From 1dc7e8f401f4e95c3ec64855227efd38453e0eba Mon Sep 17 00:00:00 2001 From: Jeremy Adams Date: Wed, 15 Dec 2021 14:35:46 -0500 Subject: [PATCH 1/2] increment import common library version, explicitly call v2.16.0 log4j artifacts --- build.gradle | 10 ++++++- gradle/wrapper/gradle-wrapper.jar | Bin 58695 -> 59203 bytes gradle/wrapper/gradle-wrapper.properties | 2 +- gradlew | 2 ++ gradlew.bat | 25 +++++------------- .../ga4gh/starterkit/drs/app/DrsServer.java | 3 ++- .../drs/app/DrsServerSpringConfig.java | 3 ++- .../starterkit/drs/model/DrsServiceInfo.java | 8 +++--- 8 files changed, 26 insertions(+), 27 deletions(-) diff --git a/build.gradle b/build.gradle index 6a5db9b..8811914 100644 --- a/build.gradle +++ b/build.gradle @@ -26,6 +26,14 @@ plugins { id 'io.codearte.nexus-staging' version '0.30.0' } +configurations.all { + resolutionStrategy.eachDependency { DependencyResolveDetails details -> + if (details.requested.group == 'org.apache.logging.log4j') { + details.useVersion '2.16.0' + } + } +} + archivesBaseName = 'ga4gh-starter-kit-drs' group 'org.ga4gh' version '0.2.1' @@ -54,7 +62,7 @@ dependencies { implementation 'javax.xml.bind:jaxb-api:2.2.8' implementation 'org.springdoc:springdoc-openapi-ui:1.2.33' implementation 'org.xerial:sqlite-jdbc:3.8.11.2' - implementation 'org.ga4gh:ga4gh-starter-kit-common:0.5.4' + implementation 'org.ga4gh:ga4gh-starter-kit-common:0.5.6' testImplementation 'org.testng:testng:7.0.0' testImplementation 'org.springframework.boot:spring-boot-starter-test:2.5.0' diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index f3d88b1c2faf2fc91d853cd5d4242b5547257070..e708b1c023ec8b20f512888fe07c5bd3ff77bb8f 100644 GIT binary patch delta 12842 zcmY+q1ymhDmoSOmQr324hm`&0SZbS3R18r37J8Z0F-T>@gIK` zatajf2b1lO#&E_RnGDF51uk%8Wcxm3`%Yhe7Psx?*?eZ?8M9_+G(?L=s^OG1n#S(NP3gF?2Mr2^f5E7sM~iVC`Rn;(-^MZ zZu*ZXB;XmgvPls(e#)MMTObsEx9oNz-K?AmQ8pP&P7vqx*=5zxjU+ye_1R<%KSg1? z7H&Yh))(Ke!Pa+aVuWxPKa_~Qo_IH}*;tV8n~O*Xa?t3P^9=L%=wOL1=~{LVv}mU8Q#e6s>v}iV8cDP|EdY)`dp≶7^21 ziF~qst3+S0y_IcTmzBD?t^AL=8|hpx>4aXc#L1YriEI=T#&IZ=SoAEyLg|^3d~uWZ zL(@1$!3on^gfz^e5VdZe5qx_>I%?g|J-FS>NG7S8Uwqt9t6KDa`8Nu!bDng+bM`&i zd>s2#sQ2Dsh6c}3YYi}8DqsK)DG!%;@xqz(<#=W`C`X+!HhtF~r~9OsI`@n36>D}N zz^HjPst0d<*2#=afSFiYwBeNZDk>BahnaW;GkQDA235(RJ%j;vVg80O#gk|q<#+OO z!F(BArIYDQG-{DlHpf+F=!)yw08zWccjd6DKgR+zJ(0X3zS;mzg+Na{$2N+AhF7`& zXj`aBWy{YG#8s$C5=GZH$a@!+F42?=O~WoaIjO;k;0P0nE5|ma;I^@xN`kKvIjTQe z1!_si%O1V@BP`r(WwTpr7HN&p#_-)5!T z%!r5ZL79g`v%i29=J2rPglr;%LCc+ZSZeh71?CfOgZ&EJdacV35*58xwhWGhyMhx{ z5KAVHq&&zae)(vc?T~KB9rtcfzy#SAUvce5`+$`_U7}=j*;@5(PyBoTp#IwDtV?s% zQ%T#rekISAFx`AeHyBx6BP^4OtUo>VhbksSk&W=OkQIO#SJ13R8z6r|HNM}$TK=58 z^$>Cg`+P;E@||v&RXQ8dF?fqSS3;wKND5tF(tf3C`q!LEI9_~9LgscI=n#Q>Vl6%6 z^xQ<;f6C*>yStD8WZ4LPzJjmeuu1L`A4BDvEy6DgDMC)PB+3}KWft<^5DPgko{>P8 zJL=zIrDlQ3l54nAxi=;0*HF+cQ`|0Z;~#mt0NHndDI8Ft6^Gp+Lz!19<=L3-abvfX zelFvqpMs+)n2}tXR2j_UG99=i2A)GzpZxTtF=_i+PyVcT4m=oLbh0j3wb~T*1D(f! 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zR)+>b|Lu|n2QOL@{#O&^KW&l!`{nz8Mh5%SWBqNPrd^^Y{J))U5D=vQ>-uNR_jg47 z*Z3J6vBV6hAo&knUHS&d`0|&Iefhmj@^~fw$LH0Vz&k&JA9`@ITB22u9sR1vhQr1C(9= zp?Ki)4LJam7kDS05UjB&1W5J%3nzV1{u&oI@c}PBeL^e2h{yt0J~uHVK7;Ku%yZnxzDBXR#gL9qNjDj2+j z54cPD8(~T(0AK9T0&dg)(r-mDV74smzb^A#e85xIf8>f?9>C|k|4_*Sw7)Lk9zFoN z;9nX2@8Kep{=b{{srcU@B6w?$2XIyTmkR9j0z@nRLQoa)-NUL 2>&1 -if "%ERRORLEVEL%" == "0" goto init +if "%ERRORLEVEL%" == "0" goto execute echo. echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. @@ -51,7 +54,7 @@ goto fail set JAVA_HOME=%JAVA_HOME:"=% set JAVA_EXE=%JAVA_HOME%/bin/java.exe -if exist "%JAVA_EXE%" goto init +if exist "%JAVA_EXE%" goto execute echo. echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% @@ -61,28 +64,14 @@ echo location of your Java installation. goto fail -:init -@rem Get command-line arguments, handling Windows variants - -if not "%OS%" == "Windows_NT" goto win9xME_args - -:win9xME_args -@rem Slurp the command line arguments. -set CMD_LINE_ARGS= -set _SKIP=2 - -:win9xME_args_slurp -if "x%~1" == "x" goto execute - -set CMD_LINE_ARGS=%* - :execute @rem Setup the command line set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + @rem Execute Gradle -"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS% +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* :end @rem End local scope for the variables with windows NT shell diff --git a/src/main/java/org/ga4gh/starterkit/drs/app/DrsServer.java b/src/main/java/org/ga4gh/starterkit/drs/app/DrsServer.java index ed33925..66e63a8 100644 --- a/src/main/java/org/ga4gh/starterkit/drs/app/DrsServer.java +++ b/src/main/java/org/ga4gh/starterkit/drs/app/DrsServer.java @@ -29,6 +29,7 @@ public static void main(String[] args) { private static boolean setup(String[] args) { Options options = new DrsServerSpringConfig().getCommandLineOptions(); - return ServerPropertySetter.setServerProperties(DrsServerYamlConfigContainer.class, args, options, "config"); + ServerPropertySetter setter = new ServerPropertySetter(); + return setter.setServerProperties(DrsServerYamlConfigContainer.class, args, options, "config"); } } diff --git a/src/main/java/org/ga4gh/starterkit/drs/app/DrsServerSpringConfig.java b/src/main/java/org/ga4gh/starterkit/drs/app/DrsServerSpringConfig.java index dc02207..48f54d9 100644 --- a/src/main/java/org/ga4gh/starterkit/drs/app/DrsServerSpringConfig.java +++ b/src/main/java/org/ga4gh/starterkit/drs/app/DrsServerSpringConfig.java @@ -153,7 +153,8 @@ public DrsServerYamlConfigContainer mergedDrsConfigContainer( @Qualifier(DrsServerConstants.DEFAULT_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer defaultContainer, @Qualifier(DrsServerConstants.USER_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer userContainer ) { - DeepObjectMerger.merge(userContainer, defaultContainer); + DeepObjectMerger merger = new DeepObjectMerger(); + merger.merge(userContainer, defaultContainer); return defaultContainer; } diff --git a/src/main/java/org/ga4gh/starterkit/drs/model/DrsServiceInfo.java b/src/main/java/org/ga4gh/starterkit/drs/model/DrsServiceInfo.java index ab511ec..240fee0 100644 --- a/src/main/java/org/ga4gh/starterkit/drs/model/DrsServiceInfo.java +++ b/src/main/java/org/ga4gh/starterkit/drs/model/DrsServiceInfo.java @@ -10,16 +10,14 @@ import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.UPDATED_AT; import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ENVIRONMENT; import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.VERSION; - -import com.fasterxml.jackson.annotation.JsonInclude; -import com.fasterxml.jackson.databind.PropertyNamingStrategies; -import com.fasterxml.jackson.databind.annotation.JsonNaming; - import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ORGANIZATION_NAME; import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ORGANIZATION_URL; import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_GROUP; import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_ARTIFACT; import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_VERSION; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.databind.PropertyNamingStrategies; +import com.fasterxml.jackson.databind.annotation.JsonNaming; /** * Extension of the GA4GH base service info specification to include DRS-specific From 94f1434cea06e4d4f0f254af1febf80e85acd7b7 Mon Sep 17 00:00:00 2001 From: Jeremy Adams Date: Wed, 15 Dec 2021 15:25:05 -0500 Subject: [PATCH 2/2] increment version to 0.2.2, add changelog to README --- README.md | 7 ++++++- build.gradle | 2 +- .../starterkit/drs/constant/DrsServiceInfoDefaults.java | 2 +- src/test/resources/responses/service-info/show/00.json | 2 +- 4 files changed, 9 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index fd26a67..7c8c547 100644 --- a/README.md +++ b/README.md @@ -182,4 +182,9 @@ Multiple datasets are currently contained in this repo for development and testi - see the [datasets page](./DATASETS.md#htsjdk) for a list of `DRS IDs` for `DrsObjects` in the htsjdk dataset * Open dataset of 384 Phenopackets: [Paper](https://pubmed.ncbi.nlm.nih.gov/32755546/), [Dataset homepage](https://zenodo.org/record/3905420#.YArkBzpKhPZ) - - see the [datasets page](./DATASETS.md#Phenopackets) for a list of `DRS IDs` for `DrsObjects` in the Phenopackets dataset \ No newline at end of file + - see the [datasets page](./DATASETS.md#Phenopackets) for a list of `DRS IDs` for `DrsObjects` in the Phenopackets dataset + +## Changelog + +### v0.2.2 +* patched log4j dependencies to v2.16.0 to avoid [Log4j Vulnerability](https://www.cisa.gov/uscert/apache-log4j-vulnerability-guidance) \ No newline at end of file diff --git a/build.gradle b/build.gradle index 8811914..50c0c02 100644 --- a/build.gradle +++ b/build.gradle @@ -36,7 +36,7 @@ configurations.all { archivesBaseName = 'ga4gh-starter-kit-drs' group 'org.ga4gh' -version '0.2.1' +version '0.2.2' repositories { // Use jcenter for resolving dependencies. diff --git a/src/main/java/org/ga4gh/starterkit/drs/constant/DrsServiceInfoDefaults.java b/src/main/java/org/ga4gh/starterkit/drs/constant/DrsServiceInfoDefaults.java index 34ec61a..a1af528 100644 --- a/src/main/java/org/ga4gh/starterkit/drs/constant/DrsServiceInfoDefaults.java +++ b/src/main/java/org/ga4gh/starterkit/drs/constant/DrsServiceInfoDefaults.java @@ -54,7 +54,7 @@ public class DrsServiceInfoDefaults { /** * Default service version */ - public static final String VERSION = "0.2.1"; + public static final String VERSION = "0.2.2"; /** * Default service organization name diff --git a/src/test/resources/responses/service-info/show/00.json b/src/test/resources/responses/service-info/show/00.json index fa01d2f..515a7a5 100644 --- a/src/test/resources/responses/service-info/show/00.json +++ b/src/test/resources/responses/service-info/show/00.json @@ -1 +1 @@ -{"id":"org.ga4gh.starterkit.drs","name":"GA4GH Starter Kit DRS Service","description":"An open source, community-driven implementation of the GA4GH Data Repository Service (DRS) API specification.","contactUrl":"mailto:info@ga4gh.org","documentationUrl":"https://github.com/ga4gh/ga4gh-starter-kit-drs","createdAt":"2020-01-15T12:00:00Z","updatedAt":"2020-01-15T12:00:00Z","environment":"test","version":"0.2.1","type":{"group":"org.ga4gh","artifact":"drs","version":"1.1.0"},"organization":{"name":"Global Alliance for Genomics and Health","url":"https://ga4gh.org"}} \ No newline at end of file +{"id":"org.ga4gh.starterkit.drs","name":"GA4GH Starter Kit DRS Service","description":"An open source, community-driven implementation of the GA4GH Data Repository Service (DRS) API specification.","contactUrl":"mailto:info@ga4gh.org","documentationUrl":"https://github.com/ga4gh/ga4gh-starter-kit-drs","createdAt":"2020-01-15T12:00:00Z","updatedAt":"2020-01-15T12:00:00Z","environment":"test","version":"0.2.2","type":{"group":"org.ga4gh","artifact":"drs","version":"1.1.0"},"organization":{"name":"Global Alliance for Genomics and Health","url":"https://ga4gh.org"}} \ No newline at end of file