Fix response for 1.5.4 (#2369)

dockstore-common/src/main/java/io/dockstore/common/PipHelper.java

@@ -14,6 +14,7 @@
  */
 public final class PipHelper {
     public static final String DEV_SEM_VER = "development-build";
+
     private PipHelper() { }
 
     /**
@@ -24,18 +25,10 @@ private PipHelper() { }
      */
     public static String convertSemVerToAvailableVersion(String semVerString) {
         if (semVerString == null || DEV_SEM_VER.equals(semVerString)) {
-            semVerString = "9001.9001.9001";
-        }
-        Version semVer = Version.valueOf(semVerString);
-        // Use the 1.6.0 even for snapshot
-        if (semVer.greaterThan(Version.valueOf("1.5.0"))) {
             return "1.6.0";
         }
-        if (semVer.greaterThan(Version.valueOf("1.4.0"))) {
-            return "1.5.0";
-        } else {
-            return "1.4.0";
-        }
+        Version semVer = Version.valueOf(semVerString);
+        return "1." + semVer.getMinorVersion() + ".0";
     }
 
     /**

dockstore-common/src/test/java/io/dockstore/common/PipHelperTest.java

@@ -3,24 +3,26 @@
 import org.junit.Assert;
 import org.junit.Test;
 
-import static org.junit.Assert.*;
-
 /**
  * @author gluu
  * @since 14/08/18
  */
 public class PipHelperTest {
     @Test
-    public void convertSemVerToAvailableVersion() throws Exception {
+    public void convertSemVerToAvailableVersion() {
+        Assert.assertEquals("1.7.0", PipHelper.convertSemVerToAvailableVersion("1.7.0-snapshot"));
+        Assert.assertEquals("1.6.0", PipHelper.convertSemVerToAvailableVersion("1.6.4"));
+        // TODO: expect 1.7.0 on develop
         Assert.assertEquals("1.6.0", PipHelper.convertSemVerToAvailableVersion(PipHelper.DEV_SEM_VER));
         Assert.assertEquals("1.6.0", PipHelper.convertSemVerToAvailableVersion(null));
         Assert.assertEquals("1.6.0", PipHelper.convertSemVerToAvailableVersion("1.6.0-snapshot"));
         Assert.assertEquals("1.6.0", PipHelper.convertSemVerToAvailableVersion("1.6.0"));
+        Assert.assertEquals("1.5.0", PipHelper.convertSemVerToAvailableVersion("1.5.4"));
         Assert.assertEquals("1.5.0", PipHelper.convertSemVerToAvailableVersion("1.5.0-snapshot"));
         Assert.assertEquals("1.5.0", PipHelper.convertSemVerToAvailableVersion("1.5.0"));
         Assert.assertEquals("1.4.0", PipHelper.convertSemVerToAvailableVersion("1.4.0-snapshot"));
         Assert.assertEquals("1.4.0", PipHelper.convertSemVerToAvailableVersion("1.4.0"));
-        Assert.assertEquals("1.4.0", PipHelper.convertSemVerToAvailableVersion("1.3.0-snapshot"));
-        Assert.assertEquals("1.4.0", PipHelper.convertSemVerToAvailableVersion("1.3.0"));
+        Assert.assertEquals("1.3.0", PipHelper.convertSemVerToAvailableVersion("1.3.0-snapshot"));
+        Assert.assertEquals("1.3.0", PipHelper.convertSemVerToAvailableVersion("1.3.0"));
     }
 }

dockstore-integration-testing/src/test/java/io/dockstore/client/cli/MetadataIT.java

@@ -0,0 +1,57 @@
+/*
+ *    Copyright 2019 OICR
+ *
+ *    Licensed under the Apache License, Version 2.0 (the "License");
+ *    you may not use this file except in compliance with the License.
+ *    You may obtain a copy of the License at
+ *
+ *        http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *    Unless required by applicable law or agreed to in writing, software
+ *    distributed under the License is distributed on an "AS IS" BASIS,
+ *    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *    See the License for the specific language governing permissions and
+ *    limitations under the License.
+ */
+package io.dockstore.client.cli;
+
+import io.swagger.client.ApiClient;
+import io.swagger.client.api.MetadataApi;
+import org.junit.Assert;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.contrib.java.lang.system.ExpectedSystemExit;
+import org.junit.contrib.java.lang.system.SystemErrRule;
+import org.junit.contrib.java.lang.system.SystemOutRule;
+import org.junit.rules.ExpectedException;
+
+public class MetadataIT extends BaseIT {
+    @Rule
+    public final SystemOutRule systemOutRule = new SystemOutRule().enableLog().muteForSuccessfulTests();
+
+    @Rule
+    public final SystemErrRule systemErrRule = new SystemErrRule().enableLog().muteForSuccessfulTests();
+
+    @Rule
+    public final ExpectedSystemExit systemExit = ExpectedSystemExit.none();
+
+    @Rule
+    public ExpectedException thrown= ExpectedException.none();
+
+
+
+
+    @Test
+    public void testRunnerDependencies() {
+        ApiClient apiClient = getWebClient();
+        MetadataApi metadataApi = new MetadataApi(apiClient);
+        String runnerDependencies = metadataApi.getRunnerDependencies("1.5.4", "2", "cwltool", "text");
+        Assert.assertTrue(runnerDependencies.contains("cwltool==1.0.20180403145700"));
+        runnerDependencies = metadataApi.getRunnerDependencies("1.6.0", "2", "cwltool", "text");
+        Assert.assertTrue(runnerDependencies.contains("cwltool==1.0.20181217162649"));
+        runnerDependencies = metadataApi.getRunnerDependencies("1.6.4", "2", "cwltool", "text");
+        Assert.assertTrue(runnerDependencies.contains("cwltool==1.0.20181217162649"));
+    }
+
+
+}

dockstore-webservice/src/main/java/io/dockstore/webservice/resources/MetadataResource.java

@@ -231,6 +231,9 @@ public Response getRunnerDependencies(
         }
         boolean unwrap = !("json").equals(output);
         String fileVersion = PipHelper.convertSemVerToAvailableVersion(clientVersion);
+        if (fileVersion == null) {
+            throw new CustomWebApplicationException("Invalid version, could not retrieve runner dependencies file", HttpStatus.SC_BAD_REQUEST);
+        }
         try {
             String content = Resources.toString(this.getClass().getClassLoader()
                     .getResource("requirements/" + fileVersion + "/requirements" + (pythonVersion.startsWith("3") ? "3" : "") + ".txt"), StandardCharsets.UTF_8);

dockstore-webservice/src/main/resources/requirements/1.3.0/requirements.txt

@@ -0,0 +1,7 @@
+setuptools==36.5.0
+cwl-runner
+cwltool==1.0.20170828135420
+schema-salad==2.6.20170806163416
+avro==1.8.1
+ruamel.yaml==0.14.12
+requests==2.18.4

dockstore-webservice/src/main/resources/requirements/1.3.0/requirements3.txt

@@ -0,0 +1,7 @@
+setuptools==36.5.0
+cwl-runner
+cwltool==1.0.20170828135420
+schema-salad==2.6.20170806163416
+avro-cwl==1.8.3
+ruamel.yaml==0.14.12
+requests==2.18.4

dockstore-webservice/src/main/resources/requirements/1.7.0/requirements.txt

@@ -0,0 +1,32 @@
+bagit==1.7.0
+CacheControl==0.11.7
+certifi==2019.3.9
+chardet==3.0.4
+cwltool==1.0.20181217162649
+decorator==4.4.0
+idna==2.8
+isodate==0.6.0
+lockfile==0.12.2
+lxml==4.3.3
+mistune==0.8.4
+mypy-extensions==0.4.1
+networkx==2.2
+pathlib2==2.3.2
+pkg-resources==0.0.0
+prov==1.5.1
+psutil==5.6.1
+pyparsing==2.4.0
+python-dateutil==2.8.0
+rdflib==4.2.2
+rdflib-jsonld==0.4.0
+requests==2.21.0
+ruamel.ordereddict==0.4.13
+ruamel.yaml==0.15.77
+scandir==1.10.0
+schema-salad==3.0.20181206233650
+shellescape==3.4.1
+six==1.12.0
+subprocess32==3.5.3
+typing==3.6.6
+typing-extensions==3.7.2
+urllib3==1.24.1

dockstore-webservice/src/main/resources/requirements/1.7.0/requirements3.txt

@@ -0,0 +1,29 @@
+bagit==1.7.0
+CacheControl==0.11.7
+certifi==2019.3.9
+chardet==3.0.4
+cwltool==1.0.20181217162649
+decorator==4.4.0
+idna==2.8
+isodate==0.6.0
+lockfile==0.12.2
+lxml==4.3.3
+mistune==0.8.4
+mypy-extensions==0.4.1
+networkx==2.2
+pkg-resources==0.0.0
+prov==1.5.1
+psutil==5.6.1
+pyparsing==2.4.0
+python-dateutil==2.8.0
+rdflib==4.2.2
+rdflib-jsonld==0.4.0
+requests==2.21.0
+ruamel.yaml==0.15.77
+scandir==1.10.0
+schema-salad==3.0.20181206233650
+shellescape==3.4.1
+six==1.12.0
+typing==3.6.6
+typing-extensions==3.7.2
+urllib3==1.24.1