Updating cwltool dependencies (#291)

* Remove dead ICGC link and update synapse link

* Bump artifact version

* Try updating circle image

* Update encrypted bundle for gitlab/bitbucket keys

* Add .DS_Store to gitignore
having returned to mac these end up everywhere

* Update version installed for integration testing

* Try reverting docker image
Annoying test failure for noInternetTest

* Set back webservice version

* other POM updates as well

* Typos in README and point to new script

* Point to new release off hotfix branch

.gitignore

@@ -2,6 +2,7 @@
 .idea
 *.class
 *.swp
+.DS_Store
 
 # Contains SQL statements to initialize testing DB with a confidential user and tokens
 # Contains SQL statements to initialize testing DB with a confidential user, assuming they followed the dockstore setup tutorial

README.md

@@ -45,8 +45,7 @@ server-url = https://www.dockstore.org/api
 
 By default, cwltool reads input files from the local filesystem. Dockstore also adds support for additional file systems
 such as http, https, and ftp. Through a plug-in system, Dockstore also supports 
-the Amazon S3, [Synapse](http://docs.synapse.org/articles/downloading_data.html), and 
-[ICGC Score Client](https://docs.icgc.org/download/guide/#score-client-usage) via [plugins](https://github.com/dockstore).
+Amazon S3 and [Synapse](https://help.synapse.org/docs/Downloading-Data-Programmatically.2003796248.html) via [plugins](https://github.com/dockstore).
 
 Download the above set of default plugins via: 
 ```

dockstore-cli-integration-testing/generated/src/main/resources/pom.xml

@@ -36,7 +36,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-integration-testing</artifactId>
-      <version>1.15.0-rc.1</version>
+      <version>1.15.4-alpha.2</version>
       <classifier>tests</classifier>
       <scope>compile</scope>
       <exclusions>
@@ -49,13 +49,13 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-common</artifactId>
-      <version>1.15.0-rc.1</version>
+      <version>1.15.4-alpha.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-webservice</artifactId>
-      <version>1.15.0-rc.1</version>
+      <version>1.15.4-alpha.2</version>
       <scope>compile</scope>
       <exclusions>
         <exclusion>
@@ -67,7 +67,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>openapi-java-client</artifactId>
-      <version>1.15.0-rc.1</version>
+      <version>1.15.4-alpha.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

dockstore-cli-reports/generated/src/main/resources/pom.xml

@@ -30,13 +30,13 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-webservice</artifactId>
-      <version>1.15.0-rc.1</version>
+      <version>1.15.4-alpha.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-common</artifactId>
-      <version>1.15.0-rc.1</version>
+      <version>1.15.4-alpha.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

dockstore-client/generated/src/main/resources/pom.xml

@@ -66,7 +66,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-common</artifactId>
-      <version>1.15.0-rc.1</version>
+      <version>1.15.4-alpha.2</version>
       <scope>compile</scope>
       <exclusions>
         <exclusion>
@@ -78,7 +78,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>openapi-java-client</artifactId>
-      <version>1.15.0-rc.1</version>
+      <version>1.15.4-alpha.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

pom.xml

@@ -38,7 +38,7 @@
 
         <github.url>scm:git:[email protected]:dockstore/dockstore-cli.git</github.url>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <dockstore-core.version>1.15.0-rc.1</dockstore-core.version>
+        <dockstore-core.version>1.15.4-alpha.2</dockstore-core.version>
         <maven-failsafe.version>2.22.2</maven-failsafe.version>
         <maven-surefire.version>2.22.2</maven-surefire.version>
         <skipTests>false</skipTests>

scripts/install-tests.sh

@@ -14,7 +14,7 @@ fi
 if [ "${TESTING_PROFILE}" = "toil-integration-tests" ]; then
     pip3 install --user toil[cwl]==3.15.0
 else
-    pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.14.0/requirements3.txt
+    pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/hotfix/1.15.4/dockstore-webservice/src/main/resources/requirements/1.15.0/requirements3.txt
 fi
 
 if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then