cgds.sql and migration.sql. It is good to bring them into sync, but we should keep in mind now that anybody who has performed a fresh install of the cbioportal database using db_schema_version between 2.6.1 and now (2.7.3) .. they will have a shorter KEYWORD field, and it will never be upgraded by future migrations because their schema version is "new" enough to think it is not necessary. Maybe we should (unfortunately) add another db migration step which again makes an ALTER TABLE statement in migration.sql to convert the KEYWORD field to width 255. I assume altering a table to be the same that it currently is will not throw an error.

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I have confirmed .. an alter table statement which keeps the same data definition for a column does not cause an error. Such as : alter table info modify column DB_SCHEMA_VERSION varchar(24) default null;

@ao508
Resolve issue #5242
a61185b 
Resolve mismatch in cgds.sql and migration.sql varchar size for `mutation_count_by_keyword.KEYWORD` (issue #5242)
@ao508 ao508 merged commit a39d1e6 into master Jan 11, 2019
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inodb commented Jan 15, 2019

@sheridancbio @angelicaochoa we should prolly still create a new migration for this right? Maybe we can add it as part of the migration currently in release-2.1.0 branch?

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ao508 commented Jan 15, 2019 •
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@inodb the mutation piece is already present, it was just left out of the cgds.sql by accident.

It was part of version 2.6.1

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inodb commented Jan 15, 2019

@angelicaochoa isn't the issue @sheridancbio mentioned unresolved? If somebody recently installed a seed cgds.sql from e.g. v2.6.1, they would never have this varchar increase?

If that's indeed the case it might be good to duplicate the same migration as part of v2.7.4 (which is currently in release-2.1.0 branch). Basically add the statement ALTER TABLE `mutation_count_by_keyword` MODIFY COLUMN `KEYWORD` VARCHAR(255); to the v2.7.4 migration.

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ao508 commented Jan 16, 2019

@inodb ah, I see. Good point. Think I should just move the original migration statement to the appropriate place then or duplicate it?

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inodb commented Jan 16, 2019

@angelicaochoa duplicating it should be fine, maybe with a comment in the migration.sql referring to this PR

@sheridancbio sheridancbio deleted the mut-count-keyword-varchar branch January 17, 2019 15:46
sheridancbio added a commit to sheridancbio/cbioportal that referenced this pull request May 29, 2019
@sheridancbio
StudyViewController changed to use Interceptor for arg parsing
badbf94 
- now that the separation of the web and security module work is merged to master, this controller needed to be updated to use the InvolvedCancerStudyExtractorInterceptor functionality before passing the argumentes for pre-authorization. (as is done currently in the release-3.0.0 branch)
- the necessary functionality in InvolvedCancerStudyExtractorInterceptor from the release-3.0.0 branch is also added
- some model changes in the 3.0.0 branch were not yet available, so those are left unchanged here
- the updates in this PR were already done in release-3.0.0 branch and rc. If the changes introduced here do not show up as conflicts during automated merger of master into release-3.0.0 branch, release-3.0.0 may break. However, conflicts are predicted, and will need to be resolved again manualy by discarding these changes and keeping the head of release-3.0.0 intact.
- the code included here was mainly introduced in commit 380d687aa642969e7e655ab6e187a9ab85803c47 to release-3.0.0 (Feb 21) by Karthik Kalletla <[email protected]>

Co-authored-by: Karthik Kalletla <[email protected]>

commit f7e11c820ecef6dd9442b8637c730a2f91584b7d
Author: Robert Sheridan <[email protected]>
Date:   Tue May 28 18:16:29 2019 -0400

    StudyViewController changed to use Interceptor for arg parsing
    - now that the separation of the web and security module work is merged to master, this controller needed to be updated to use the InvolvedCancerStudyExtractorInterceptor functionality before passing the argumentes for pre-authorization. (as is done currently in the release-3.0.0 branch)
    - the necessary functionality in InvolvedCancerStudyExtractorInterceptor from the release-3.0.0 branch is also added
    - some model changes in the 3.0.0 branch were not yet available, so those are left unchanged here
    - the updates in this PR were already done in release-3.0.0 branch and rc. If the changes introduced here do not show up as conflicts during automated merger of master into release-3.0.0 branch, release-3.0.0 may break. However, conflicts are predicted, and will need to be resolved again manualy by discarding these changes and keeping the head of release-3.0.0 intact.

commit 8f7a1d57ae81f902b273257c73abce2eacf2c84c
Merge: 9077178 4bb297e
Author: alisman <[email protected]>
Date:   Tue May 28 10:18:42 2019 -0400

    Merge pull request #6166 from cBioPortal/fix-bean-not-found-error-in-master

    change ObjectMapper in InvolvedCancerStudyExtractorInterceptor

commit 4bb297e0367a12b067f6b7bd274379f425709617
Author: Avery Wang <[email protected]>
Date:   Thu Apr 18 15:22:33 2019 -0400

    change ObjectMapper in InvolvedCancerStudyExtractorInterceptor to not using Autowiring/Bean
    Just instantiate an ObjectMapper to use
    resolves "bean not found of type" error message in tomcat catalina.out

    Signed-off-by: Avery Wang <[email protected]>

commit 907717816ed2e1fefb44e834a26da8b495062896
Merge: f87e5c8 6b71c75
Author: Ino de Bruijn <[email protected]>
Date:   Fri May 24 14:48:34 2019 -0400

    Merge pull request #6159 from cBioPortal/update-tools-jsp-link

    update tools.jsp link

commit 6b71c754f2b577852aa7590f587d9fa96807be6a
Author: Ino de Bruijn <[email protected]>
Date:   Fri May 24 13:55:57 2019 -0400

    update tools.jsp link

commit f87e5c8e8c66f15dc4a164db9e1642e66c526fab
Merge: ea33422 00f636d
Author: alisman <[email protected]>
Date:   Tue May 21 11:28:50 2019 -0400

    Merge pull request #6124 from alisman/release-221

    Update frontend to release v2.2.1

commit 00f636d68d401ff5a508d3c75a26fdd15b8a9d83
Author: lismana <[email protected]>
Date:   Tue May 21 10:30:59 2019 -0400

    Update frontend to release v2.2.1

commit ea3342206abf90bc04e8315d5c71afffaf313b7f
Merge: 9cc6b2d c27be64
Author: Ino de Bruijn <[email protected]>
Date:   Wed May 15 12:45:32 2019 -0400

    update biogene url (#6102)

    update biogene url

commit 9cc6b2d2a386cf281bab0e6f31bfbb048583a233
Merge: c3601a8 cdc109f
Author: JianJiong Gao <[email protected]>
Date:   Tue May 14 17:21:38 2019 -0400

    Fix description in Copy Number Enrichments (#6089)

    Fix description in Copy Number Enrichments

commit c27be647ebb93cf3a81b0f01cacbbccf4a8f8098
Author: Ino de Bruijn <[email protected]>
Date:   Tue May 14 14:52:22 2019 -0400

    update biogene url

commit cdc109fb2ea2680933cc686153872b6c05332cc1
Author: kojix2 <[email protected]>
Date:   Mon May 13 15:14:06 2019 +0900

    Fix description in Copy Number Enrichments

commit c3601a875ede8e6a897abf61400256ba63107a87
Merge: 08a16db 77ecb8e
Author: Ino de Bruijn <[email protected]>
Date:   Wed May 8 18:02:53 2019 -0400

    Add PTM news (#6072)

    Add PTM news

commit 77ecb8e2cf6d5232953a48761bdadcc0ce74b016
Author: Ino de Bruijn <[email protected]>
Date:   Wed May 8 13:25:01 2019 -0400

    add colon in news

commit 9845279fcf576745798de0458efc5169de036bb3
Author: Ino de Bruijn <[email protected]>
Date:   Wed May 8 13:24:00 2019 -0400

    add link to ptm query

commit d1db7eac666e4622c7ced9f1b2d36d9bd1598777
Author: Ino de Bruijn <[email protected]>
Date:   Wed May 8 12:27:09 2019 -0400

    Add PTM news

commit 08a16dbaddc257ad8e8b13ac11059289e94d56f6
Merge: 4eda4ab eb577a1
Author: Ino de Bruijn <[email protected]>
Date:   Mon May 6 12:05:10 2019 -0400

    fix gene panel matrix hyperlink (#6037)

    fix gene panel matrix hyperlink

commit 4eda4abf773e7a78fd3e960ae94373a8f6f01bc1
Merge: c146883 1e48a5c
Author: alisman <[email protected]>
Date:   Mon May 6 11:20:45 2019 -0400

    Merge pull request #6061 from lemccarthy/master-analytics-config

    Added configuration entry for analytics report url

commit 1e48a5ce4d4d70cdee0479080dfaa80c72dd1b2d
Author: Lloyd McCarthy <[email protected]>
Date:   Mon May 6 10:58:06 2019 -0400

    Added configuration entry for analytics report url

commit eb577a15d14e94a10d0e5983d816eebe8feca537
Author: gaofei zhao <[email protected]>
Date:   Wed May 1 11:44:57 2019 -0400

    fix gene panel matrix hyperlink

commit c1468832fca041bbe8b0c00342eba19dd821ed2c
Merge: b331932 7d7728a
Author: Ino de Bruijn <[email protected]>
Date:   Mon Apr 29 11:45:24 2019 -0400

    Merge pull request #6026 from sheridancbio/break-security-module-dependency-on-web-in-master

    Security module dependency on web module is eliminated

commit 7d7728a7b47710cf46cdd4b9abc29cf0aba135a5
Author: Robert Sheridan <[email protected]>
Date:   Tue Nov 6 10:45:30 2018 -0500

    Security module dependency on web module is eliminated

    - security/spring-security is now dependent on persistence/persistence-mybatis instead
    - CancerStudyPermissionEvaluator awareness of Web API request filters has been removed
        - instead, the logic for parsing user supplied filter arguments to Web API endpoints has been moved to a web module interceptor class (InvolvedCancerStudyExtractorInterceptor)
        - when authorization of Web API requests is necessary, this interceptor will parse user supplied filter arguments and set a request attribute with the involved cancer studies
        - CancerStudyPermissionEvaluator will now authorize requests based on cancer study identifier lists stored in a request attribute (named involvedCancerStudies)
        - parsed filter types:
            - ClinicalAttributeCountFilter
            - ClinicalDataIdentifier
            - ClinicalDataMultiStudyFilter
            - GenePanelMultipleStudyFilter
            - MolecularDataMultipleStudyFilter
            - MolecularProfileFilter
            - MutationMultipleStudyFilter
            - PatientFilter
            - SampleFilter
        - to avoid an error where a parsed/read POST request body was failing to be re-read, the request body parameter is also saved as an attribute and referenced in the handler through the attribute
    - CancerStudyPermissionEvaluator has been clarified / simplified
        - caching of maps from identifiers to modeled objects {CancerStudy, MolecularProfile, SampleList} has been encapsulated in persistence layer utility CacheMapUtil
        - 3 direct model object authorization modes and 8 indirect (by reference to an id) target types can be evaluated with hasPermission()
        - all indirect types are identified by string comparison to symbolic constants with more accurate names:
            - TARGET_TYPE_CANCER_STUDY_ID = "CancerStudyId";
            - TARGET_TYPE_MOLECULAR_PROFILE_ID = "MolecularProfileId";
            - TARGET_TYPE_GENETIC_PROFILE_ID = "GeneticProfileId"; (synonym for MolecularProfileId)
            - TARGET_TYPE_SAMPLE_LIST_ID = "SampleListId";
            - TARGET_TYPE_COLLECTION_OF_SAMPLE_LIST_IDS = "Collection<SampleListId>";
            - TARGET_TYPE_COLLECTION_OF_CANCER_STUDY_IDS = "Collection<CancerStudyId>";
            - TARGET_TYPE_COLLECTION_OF_MOLECULAR_PROFILE_IDS = "Collection<MolecularProfileId>";
            - TARGET_TYPE_COLLECTION_OF_GENETIC_PROFILE_IDS = "Collection<GeneticProfileId>"; (synonym for MolecularProfileId)
        - determination of target type has been separated from the processing of different target types
        - target type processing functions have been made more parallel
    - all controller (and service) classes have been updated to use updated target type identifiers in @PreAuthorize annotations
    - controllers for endpoints with user supplied POST body filters have been udpated to use extracted involvedCancerStudies attribute
            - ClinicalAttributeController
            - ClinicalDataController
            - CopyNumberSegmentController
            - GenePanelController
            - MolecularDataController
            - MolecularProfileController
            - MutationController
            - PatientController
            - SampleController
    - Authorization is now implied by Authentication profile
        - the available authentication profiles are now summarized in a comment in applicationContext-security.xml
        - three profiles do not perform authorization via spring method security pre-post-annotations : {false, social_auth, noauthsessionservice}. All others do.
        - it was observed that the independent behavior of the authorization property was no longer supported.
            - setting authorization=true with authentication=social_auth was not supported
            - setting authorization=false with authentication=googleplus was not supported
            - in general, the authorization setting was already being ignored, and the authentication setting was determining the use (or non-use) of pre-post-annotations
            - as this seemed to not be a feature needed by current users, and because it would be difficult to work out
                    the semantics of a system where authorization=true where authentication is optional (social_auth),
                    it was decided to continue allowing authentication profile to determine the authorization mode.
                    Therefore no functional change is made here, other than to drop the unsupported/unenforced authorization property.
    - Documentation pages have been updated to reflect the dropping of an authorization property
    - Authorization infrastructure is (nearly) inactive when not needed
        - needed identifier map caches are not constructed
        - Web API filter parameters in post bodies are not parsed to derive the involvedCancerStudies attribute
    - Web layer unit tests
        - done without authentication (as before)
        - null mocks of the necessary interceptor classes are provided for spring wiring only. (created in reused (web and weblegacy) Configuration class)
        - travis CI configuration now specifies testing with -Dauthentication=none profile
        - ObjectMapper now autowired (rather than manually instantiated in each class)
    - bug fixes
        - wrong paging constants have been replaced with repository limit/offset arguments in CacheMapUtil repository requests
        - path to patient fetch endpoint has been corrected
        - added missing drop table line in cgds.sql for reference_genome_gene (allows use of persistent/external database for unit testing)
    - some whitespace cleanup / style standardization
    - drop unused classes
        - TestGenePanelUtil
        - TestImportUtil

    Key files to review:
    - persistence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/util/CacheMapUtil.java
        (stores identifier to model object maps for pre-post-annotation checking, determines if pre-post-annotations are active using authentication profile)
    - security/security-spring/src/main/java/org/cbioportal/security/spring/CancerStudyPermissionEvaluator.java
        (approves or denies access to resources based on authenticated user identity, user authorities to cancer studies in cbioportal database, set of requested resources)
    - web/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java
        (now parses POST body filter parameters (inferring the arriving filter type from the request endpoint) and computes/stores involvedCancerStudies in attribute)
    - security/security-spring/src/main/resources/applicationContext-security.xml
        (documents available authentication filter profiles)
    - web/src/main/resources/applicationContext-web.xml
        (adds interceptor to spring-mvc)
    - web controller classes involved in POST body filter parameter requests (see list above)
        (shows the annotation of RequestAttributes to hold passed parameter and computed involvedCancerStudies attribute)

    Co-authored-by: Angelica Ochoa <[email protected]>

commit b331932db1011611e38ccd085fbbdbd5d2dc92b0
Merge: 0bd0171 9582971
Author: Ino de Bruijn <[email protected]>
Date:   Fri Apr 26 17:31:26 2019 -0400

    Update News.md (#6022)

    Update News.md

commit 9582971f68cfde77793cb35c0bd27602b8b5cfb9
Merge: 7628514 0bd0171
Author: ritikakundra <[email protected]>
Date:   Fri Apr 26 17:11:18 2019 -0400

    Merge branch 'master' into ritikakundra-patch-3

commit 0bd017137bb9a02161b222965b46efa0030eca77
Merge: e34f262 a8b31bd
Author: Ino de Bruijn <[email protected]>
Date:   Fri Apr 26 17:03:48 2019 -0400

    Load applicationContext-business.xml first (#6012)

    Load applicationContext-business.xml first

commit 7628514328e15d6a5afaba95e0ebeeae284a0abd
Author: ritikakundra <[email protected]>
Date:   Fri Apr 26 16:51:38 2019 -0400

    Update News.md

commit fa970f1e834f01f8b23a817bc31bc14894f4ec0f
Author: ritikakundra <[email protected]>
Date:   Fri Apr 26 15:07:04 2019 -0400

    Update News.md

commit e34f2622cec03f3b98cd68bfeac4861a30826aba
Merge: 1f2c6be cc15754
Author: Ino de Bruijn <[email protected]>
Date:   Fri Apr 26 10:43:27 2019 -0400

    Merge pull request #5900 from inodb/add-release-n-deployment-procedure

    Add documentation describing release + deployment

commit cc15754230b7976549dc7087fece6d1c281a0f2f
Author: Ino de Bruijn <[email protected]>
Date:   Fri Apr 26 10:29:05 2019 -0400

    deploy docs add netlify note

commit be00f10a4e05fd1af2e3c632aab2516e950f55cc
Author: Ino de Bruijn <[email protected]>
Date:   Tue Mar 26 19:32:48 2019 -0400

    Add documentation describing release + deployment

    This describes our internal release and deployment procedures.

commit 1f2c6beb822b568f2c62e8e2fca4fa0673ee2569
Author: Fedde Schaeffer <[email protected]>
Date:   Thu Apr 25 18:18:15 2019 +0200

    Document clarified guidelines for code review (#5746)

    * Document the practice of requesting PR review
    * Suggest explicit review requesting guidelines
         Aiming to avoid the situation in which it's unclear whether someone is
    still writing  a review or has decided not to prioritise it since they
    wouldn't find much that other reviewers haven't already found.
         Also documenting the practice of notifying reviewers who know more about
    use-cases and architectural decisions related to the logic/docs being
    changed.
    * Remove the requirement for Signed-off-by commits
        Most commits being accepted into cBioPortal do not contain such a
    string, and since the project does not define what it means by it,
    they do not add clarity to the legal intentions of the contributor.
    * Ask contributors not to squash during review
        This makes it easier for reviewers to see what changed since the last
    time they looked.
    * Document asking to squash amendments after review

commit a8b31bd1d8c04b46d21a5d11a6cb0505df66da7a
Author: oplantalech <[email protected]>
Date:   Fri Apr 19 17:00:13 2019 +0200

    Load applicationContext-business.xml first

commit 760e8e176584b047ad412319d523579f7f3445b7
Merge: 8ae5ac3 57a61c3
Author: Hongxin <[email protected]>
Date:   Wed Apr 24 11:41:06 2019 -0400

    Merge pull request #6008 from kalletlak/sv-fixes

    Fix mutationCountVsCNASelection filtering in study view api's

commit 57a61c37f1e949ec7c379c8c533cf1443ee402e5
Author: Karthik Kalletla <[email protected]>
Date:   Tue Apr 23 16:21:06 2019 -0400

    Fix mutationCountVsCNASelection filtering in study view api's

commit 8ae5ac3ccc5f0b7b0bada33851ffcfd8ca7325de
Merge: ff2c049 690f5ae
Author: Ino de Bruijn <[email protected]>
Date:   Tue Apr 23 16:14:02 2019 -0400

    fix hyperlink broken (#5976)

    fix hyperlink broken

commit ff2c0499e09a7f608b389a301e30d7fb21ff9b44
Merge: cb8e474 feabd77
Author: Hongxin <[email protected]>
Date:   Fri Apr 19 11:51:24 2019 -0400

    Merge pull request #5983 from zhx828/update-doc

    Update tutorials page link; Update all portal link to https://www.cbioportal.org

commit feabd77aaddd055f35832555e2b0874da55ad0ae
Author: Hongxin Zhang <[email protected]>
Date:   Thu Apr 18 10:26:11 2019 -0400

    Update tutorials page link; Update all portal link to https://www.cbioportal.org

commit 690f5ae8668eb6da0c310dedd7edb1223cc8947f
Author: gaofei zhao <[email protected]>
Date:   Tue Apr 16 11:16:19 2019 -0400

    fix hyperlink broken

commit cb8e474c52a0bc90ccd9914f380fcacdad8fd343
Merge: f35c58c 62ed702
Author: Ersin Ciftci <[email protected]>
Date:   Mon Apr 15 14:03:24 2019 -0400

    Merge pull request #5973 from lemccarthy/swagger-fix

    Added prefixes to the swagger endpoint tags

commit 62ed7026cd70a97823052203d92575e344450f0e
Author: Lloyd McCarthy <[email protected]>
Date:   Mon Apr 15 12:55:17 2019 -0400

    Added prefixes to the swagger endpoints to enforce a visual ordering in the swagger ui

commit f35c58c8dd92c48462021f59819aea39c7be3cec
Merge: 9204b8a 6cf798a
Author: Ersin Ciftci <[email protected]>
Date:   Thu Apr 11 16:11:47 2019 -0400

    Merge pull request #5959 from lemccarthy/master-quicksearch

    Fixed a bug with the ordering of quicksearch trial results

commit 6cf798afefce381439ddaa749e2670eb3e6fcd3e
Author: Lloyd McCarthy <[email protected]>
Date:   Thu Apr 11 15:34:03 2019 -0400

    Fixed a bug with the ordering of quicksearch results

commit 9204b8ac5d479132459e3a6053955cff8c2cb832
Merge: e766dfa 6c776a8
Author: alisman <[email protected]>
Date:   Mon Apr 8 15:38:53 2019 -0400

    Merge pull request #5946 from kalletlak/fix-5944

    Fix patient API issue in private portal

commit 6c776a87e74ba222535459767c0ec9fc665a9e1d
Author: Karthik Kalletla <[email protected]>
Date:   Mon Apr 8 14:40:45 2019 -0400

    Fix patient API issue in private portal

commit e766dfaa080d2036db8f930b5fc5213bb0379649
Merge: a099f25 f343178
Author: Ino de Bruijn <[email protected]>
Date:   Wed Apr 3 15:17:33 2019 -0400

    Merge pull request #5927 from lemccarthy/master

    Fixed bugged document display

commit f343178d078918ffd643aedb8f849f2faae3716d
Author: Lloyd McCarthy <[email protected]>
Date:   Wed Apr 3 13:15:13 2019 -0400

    Fixed bugged document display

commit a099f259e08b76e296f270846c11aaac56f02cf7
Merge: a3c9bb0 b521912
Author: Ersin Ciftci <[email protected]>
Date:   Wed Apr 3 01:52:31 2019 -0400

    Merge pull request #5905 from ersinciftci/coexp-opt

    Co-expression memory optimization

commit b5219125d8453c4a7676583a843009eb25328196
Author: Ersin Ciftci <[email protected]>
Date:   Wed Mar 27 15:49:41 2019 -0400

    Co-expression memory optimization

commit a3c9bb0f467486fa790438d3a10539d58e8ee478
Merge: 08eee8d 6405b36
Author: Ino de Bruijn <[email protected]>
Date:   Thu Mar 28 23:53:33 2019 -0400

    Merge pull request #5914 from cBioPortal/release-2.2.0

    Release 2.2.0

commit 6405b36d0a9d392a366a7061c4b03e6ce7a7d1b5
Author: Ino de Bruijn <[email protected]>
Date:   Thu Mar 28 23:37:52 2019 -0400

    update frontend to v2.2.0

commit 7904e7958e2868a4a2ad2d1a08031ed81ac25491
Merge: 09d0e83 08eee8d
Author: Ino de Bruijn <[email protected]>
Date:   Thu Mar 28 19:19:25 2019 -0400

    Merge remote-tracking branch 'origin/master' into release-2.2.0

commit 08eee8d189bbfbabbe7a77a2d8502b82fe15c384
Merge: 307e8dd 8f9f129
Author: Ino de Bruijn <[email protected]>
Date:   Thu Mar 28 18:25:20 2019 -0400

    Merge pull request #5913 from alisman/release-2.1.1

    release-2.1.1

commit 8f9f129b753cbf831987563eb51ee87228737b80
Author: aaronlisman <[email protected]>
Date:   Thu Mar 28 17:13:09 2019 -0400

    release-2.1.1

commit 09d0e83823f22bb0730939abf2d90be7b0ce6daf
Author: Ino de Bruijn <[email protected]>
Date:   Wed Mar 27 17:54:17 2019 -0400

    Add quick search news section (#5906)

commit afce285ca05c68f09d1cf5adc8f94b4dda910bcd
Merge: cfaf781 307e8dd
Author: Ino de Bruijn <[email protected]>
Date:   Wed Mar 27 00:00:01 2019 -0400

    Automated master to release-2.2.0 merge

commit cfaf78146449662deecd9ccab2cf1d91b565e6d7
Author: Ino de Bruijn <[email protected]>
Date:   Tue Mar 26 14:56:47 2019 -0400

    Add quick search beta configuration and docs (#5863)

    * Add quick search beta configuration and docs

    * Remove linkout, let frontend handle this

    handle e.g. /ln?q=TP53:MUT on frontend

    * Update frontend version - Handle /ln? links

    * update /ln? documentation

commit 307e8dd91cc99367696cb531141cf90a78d3eabb
Merge: e7a861c 4916181
Author: Ino de Bruijn <[email protected]>
Date:   Tue Mar 26 11:45:03 2019 -0400

    Merge pull request #5821 from cBioPortal/jjgao-patch-7

    fixed #5812

commit e7a861cec60050bd8f63949908df9d01dbad66b8
Merge: 46010cb 1cb945d
Author: Ino de Bruijn <[email protected]>
Date:   Tue Mar 26 11:15:52 2019 -0400

    Merge pull request #5868 from cBioPortal/jjgao-patch-11

    Update About-Us.md

commit 20efd06f90e91649f8f10ab66af68e3482e75398
Merge: 7ce99a3 46010cb
Author: Ino de Bruijn <[email protected]>
Date:   Tue Mar 26 00:00:02 2019 -0400

    Automated master to release-2.2.0 merge

commit 46010cbd07422c1b481a8078221a687ba0435387
Merge: f249a40 26c4f64
Author: Hongxin <[email protected]>
Date:   Mon Mar 25 17:43:28 2019 -0400

    Merge pull request #5842 from zhx828/issue-4277

    Remove oncokb.api.url property; Remove cross_cancer_results servlet

commit 26c4f64dee41debee447318dd693a2841499cf08
Author: Hongxin Zhang <[email protected]>
Date:   Thu Mar 7 13:54:46 2019 -0500

    Remove oncokb.api.url property; Remove cross_cancer_results servlet

commit 7ce99a37008c8daa25235223789595e96203c3ae
Merge: 13aa67e 56de1cb
Author: Ino de Bruijn <[email protected]>
Date:   Fri Mar 22 14:01:23 2019 -0400

    Merge pull request #5885 from inodb/fix-cancer-studies-by-keyword-endpoint

    Fix /api/studies/ keyword+pageSize resp size

commit 56de1cb5f9766d3c7a157c975da8d716bb8f2eef
Author: Ino de Bruijn <[email protected]>
Date:   Fri Mar 22 12:15:45 2019 -0400

    Fix /api/studies/ keyword+pageSize resp size

    The primary site keyword search would not disregard duplicates when determining
    how many studies to add. This fixes that. As an example: on current public
    portal querying with keyword head and selecting a pageSize of 15 would not
    return a response with all 13 studies, it would return fewer.

commit 13aa67ec12929bac1a7a2165c7fe03d0374ef385
Merge: c112c6c f249a40
Author: Ino de Bruijn <[email protected]>
Date:   Fri Mar 22 00:00:02 2019 -0400

    Automated master to release-2.2.0 merge

commit f249a409ae112f18d4f4df578d35abf74bdad7fc
Merge: 3eb7c74 451cdea
Author: ao508 <[email protected]>
Date:   Thu Mar 21 17:01:29 2019 -0400

    Merge pull request #5765 from sheridancbio/make-db-schema-mysql8-friendly

    reduce prefix length of tumor_seq_allele field in db key

commit 451cdeacb06606369ff13b64219fce70388c679b
Author: Robert Sheridan <[email protected]>
Date:   Wed Feb 20 11:50:58 2019 -0500

    reduce prefix length of tumor_seq_allele field in db key

commit c112c6cb8251e3199ce792ba0ea65d6f3c0b7743
Merge: ce0f59c 3eb7c74
Author: Ino de Bruijn <[email protected]>
Date:   Thu Mar 21 00:00:02 2019 -0400

    Automated master to release-2.2.0 merge

commit 3eb7c745c40449f5e6cb756eb495ff113d56669d
Merge: a0995c1 0e07517
Author: n1zea144 <[email protected]>
Date:   Wed Mar 20 19:51:31 2019 -0400

    Merge pull request #5876 from n1zea144/molecular-data-service-opt-2

    Replace list.indexOf() with map.get() speeds up MolecularDataServiceImpl.fetchMolecularData

commit 0e07517500913f4297658d1a9c2e5068b923d908
Author: n1zea144 <[email protected]>
Date:   Wed Mar 20 14:52:37 2019 -0400

    Replace list.indexOf() with map.get() speeds up MolecularDataServiceImpl.fetchMolecularData()

commit a0995c150ef282b7bff96c187551002521efb076
Merge: f74d03a ef8ad33
Author: alisman <[email protected]>
Date:   Wed Mar 20 15:46:23 2019 -0400

    Merge pull request #5877 from alisman/addQuickConfig

    Add skin.quick_select_buttons configuration to config service

commit ef8ad33a7b240e858b8a02e06a890ba6ae56130d
Author: aaronlisman <[email protected]>
Date:   Wed Mar 20 15:15:03 2019 -0400

    Add skin.quick_select_buttons configuration to config service

commit f74d03ae79cd71a1363c41b2d21b44686bf77ee6
Merge: 3c88f48 166d732
Author: n1zea144 <[email protected]>
Date:   Wed Mar 20 09:47:03 2019 -0400

    Merge pull request #5871 from n1zea144/molecular-data-service-opt

    Replace list.indexOf() with map.get() speeds up MolecularDataServiceImpl.getMolecularDataInMultipleProfiles()

commit 166d732533b9ea6b739a0ae9c17fd329f26bf6f2
Author: n1zea144 <[email protected]>
Date:   Tue Mar 19 10:37:39 2019 -0400

    Replace list.indexOf() with map.get()

commit ce0f59c16ae31c9d7229d34e62068f2a47561196
Merge: 230fe79 3c88f48
Author: Ino de Bruijn <[email protected]>
Date:   Tue Mar 19 00:00:02 2019 -0400

    Automated master to release-2.2.0 merge

commit 3c88f48025084eaf750da18df1a423d2d14b8345
Merge: ebd29b9 b449f59
Author: JianJiong Gao <[email protected]>
Date:   Mon Mar 18 10:06:59 2019 -0400

    Merge pull request #5870 from agarwalrounak/doc-links

    Fix broken links in documentation

commit b449f59ec31223e3762022dba67a56a5e2e21696
Merge: 906aa98 ebd29b9
Author: Rounak Agarwal <[email protected]>
Date:   Sun Mar 17 16:45:21 2019 +0530

    Merge branch 'master' into doc-links

commit 906aa983eb7d55c3987c21d8e206978196edf6c8
Author: agarwalrounak <[email protected]>
Date:   Sun Mar 17 16:43:22 2019 +0530

    Fix broken links in documentation

commit 230fe79e76a63fc58b761e36fd8ae1c87c1093f5
Merge: bd8bf52 ebd29b9
Author: Ino de Bruijn <[email protected]>
Date:   Sat Mar 16 00:00:02 2019 -0400

    Automated master to release-2.2.0 merge

commit 1cb945d9e43fbc42548d812b5c11712529865e01
Author: JianJiong Gao <[email protected]>
Date:   Fri Mar 15 16:14:06 2019 -0400

    Update About-Us.md

commit ebd29b951769ddd3393b5572444d77472b49b5de
Merge: bd8bf52 b4993f6
Author: ritikakundra <[email protected]>
Date:   Fri Mar 15 13:43:16 2019 -0400

    Merge pull request #5866 from cBioPortal/ritikakundra-patch-3

    Update News.md

commit b4993f6c5ef38ed60d373827eb08b5ee66da3f25
Author: ritikakundra <[email protected]>
Date:   Fri Mar 15 13:05:53 2019 -0400

    Update News.md

commit bd8bf52964fdb120b56d93067fc8e6c9467ca2f0
Merge: bac1dce ed6a65d
Author: n1zea144 <[email protected]>
Date:   Tue Mar 12 12:58:08 2019 -0400

    Merge pull request #5858 from n1zea144/study-view-controller-sample-counts-opt

    Use of hashset instead of list speeds up SampleServiceImpl.processSam…

commit ed6a65ddc861d29dc1a14da88083c80eeada99c2
Author: n1zea144 <[email protected]>
Date:   Tue Mar 12 12:11:39 2019 -0400

    Use of hashset instead of list speeds up SampleServiceImpl.processSamples.

commit bac1dce3fd71948a2a9a1e18e7eee2a85cfb5113
Merge: b73c8a6 3192e6e
Author: n1zea144 <[email protected]>
Date:   Tue Mar 12 09:39:55 2019 -0400

    Merge pull request #5840 from ao508/drop-add-samples-on-fly

    Removing code adding samples to db on the fly during import

commit 3192e6e164f2c790ef96605d7b7b86ace670ff10
Author: Angelica Ochoa <[email protected]>
Date:   Thu Feb 28 16:40:35 2019 -0500

    Removing code adding samples to db on the fly during import

    Signed-off-by: Angelica Ochoa <[email protected]>

commit b73c8a662b8d7eaf4d3fabe7c17f32f9d2d7d8b3
Merge: c29493f 2ec46d0
Author: JianJiong Gao <[email protected]>
Date:   Thu Mar 7 17:52:05 2019 -0500

    Merge pull request #5843 from cBioPortal/jjgao-patch-9

    updating/removing links to wiki.nci.nih.gov

commit 2ec46d0630ed0075178e1ccf21a7b9b5ceb9df53
Author: JianJiong Gao <[email protected]>
Date:   Thu Mar 7 16:29:55 2019 -0500

    Update Using-the-dataset-validator.md

commit c8826bdbcb325a833cf09509c2fbac67f951068c
Author: JianJiong Gao <[email protected]>
Date:   Thu Mar 7 16:24:19 2019 -0500

    updating/removing links to wiki.nci.nih.gov

commit c29493f4c062dc6439592e66685f3663dedce512
Merge: d11261e 945ad74
Author: JianJiong Gao <[email protected]>
Date:   Wed Mar 6 08:43:07 2019 -0500

    Merge pull request #5715 from kalletlak/fix-5695

    Fix broken LDAP integration

commit d11261e28216e9332ecec89fe1108b4094eeea8e
Merge: c488f89 74f2b9d
Author: Ino de Bruijn <[email protected]>
Date:   Tue Mar 5 18:08:35 2019 -0500

    Merge pull request #5833 from alisman/fixLN

    /ln links should expand to pan can atlas studies instead of all stds

commit c488f8928132e8fbb26247eb3b1219771314f34c
Merge: ffe66a8 12c80a3
Author: Ino de Bruijn <[email protected]>
Date:   Tue Mar 5 11:01:02 2019 -0500

    Merge pull request #5832 from cBioPortal/jjgao-patch-8

    Update About-Us.md

commit 74f2b9d438040f90d2f7b3ccbd73054360994d83
Author: aaronlisman <[email protected]>
Date:   Tue Mar 5 10:56:01 2019 -0500

    /ln links should expand to pan can atlast study set instead of all studies (temporary fix)

commit 12c80a39ae5d70504059adafb0927dfb5c2026de
Author: JianJiong Gao <[email protected]>
Date:   Tue Mar 5 10:37:35 2019 -0500

    Update About-Us.md

commit 49161818d1ad583891b82a70ea39740201390544
Author: JianJiong Gao <[email protected]>
Date:   Mon Mar 4 15:10:03 2019 -0500

    fixed #5812

commit ffe66a82351a1c813fd2bc3522d09005e5a1a6ec
Merge: fbd6921 7640ae9
Author: Ino de Bruijn <[email protected]>
Date:   Mon Mar 4 14:11:43 2019 -0500

    Merge pull request #5817 from alisman/fiReload

    DevTool: window.location.reload, not window.reload

commit 7640ae993c0491f3ffd84ef187d8eb98618aaeb5
Author: aaronlisman <[email protected]>
Date:   Mon Mar 4 11:01:20 2019 -0500

    DevTool: window.location.reload, not window.reload

commit fbd69216311e484947f55e30b180ba7244b6d824
Merge: c52f989 a8f7834
Author: Ino de Bruijn <[email protected]>
Date:   Mon Mar 4 10:38:17 2019 -0500

    Merge pull request #5808 from inodb/jdbc-remove-pool-prepared-statements

    Disable Pool Prepared Statement JDBC

commit a8f7834547ad620f520f460c32a8e651915bb438
Author: Ino de Bruijn <[email protected]>
Date:   Fri Mar 1 16:15:22 2019 -0500

    Disable Pool Prepared Statement JDBC

    We are using -Ddbconnector=jdbc on AWS in production. Before the dbcp was only
    being used for the importer. It seems that enabling this when serving the
    webapp results in a huge number of queries being stored in memory. We might
    eventually want to make this some property that one can only enable when using
    the importer.

commit c52f9891f04a4d7cd7d8c2983dd496ef75f2150c
Merge: 775deaa 72fe5e8
Author: n1zea144 <[email protected]>
Date:   Mon Mar 4 08:37:15 2019 -0500

    Merge pull request #5602 from thehyve/improve_gene_panel_data_importer

    Fix gene panel importer, add validation and improve documentation

commit 72fe5e88250b90c3a0ba60224d2e19716ad9de5b
Author: Sander Tan <[email protected]>
Date:   Mon Mar 4 10:04:15 2019 +0100

    Fix gene panel importer; add validation for gene panels; add docu

commit 775deaa83b4ff92a5a8fd476fdaf441808b8a9bc
Merge: 62ccd52 a6585c9
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 26 18:38:04 2019 -0500

    Merge pull request #5787 from inodb/add-netlify-dev-load-frontend

    Add netlify as another place for loading frontend

commit 62ccd522ab30a578690f67cf754e9d2ccf23043a
Merge: 2c869e6 60e1d41
Author: Robert Sheridan <[email protected]>
Date:   Tue Feb 26 13:27:01 2019 -0500

    Merge pull request #5734 from averyniceday/ssl-db-prop

    Add ssl prop for db connection

commit a6585c947dab703668f9f455a626f4cf62e33e35
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 26 11:53:39 2019 -0500

    Add netlify as another place for loading frontend

    Similar to Heroku, but use Netlify. Netlify builds frontend artifacts
    automatically, so it will save some time having to wait for heroku deployments
    to build. The instances don't sleep either, so this makes the testing
    experience a little smoother.

commit 60e1d41db3acaaf8fa7138be1173e4496e6a03d3
Author: Avery Wang <[email protected]>
Date:   Wed Feb 13 15:30:10 2019 -0500

    updated ssl arguments

commit 2c869e62c985102d3ce14b082d0005f9a86c5583
Merge: 4298b87 773b2bc
Author: Ino de Bruijn <[email protected]>
Date:   Mon Feb 25 18:21:34 2019 -0500

    Merge pull request #5784 from dippindots/add_time_to_mskSlideViewer

    add timestamp to the msk slide viewer token information

commit 773b2bc2178c103dd528d1757f7697615a2ac0b8
Author: gaofei zhao <[email protected]>
Date:   Mon Feb 25 14:19:59 2019 -0500

    add timestamp to the msk slide viewer token information

commit 4298b870aa127277d135581b4d486684190d8a21
Author: JianJiong Gao <[email protected]>
Date:   Fri Feb 22 15:25:07 2019 -0500

    news about regression line (#5775)

commit a078b3c38b2f34349aac8585edc08ac16c2b6da6
Merge: df2038b 15ca61b
Author: Ino de Bruijn <[email protected]>
Date:   Thu Feb 21 21:09:41 2019 -0500

    Merge pull request #5774 from cBioPortal/jjgao-patch-6

    fixed #5772 - typo

commit 15ca61b5339ccf6f86be9b99488d0db9999c3f52
Author: JianJiong Gao <[email protected]>
Date:   Thu Feb 21 13:14:43 2019 -0500

    fixed #5772 - typo

commit df2038bff5baca9bc50a491317efe735baa91ad6
Merge: 9202a7c c1abf5f
Author: JianJiong Gao <[email protected]>
Date:   Thu Feb 21 12:57:06 2019 -0500

    Merge pull request #5764 from cBioPortal/update-news

    update news

commit c1abf5fe0924eaa925c76a4328a6d5e97fa122b9
Author: Ino de Bruijn <[email protected]>
Date:   Wed Feb 20 11:35:20 2019 -0500

    remove old news

commit 6a3bf58b4b0f256f07bbedeeb12319b59d736d26
Author: Ino de Bruijn <[email protected]>
Date:   Wed Feb 20 11:33:57 2019 -0500

    update news

    Incorporate changes proposed by Niki: https://github.com/cBioPortal/cbioportal/pull/5763#issuecomment-465417017

commit 9202a7c12584ab8a8794e319bb9e383d070b1f6a
Merge: 6c6e867 e08e06f
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 22:18:57 2019 -0500

    Merge pull request #5762 from cBioPortal/release-2.1.0

    Release 2.1.0

commit e08e06fcb6dd5be890724d714cae6badba2e1696
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 22:17:45 2019 -0500

    v2.1.0

commit 8d78e0e347c6596d947a10e8030921127669d619
Merge: 2de4cbd 6c6e867
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 22:05:33 2019 -0500

    Merge remote-tracking branch 'origin/master' into release-2.1.0

commit 6c6e867b68846483b1faebab19a531f4ea3b8000
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 21:56:26 2019 -0500

    v2.0.2

commit 2de4cbd94328c552684c6c53d636ca2e2cbd248e
Merge: 0d64eaa 46f1ced
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 21:45:54 2019 -0500

    Merge pull request #5763 from cBioPortal/jjgao-patch-5

    release-2.1.0 news

commit 0d64eaae4f32b005f8f45a0620f31875db968b3b
Merge: c36901c 0844418
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 20:46:03 2019 -0500

    Merge remote-tracking branch 'origin/master' into release-2.1.0

commit 08444187c901ce39397ecde734e30b29dd612558
Merge: 71dd656 b93f5bc
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 20:43:55 2019 -0500

    Merge pull request #5747 from kalletlak/fix-5702

    Add authentication to studyView API's

commit 71dd6569415573c9d0294485e47eb940aaf96269
Merge: 84f822b 69de9ab
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 20:38:24 2019 -0500

    Merge pull request #5717 from zhx828/remove-cancer-genes-page

    Remove cancer gene page

commit 84f822b3d135ac4eb9038216aaa036f8bb2709a6
Merge: 4a67746 1dfab35
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 20:37:11 2019 -0500

    Merge pull request #5722 from dippindots/viewer_token_generator

    whole slide viewer token generator

commit 4a6774648c340badd2068828c683480315e2a73b
Merge: 5327dbf 629814b
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 20:36:28 2019 -0500

    Merge pull request #5718 from zhx828/remove-legacy-study-view

    Remove study view legacy code

commit 5327dbf24eef2acb4cabd3734dd8a9e18895df66
Merge: 848f6d1 5f5c327
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 19 20:32:35 2019 -0500

    Merge pull request #5725 from onursumer/study-view-filter-order-fix

    Applying patient filters before applying sample filters

commit b93f5bc5297855e96d5ed7297fbafcb166f0bee6
Author: Karthik Kalletla <[email protected]>
Date:   Fri Feb 15 11:43:36 2019 -0500

    Add authentication to studyView API's

commit 46f1ced887d6785e48bea70bf03c68368eb46d64
Author: JianJiong Gao <[email protected]>
Date:   Tue Feb 19 19:40:41 2019 -0500

    Update News.md

commit 0af4f1c03f2ea020c43a5be2bf4423caa1034eb7
Author: JianJiong Gao <[email protected]>
Date:   Tue Feb 19 18:33:13 2019 -0500

    release-2.1.0

commit 5f5c32733cec3415543c7778aace5aa8c08814bc
Author: Onur Sumer <[email protected]>
Date:   Mon Feb 11 17:36:56 2019 -0500

    applying patient filters before applying sample filters (fix #5710)

commit 1dfab35103b0f4173f588b54aec152e924c71f99
Author: gaofei zhao <[email protected]>
Date:   Mon Feb 11 11:57:17 2019 -0500

    whole slide viewer token generator

commit 848f6d1a119085312880fdbf95d154493df77a99
Merge: d433408 839fac4
Author: Onur Sumer <[email protected]>
Date:   Tue Feb 19 15:31:37 2019 -0500

    Merge pull request #5593 from kalletlak/sv-updates

    Update virtual study data object

commit 839fac442ae03261fcb370d7f8cc2c18667df7c1
Author: Karthik Kalletla <[email protected]>
Date:   Thu Jan 10 11:17:20 2019 -0500

    Update virtual study data object

commit c36901c8dda33047b8a49e0334716d7635454d87
Merge: 30e5b3c d433408
Author: Ino de Bruijn <[email protected]>
Date:   Sat Feb 16 00:00:03 2019 -0500

    Automated master to release-2.1.0 merge

commit d433408852cdc9c1c382e1f25c1757dad93fe513
Merge: 80707d8 34e635d
Author: JianJiong Gao <[email protected]>
Date:   Fri Feb 15 18:31:52 2019 -0500

    Merge pull request #5752 from cBioPortal/tmazor-oql-updates

    update OQL page with high/low expression

commit 34e635dbb1bbde2730c46471445d9aeb2f2e381b
Author: Tali Mazor <[email protected]>
Date:   Fri Feb 15 16:49:46 2019 -0500

    update OQL screenshots

commit 7ab63e38dcbed544feb8849629572f09b91ecbca
Author: Tali Mazor <[email protected]>
Date:   Fri Feb 15 15:39:31 2019 -0500

    update OQL page with high/low expression

commit 30e5b3c42654cd46b0b805ce13790ca5e37a8ac4
Merge: 3b13693 80707d8
Author: Ino de Bruijn <[email protected]>
Date:   Fri Feb 15 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 80707d8f72ffdfdc8a6a1972838ca999ef155670
Merge: 8af1352 6a1f3ee
Author: Ino de Bruijn <[email protected]>
Date:   Thu Feb 14 20:17:32 2019 -0500

    Merge pull request #5741 from cBioPortal/jjgao-patch-3

    Update Import-the-Seed-Database.md

commit 3b1369362dc85000f922d47375cf6b21cf2a666e
Merge: ed6de4e 532d15d
Author: Robert Sheridan <[email protected]>
Date:   Thu Feb 14 13:01:29 2019 -0500

    Merge pull request #5658 from angelicaochoa/drop-uk-mutevent

    Drop UNIQUE KEY from mutation_event. Set ALLELE fields to TEXT

commit 532d15d19df7793be6ec3e7a247cf96fc59e39ae
Author: Angelica Ochoa <[email protected]>
Date:   Fri Jan 25 14:53:19 2019 -0800

    Drop UNIQUE KEY from mutation_event. Set ALLELE fields to TEXT

    * Added unit test and integration test
    * Generate temp test DB schema to accommodate H2 MySQL driver not supporting partial indexes

    Signed-off-by: Angelica Ochoa <[email protected]>

commit ed6de4e0f850502ee817053859e92cdd8aec3c79
Merge: f084bce 8af1352
Author: Ino de Bruijn <[email protected]>
Date:   Thu Feb 14 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 6a1f3ee691c5e1cdc0f708854b4d4ffa12cfcc80
Author: JianJiong Gao <[email protected]>
Date:   Wed Feb 13 17:35:35 2019 -0500

    Update Import-the-Seed-Database.md

commit 8af1352345ac44d9ba4de5cc03703b8f62498248
Merge: d683b6f a68c8a4
Author: Ino de Bruijn <[email protected]>
Date:   Wed Feb 13 17:25:49 2019 -0500

    Merge pull request #5732 from inodb/remove-more-public-portal-links

    Remove old files with /public-portal/ links

commit f084bcea02b9ba88d9624ddea73f740d9c30e707
Merge: fc07cad 44cb9b5
Author: Onur Sumer <[email protected]>
Date:   Wed Feb 13 15:08:32 2019 -0500

    Merge pull request #5735 from onursumer/copy-number-segment-count

    Added copy number segment count for samples

commit 44cb9b5d8ca541c2b8c63efd598d3a59b9532f37
Author: Onur Sumer <[email protected]>
Date:   Tue Feb 12 17:33:25 2019 -0500

    added copy number segment count for samples

commit d683b6faeb224dbaa3140800ba27c620d1b400a5
Merge: ad023a5 69b3ba1
Author: Ino de Bruijn <[email protected]>
Date:   Wed Feb 13 10:45:05 2019 -0500

    Merge pull request #5736 from cBioPortal/pieterlukasse-patch-4

    adding Pim to the team!

commit 69b3ba1b530d8b2577350347cf0897ab25a351e8
Author: pieterlukasse <[email protected]>
Date:   Wed Feb 13 10:42:46 2019 +0100

    adding Pim to the team!

commit fc07cad44d9ba53e4a8457515ee288076a177814
Merge: 1df7100 ad023a5
Author: Ino de Bruijn <[email protected]>
Date:   Wed Feb 13 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit a68c8a47025f7a4bb1b4066e7c13ea33e9527d95
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 12 11:43:42 2019 -0500

    Remove old files with /public-portal/ links

commit ad023a5915a96f523bccbdd1903cfb6b6069f796
Merge: cf89d09 3c60faa
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 12 11:33:26 2019 -0500

    Merge pull request #5730 from cBioPortal/change-md-urls-public-portal

    remove /public-portal/ links

commit 3c60faad8be5952fef8675abf565076e23dfffdc
Author: Ino de Bruijn <[email protected]>
Date:   Tue Feb 12 11:19:59 2019 -0500

    remove /public-portal/ links

commit 1df71001ddc522f5d59715059be57ad0b5daad5d
Merge: 4db9e02 cf89d09
Author: Ino de Bruijn <[email protected]>
Date:   Mon Feb 11 17:34:09 2019 -0500

    Merge remote-tracking branch 'origin/master' into release-2.1.0

commit 69de9ab690a8ed7d90262932a6356cb28684327c
Author: Hongxin Zhang <[email protected]>
Date:   Fri Feb 8 11:14:21 2019 -0500

    Remove cancer gene page

commit cf89d09f45210d9c8248babb695bbf88f53f2e96
Merge: 82df399 7445f8b
Author: Hongxin <[email protected]>
Date:   Mon Feb 11 16:43:34 2019 -0500

    Merge pull request #5707 from zhx828/update-sitemaps

    Prevent sitemap xml file showing up in the google result

commit 7445f8bfdafc38c8247040bf7a38cde0050ded17
Author: Hongxin Zhang <[email protected]>
Date:   Thu Feb 7 11:32:03 2019 -0500

    Prevent sitemap xml file showing up in the google result

commit 82df39973f5ceae1f02314e34ad83668d720a94e
Merge: 2324d12 76a462b
Author: n1zea144 <[email protected]>
Date:   Mon Feb 11 13:32:58 2019 -0500

    Merge pull request #5677 from angelicaochoa/oauth2-user-email

    Use OAuth2Operations to fetch User email.

commit 76a462b1e47f69dad81eadd5e9d0652bdd3c4cc7
Author: Angelica Ochoa <[email protected]>
Date:   Mon Feb 11 11:59:59 2019 -0500

    Use OAuth2Operations to fetch user email

    Signed-off-by: Angelica Ochoa <[email protected]>

commit 4db9e02ce78e75b6e199a6da7f14ccbdd1cc339c
Merge: 67d046a 2324d12
Author: Ino de Bruijn <[email protected]>
Date:   Sat Feb 9 00:00:03 2019 -0500

    Automated master to release-2.1.0 merge

commit 2324d128768e2b0c71392ce2cbd5b0fc99fc3703
Merge: 8a137b1 7f41ce2
Author: JianJiong Gao <[email protected]>
Date:   Fri Feb 8 17:15:53 2019 -0500

    Merge pull request #4527 from thehyve/mouse_validator

    Allow gene symbols starting with numbers for mouse studies

commit 7f41ce20146407a93539ec1929e23131f9da194a
Author: oplantalech <[email protected]>
Date:   Sun Jul 29 10:54:57 2018 +0200

    Allow gene symbols starting with numbers for mouse studies

commit 8a137b1114efc210a531399b8ee257ebbaef0b0f
Merge: 751230e fcea59d
Author: Ino de Bruijn <[email protected]>
Date:   Fri Feb 8 14:04:22 2019 -0500

    Merge pull request #5712 from inodb/add-same-origin-header-for-network-tab

    Network tab needs X-Frame-Options: SAMEORIGIN

commit fcea59d05871918d3be4340acb2adf904b4f1c28
Author: Ino de Bruijn <[email protected]>
Date:   Thu Feb 7 20:54:52 2019 -0500

    Network tab needs X-Frame-Options: SAMEORIGIN

    - The filter is for when using authenticate=false
    - The <http><header> part is for when using authenticate=social_auth

commit 751230e379baac311e355c17b7f03f111e24a730
Merge: a89a195 a5bfa8f
Author: JianJiong Gao <[email protected]>
Date:   Fri Feb 8 12:43:43 2019 -0500

    Merge pull request #5682 from cBioPortal/oplantalech-patch-1

    Change realm name in the Keycloak documentation

commit 629814b76e683e3f77cc11f7383f21ee09bb53e3
Author: Hongxin Zhang <[email protected]>
Date:   Fri Feb 8 11:23:46 2019 -0500

    Remove study view legacy code

    - Removed the dashboard js folder
    - Removed the dashboard jsp folder
    - Removed CancerStudyView, CancerStudyViewV2 servlets

commit a5bfa8f2985c19edbab9129f59bdc305dbcc08dc
Author: Oleguer <[email protected]>
Date:   Tue Feb 5 10:00:43 2019 +0100

    Change realm name in the Keycloak documentation

    _demo_ is not a very appropriate name for the Keycloak realm name for cBioPortal, so this commit changes it to _cbioportal_ which is much self-explanatory.

commit a89a1954e2ce6d7032e2ac9660711d117f8b1a87
Merge: 4972e20 b5de49f
Author: JianJiong Gao <[email protected]>
Date:   Fri Feb 8 10:36:28 2019 -0500

    Merge pull request #5351 from cBioPortal/pieterlukasse-patch-4

    added small note regarding localhost url used

commit 945ad74cd8aba4c23c175d46abf11332d150852e
Author: Karthik Kalletla <[email protected]>
Date:   Fri Feb 8 10:28:27 2019 -0500

    Fix broken LDAP integration

commit b5de49fc3bded2262a9f8238df03dea18e1d1e83
Author: pieterlukasse <[email protected]>
Date:   Mon Dec 3 12:28:05 2018 +0100

    added small note regarding localhost url used

commit 67d046a03c49c3cfbdeb0a8a3e4e57bcaa6bd1d2
Merge: bd3285d 4972e20
Author: Ino de Bruijn <[email protected]>
Date:   Fri Feb 8 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 4972e20774531fa5ce6728c6da91c06c5d088e25
Merge: cfeba87 5973f13
Author: n1zea144 <[email protected]>
Date:   Thu Feb 7 12:23:53 2019 -0500

    Merge pull request #5686 from n1zea144/security-updates

    patient endpoint redirect is now handled by frontend.

commit 5973f1354837e216a76617fef4289ca43ef024cb
Author: Benjamin Gross <[email protected]>
Date:   Tue Feb 5 10:58:25 2019 -0500

    Access to patient endpoint should be handled by frontend.

commit bd3285d2ccdc186821b4b57213889c66001c077e
Merge: 31b0dcb cfeba87
Author: Ino de Bruijn <[email protected]>
Date:   Sat Feb 2 00:00:01 2019 -0500

    Automated master to release-2.1.0 merge

commit 31b0dcb6ec2cd3d1304d1b4c6d460b9d04f5dca2
Merge: 36f121a 705f278
Author: angelicaochoa <[email protected]>
Date:   Fri Feb 1 14:19:34 2019 -0500

    Merge pull request #5669 from averyniceday/ddp-patient-viewer

    change darwin auth check to construct ddp url for ddp patient viewer

commit 705f278d4506c351397deb0feecd09f5e100c59c
Author: Avery Wang <[email protected]>
Date:   Wed Jan 30 16:47:34 2019 -0500

    change darwin auth check to construct ddp url for ddp patient viewer

commit cfeba87456a2e75154fb1ce6d43e8b60d23dd5f5
Merge: 06e760c 5d5f33f
Author: JianJiong Gao <[email protected]>
Date:   Fri Feb 1 12:03:14 2019 -0500

    Merge pull request #5671 from cBioPortal/pieterlukasse-patch-6

    Replacing old static list by link to RFC folder

commit 5d5f33f64713e0bcf7e0b3961ea22310b0241109
Author: pieterlukasse <[email protected]>
Date:   Fri Feb 1 15:04:24 2019 +0100

    Replacing old static list by link to RFC folder

    One of our users ignored this page because he saw that the list of 20 RFCs was never changing.
    This commit solves this issue by pointing to the RFCs folder directly.

commit 36f121a85ce4714384523cfe2415d51a72fab009
Merge: 901dfc4 06e760c
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 29 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 06e760c1764c2c8371fb35a677e3484317d19a8f
Merge: 2a2f3fe 89bde72
Author: Ino de Bruijn <[email protected]>
Date:   Mon Jan 28 20:48:07 2019 -0500

    Merge pull request #5605 from inodb/update-webapp-runner

    Update webapp-runner.jar

commit 89bde726538adf1291d0d2056d0ef68a098ee569
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 15 13:22:06 2019 -0500

    Update webapp-runner.jar

    - Allow for more customization of HTTP connector, which is necessary for the
      AWS deployment of cBioPortal.
    - Upgrade to version using fstCodec to allow use of redis
      (https://github.com/jsimone/webapp-runner/pull/127)

commit 901dfc47dcb89cc27e6768f87072bff626ec8dd5
Merge: 73322fd ee66361
Author: Ino de Bruijn <[email protected]>
Date:   Mon Jan 28 13:29:25 2019 -0500

    Merge pull request #5511 from sheridancbio/enlarge_pmid_field

    enlarge cancer_study pmid field width

commit ee663612be29f2b43830022911c02b6177875fca
Author: Robert Sheridan <[email protected]>
Date:   Thu Dec 20 12:52:55 2018 -0500

    enlarge cancer_study pmid field width
    - migrate to db_schema_version 2.8.0 with cancer_study.pmid as varchar(1024)
    - update some unit tests with a comma separated string for pmid
    - update documentation pages to refer to the pmid field as a string of comma separated values
    - adjust validator to allow longer pmid field width
    - add validation for comma separated PMID list (with no WS in meta_study.txt PMID field

        Co-authored-by: Sander de Ridder <[email protected]>

commit 73322fddf13242708950cc3729a084d46e9e5d60
Merge: edb0c46 2a2f3fe
Author: Ino de Bruijn <[email protected]>
Date:   Fri Jan 25 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 2a2f3fef3dfc0552647c2df0eb7ca815f039e054
Merge: 56050cb cd32301
Author: ritikakundra <[email protected]>
Date:   Thu Jan 24 14:47:21 2019 -0500

    Merge pull request #5654 from cBioPortal/ritikakundra-patch-3

    Update News.md

commit cd32301504ae039b2ac7b8ed4d20964bc3bc7fa4
Author: ritikakundra <[email protected]>
Date:   Thu Jan 24 14:25:57 2019 -0500

    Update News.md

commit 56050cbcc9090d968c7204ba5d5146a56b75744b
Merge: da4a8d1 20eca1a
Author: ritikakundra <[email protected]>
Date:   Thu Jan 24 14:24:00 2019 -0500

    Merge pull request #5653 from cBioPortal/ritikakundra-patch-3

    Update News.md

commit 20eca1a3633fe7561243b954c54614462eb9a4a7
Author: ritikakundra <[email protected]>
Date:   Thu Jan 24 11:48:05 2019 -0500

    Update News.md

commit 83632d4af2ef2e95f27b39d8e038d07833a1e8af
Author: ritikakundra <[email protected]>
Date:   Thu Jan 24 11:37:01 2019 -0500

    Update News.md

commit edb0c46dbdd31866b517320ad457696467a68e9e
Merge: 7dd075b da4a8d1
Author: Ino de Bruijn <[email protected]>
Date:   Thu Jan 24 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit da4a8d1ca1ef68ff51507d0139123a1b7c749bfd
Merge: 385bb86 a1450a2
Author: Ersin Ciftci <[email protected]>
Date:   Wed Jan 23 11:47:16 2019 -0500

    Merge pull request #5628 from ersinciftci/fix-cna-genes

    Fix cna-genes and mutated-genes when there is no related profile in t…

commit a1450a28f3acc0f8bea3c2e188b729b56c9000a4
Author: Ersin Ciftci <[email protected]>
Date:   Fri Jan 18 13:38:55 2019 -0500

    Fix cna-genes and mutated-genes when there is no related profile in the studies

commit 7dd075b5c977a9533bd608db709f04f53b8360c2
Merge: c7a900e 385bb86
Author: Ino de Bruijn <[email protected]>
Date:   Sat Jan 19 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 385bb864340fe0d41c3b5615bddea962d8232c41
Merge: 22970fa 986e47b
Author: JianJiong Gao <[email protected]>
Date:   Fri Jan 18 16:59:46 2019 -0500

    Merge pull request #5629 from kunalchandan/patch-1

    Fixed small gramatical errors

commit 986e47b5ea1184055fc4f97d3a330cdf63c53075
Author: Kunal Chandan <[email protected]>
Date:   Fri Jan 18 16:25:35 2019 -0500

    Fixed small gramatical errors

commit c7a900ea431b6e82b7f40043abc0dcf95240ecc0
Merge: 9e1779b 22970fa
Author: Ino de Bruijn <[email protected]>
Date:   Fri Jan 18 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 22970fa5e160605bd4293b38d9a9bc6123c0041e
Merge: 86eb2f0 b6883fe
Author: JianJiong Gao <[email protected]>
Date:   Thu Jan 17 17:54:12 2019 -0500

    Merge pull request #5592 from cBioPortal/tmazor-news

    update news page with OQL

commit b6883feffe5ef8fbffc96bb44002fe729647e668
Merge: 8aaf062 86eb2f0
Author: JianJiong Gao <[email protected]>
Date:   Thu Jan 17 17:37:34 2019 -0500

    Merge branch 'master' into tmazor-news

commit 9e1779bfd966bfe22f0270d68d1bcde0cb99cf8c
Merge: be09a91 86eb2f0
Author: Ino de Bruijn <[email protected]>
Date:   Thu Jan 17 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 86eb2f01907adf872ca2616d91d22587a2110d93
Merge: 677113a 98242a0
Author: n1zea144 <[email protected]>
Date:   Wed Jan 16 15:41:48 2019 -0500

    Merge pull request #5614 from thehyve/validator_remove_hg18

    Remove hg18 exception for segment data

commit 98242a08de22687340eefc568c2a9443997b51d1
Author: Sander Tan <[email protected]>
Date:   Wed Jan 16 11:44:30 2019 +0100

    Remove hg18 from allowed reference genomes for segment data

commit be09a91e9bef621870bf8af3a3f18185ac116f6d
Merge: 157832a 03cdd9d
Author: Ino de Bruijn <[email protected]>
Date:   Wed Jan 16 12:08:53 2019 -0500

    Merge pull request #5616 from angelicaochoa/migration-mut-keyword

    Update migration script

commit 03cdd9de5c8e802762940c9152c6f177b052f4b1
Author: Angelica Ochoa <[email protected]>
Date:   Wed Jan 16 11:41:37 2019 -0500

    Update migration script

    Signed-off-by: Angelica Ochoa <[email protected]>

commit 157832ae41b6013dffb329754296a9b0d7468b5d
Merge: 5d6ed20 677113a
Author: Ino de Bruijn <[email protected]>
Date:   Wed Jan 16 00:00:02 2019 -0500

    Automated master to release-2.1.0 merge

commit 677113a6dc6063b74fa7b534c51f8e3256314fca
Merge: 955171c 0d07a01
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 15 18:27:05 2019 -0500

    Merge pull request #5611 from inodb/release-2.0.1

    update frontend to v2.0.1

commit 0d07a01e67c3110813688326b9d1bfe993ab1c90
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 15 18:08:43 2019 -0500

    update frontend v2.0.1

commit 5d6ed2068612ca8d549ab291d71f07ec3e415b61
Merge: b32405e 955171c
Author: Ino de Bruijn <[email protected]>
Date:   Sat Jan 12 00:00:02 2019 -0500

    Automated master to rc merge

commit 955171cb22b0978c0e03fe2957876a890a7e7ad4
Merge: a39d1e6 0784b84
Author: alisman <[email protected]>
Date:   Fri Jan 11 09:23:03 2019 -0500

    Merge pull request #5591 from cBioPortal/tmazor-oql-fix

    fix links to tutorial

commit b32405ed2dda3fd9ed2c9a321d1b90693a864db6
Merge: 2e645ea a39d1e6
Author: Ino de Bruijn <[email protected]>
Date:   Fri Jan 11 00:00:02 2019 -0500

    Automated master to rc merge

commit a39d1e648b37dc4420edfaf844993d419f000025
Merge: 4ae64bf a61185b
Author: angelicaochoa <[email protected]>
Date:   Thu Jan 10 19:33:14 2019 -0500

    Merge pull request #5245 from cBioPortal/mut-count-keyword-varchar

    Resolve issue #5242

commit a61185b96e5bde6508ae6d3e518cf86004607a38
Author: angelicaochoa <[email protected]>
Date:   Wed Nov 14 10:09:43 2018 -0500

    Resolve issue #5242

    Resolve mismatch in cgds.sql and migration.sql varchar size for `mutation_count_by_keyword.KEYWORD` (issue #5242)

commit 8aaf06210f304e386d735122048d4425afeed184
Author: Tali Mazor <[email protected]>
Date:   Thu Jan 10 15:13:34 2019 -0500

    add link to OQL documentation page

commit 5b2cf5c260a0424474be44ee564e7e484b5227c0
Author: Tali Mazor <[email protected]>
Date:   Thu Jan 10 11:04:56 2019 -0500

    update news page with OQL

commit 0784b8481c9c1af07096ccd3505c9c7ef59777df
Author: Tali Mazor <[email protected]>
Date:   Thu Jan 10 10:18:41 2019 -0500

    fix links to tutorial

commit 2e645ea0c3d45f3a1a904bb2ddabeb414504e656
Merge: 0cb5536 4ae64bf
Author: Ino de Bruijn <[email protected]>
Date:   Thu Jan 10 00:00:02 2019 -0500

    Automated master to rc merge

commit 4ae64bfd19ea82bbfd239c897beb21f269637421
Merge: e894ce1 8f4b988
Author: alisman <[email protected]>
Date:   Wed Jan 9 15:59:23 2019 -0500

    Merge pull request #5582 from cBioPortal/tmazor-oql-updates

    add link to tutorial to OQL documentation page

commit e894ce1c6fadc8c98c2091fa5f1b17505576cf39
Merge: 8f1875b 1cc98eb
Author: n1zea144 <[email protected]>
Date:   Wed Jan 9 12:48:08 2019 -0500

    Merge pull request #5581 from angelicaochoa/drop-axis-core-dep

    Drop axis dependencies from core pom

commit 8f4b988e338752461584e4d419f4aa7b0a9c9b04
Author: Tali Mazor <[email protected]>
Date:   Wed Jan 9 11:50:41 2019 -0500

    fix indentation

commit 797bd8d2a137f826fab4ad7dfdf91ddb4d29a7dc
Author: Tali Mazor <[email protected]>
Date:   Wed Jan 9 11:33:34 2019 -0500

    add link to tutorial to OQL documentation page

commit 1cc98eb8c4a80ac2f65dffc6e0e2732edc454a26
Author: Angelica Ochoa <[email protected]>
Date:   Wed Jan 9 10:55:06 2019 -0500

    Drop axis dependencies from core pom

    Signed-off-by: Angelica Ochoa <[email protected]>

commit 0cb5536f61e2fda8695b36422713656042c90ac3
Merge: db9a722 68b9567
Author: Ersin Ciftci <[email protected]>
Date:   Wed Jan 9 09:58:51 2019 -0500

    Merge pull request #5577 from ersinciftci/search-in-alias

    Show if there is an exact match with a gene alias in quick search

commit 68b9567e43db428c23c300016fbf79b8c201ffbc
Author: Ersin Ciftci <[email protected]>
Date:   Tue Jan 8 17:16:37 2019 -0500

    Show if there is an exact match with an alias in quick search

commit db9a722d6785210854e484487d37de3c5acee418
Merge: 590f262 8f1875b
Author: Ino de Bruijn <[email protected]>
Date:   Wed Jan 9 00:00:03 2019 -0500

    Automated master to rc merge

commit 8f1875bf3c8841c07e369d6233d3d76daedc3eab
Merge: 5c0c96f 0b4461c
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 8 13:37:13 2019 -0500

    Merge pull request #5575 from inodb/release-2.0.0

    Frontend v2.0.0

commit 0b4461cc6e4350d4c9fffde6b92bc1e349eeaab6
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 8 11:19:54 2019 -0500

    Frontend v2.0.0

commit 5c0c96f7c7c35f2276e384af9a3a3074c4283fe3
Merge: 5ed616c a222485
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 8 11:48:23 2019 -0500

    Merge pull request #5573 from cBioPortal/remove-travis-slack-token

    remove travis slack notifications

commit 590f2623de05331b8788c90f9ad0dd0b04f09549
Merge: 27c7409 7bcb939
Author: Ersin Ciftci <[email protected]>
Date:   Tue Jan 8 11:38:42 2019 -0500

    Merge pull request #5561 from ersinciftci/quick-search-primary-site

    Search in the primary site of the studies in quick search

commit a222485a82079aa87fe600ebbfafb8ff119f935b
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 8 11:07:59 2019 -0500

    remove travis slack notifications

    Revoked the token on slack as well, so people searching the history won't find it.

commit 7bcb939fc89bc668089b575c1d75dc1bb8056ab6
Author: Ersin Ciftci <[email protected]>
Date:   Mon Jan 7 13:43:30 2019 -0500

    Search in the primary site of the studies in quick search

commit 5ed616c678509097b2e2545aa76d6bef234e3f20
Merge: a7a6372 a1240ca
Author: n1zea144 <[email protected]>
Date:   Tue Jan 8 10:38:10 2019 -0500

    Merge pull request #5572 from averyniceday/update-dependencies

    update commons file-upload dependency version

commit a1240ca658549f51ca56839d26f597e912f69bb9
Author: Avery Wang <[email protected]>
Date:   Tue Jan 8 10:11:23 2019 -0500

    update commons file-upload dependency version

commit 27c74090438cd660a3857df1f645594aa2bf5d77
Merge: c0e12b2 a7a6372
Author: Ino de Bruijn <[email protected]>
Date:   Tue Jan 8 00:00:02 2019 -0500

    Automated master to rc merge

commit a7a637226fda943d353fef37f4d5027f2ba4a34c
Merge: b2573f3 59899a6
Author: Hongxin <[email protected]>
Date:   Mon Jan 7 18:27:39 2019 -0500

    Merge pull request #5531 from zhx828/update-sv-readme

    Update study view layout documentation

commit 59899a61d7fb9ed510f582c71b230c8196e0807f
Author: Hongxin Zhang <[email protected]>
Date:   Thu Dec 27 18:22:50 2018 -0500

    Update study view layout documentation

commit b2573f3df4a1a1fc6b40f6d05c5b8eaa5cff16ef
Merge: bf32607 9f91659
Author: n1zea144 <[email protected]>
Date:   Mon Jan 7 14:38:30 2019 -0500

    Merge pull request #5563 from averyniceday/update-dependencies

    Update Version for Dependencies to Fix Security Vulnerability Warnings

commit 9f91659a82bb80472c5eb4ffe3cd814e9af37f59
Author: Avery Wang <[email protected]>
Date:   Mon Jan 7 14:18:51 2019 -0500

    updated versions for various dependencies
    in response to vulnerability warning from github

commit c0e12b24d3d3f04bcf5ac750e0931ad127d75bca
Merge: f9f1d4e 68fd88d
Author: alisman <[email protected]>
Date:   Fri Jan 4 12:36:08 2019 -0500

    Merge pull request #5441 from thehyve/remove_whats_new

    Add parameter to remove What's New section

commit f9f1d4e544a7be54a1b1a71e4ad526371ea851dc
Merge: bc33ae5 bf32607
Author: Ino de Bruijn <[email protected]>
Date:   Fri Jan 4 00:00:03 2019 -0500

    Automated master to rc merge

commit bc33ae55fa64bc937b0ae39e5833197cc8f3ba3d
Merge: 523ee4e d92272f
Author: alisman <[email protected]>
Date:   Thu Jan 3 10:45:42 2019 -0500

    Merge pull request #5459 from cBioPortal/pieterlukasse-patch-5

    Documentation to help new (backend) developers with testing part

commit bf32607e156518c93012e71dcc7d43d0914c46fc
Merge: 02ecb20 1bd9593
Author: alisman <[email protected]>
Date:   Thu Jan 3 10:44:58 2019 -0500

    Merge pull request #5521 from cBioPortal/tmazor-oql

    update OQL documentation

commit 523ee4e8b9f6e8dbd18fdfff585b6cb7c559ac30
Merge: f9240c3 02ecb20
Author: Ino de Bruijn <[email protected]>
Date:   Thu Jan 3 00:00:01 2019 -0500

    Automated master to rc merge

commit 02ecb20a1c1d67551d6c022654c9077e5d56f88f
Merge: a38ceec 7042c50
Author: alisman <[email protected]>
Date:   Wed Jan 2 16:28:25 2019 -0500

    Merge pull request #5519 from alisman/killoncoprinter

    Remove oncoprinter.jsp as it now lives in frontend project

commit f9240c32276a7e8013d5b73d02b1a5cfc888e3f4
Merge: fe7f45f 332fc74
Author: Ersin Ciftci <[email protected]>
Date:   Wed Dec 26 11:41:29 2018 -0500

    Merge pull request #5523 from ersinciftci/enrich-remove-query-genes

    Remove queryGenes and qValue from enrichment and co-exp endpoints

commit 332fc74b5591b0cd44633a2e295ac5a03b113d72
Author: Ersin Ciftci <[email protected]>
Date:   Wed Dec 26 11:09:58 2018 -0500

    Remove queryGenes and qValue from enrichment and co-exp endpoints

commit 1bd9593ec4343ebc43e81de250c2ddcf7a2b274a
Author: Tali Mazor <[email protected]>
Date:   Mon Dec 24 13:17:55 2018 -0500

    updates to the top table

commit 063e492be79b3376ac629bd44325610cf3c1c3cf
Author: Tali Mazor <[email protected]>
Date:   Mon Dec 24 11:55:08 2018 -0500

    make explicit that MUT= is not required

commit 7042c5017082dcf59718eb69ba2241b88e40de33
Author: aaronlisman <[email protected]>
Date:   Fri Dec 21 17:44:10 2018 -0500

    Remove oncoprinter.jsp as it now lives in frontend project

commit fe7f45f906455ce2684b7393b7ab8922af4fbc35
Merge: 06abbe3 a38ceec
Author: Ino de Bruijn <[email protected]>
Date:   Fri Dec 21 00:00:02 2018 -0500

    Automated master to rc merge

commit a38ceec45f1b50e2af4482f74169c7f3f614f154
Merge: 6178fe5 9094c78
Author: Adam Abeshouse <[email protected]>
Date:   Thu Dec 20 17:46:38 2018 -0500

    Merge pull request #5485 from cBioPortal/tmazor-oql-updates

    add driver and germlin…
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@sheridancbio sheridancbio sheridancbio approved these changes

@pieterlukasse pieterlukasse Awaiting requested review from pieterlukasse

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cgds and migration.sql mismatch
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