minor changes in the conda readers

ypriverol · ypriverol · commit 5e35a5bc9133 · 2018-09-26T11:19:55.000+01:00
diff --git a/registries-readers/src/main/java/pro/biocontainers/readers/github/configs/GitHubConfiguration.java b/registries-readers/src/main/java/pro/biocontainers/readers/github/configs/GitHubConfiguration.java
@@ -19,7 +19,7 @@ public class GitHubConfiguration {
     @Value("${github.docker-api-containers-urls}")
     String gitHubAPIDockerFiles;
 
-    @Value("${githug.conda-api-containers-urls}")
+    @Value("${github.conda-api-containers-urls}")
     String gitHubAPICondaFiles;
 
 }
diff --git a/registry-pipelines/src/main/java/pro/biocontainers/pipelines/jobs/AnnotateToolFromContainerVersionsJob.java b/registry-pipelines/src/main/java/pro/biocontainers/pipelines/jobs/AnnotateToolFromContainerVersionsJob.java
@@ -1,4 +1,4 @@
-package pro.biocontainers.pipelines.jobs.registries;
+package pro.biocontainers.pipelines.jobs;
 
 /**
  * This code is licensed under the Apache License, Version 2.0 (the
diff --git a/registry-pipelines/src/main/java/pro/biocontainers/pipelines/jobs/ImportContainersFromCondaJob.java b/registry-pipelines/src/main/java/pro/biocontainers/pipelines/jobs/ImportContainersFromCondaJob.java
@@ -1,4 +1,4 @@
-package pro.biocontainers.pipelines.jobs.registries.bioconda;
+package pro.biocontainers.pipelines.jobs;
 
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.batch.core.Job;
@@ -57,19 +57,35 @@ public RestTemplateBuilder restTemplateBuilder() {
     @Autowired
     GitHubConfiguration gitHubConfiguration;
 
-    final GitHubFileReader fileReaderService;
+    GitHubFileReader fileReaderService;
 
-    final RestTemplateBuilder builder;
+    RestTemplateBuilder builder;
 
     @Value("${public-url.dockerhub}")
     String dockerHubRegistry;
 
     @Value("${public-url.quay-io}")
     String quayIOHubRegistry;
 
-    public ImportContainersFromCondaJob(){
+    @Value("${biocontainers-registry}")
+    String bioContainersURL;
+
+    @Value("${biocontainers-registry-version}")
+    String bioContainersVersionURL;
+
+    @Value("${biocontainers-registry-image}")
+    String bioContainersImageURL;
+
+    @Bean
+    public RestTemplateBuilder getRestTemplate() {
         builder = new RestTemplateBuilder();
+        return builder;
+    }
+
+    @Bean
+    GitHubFileReader getFileReaderService(){
         fileReaderService = new GitHubFileReader(gitHubConfiguration, builder);
+        return this.fileReaderService;
     }
 
     /**
@@ -82,7 +98,6 @@ Step readContainersFromQUAYIO() {
                 .get(PipelineConstants.StepNames.READ_QUAYIO_REGISTRY_LIST.name())
                 .tasklet((stepContribution, chunkContext) -> {
 
-
                     GitHubFileNameList condaFileList = fileReaderService.getCondaFiles();
                     Map<String, Set<CondaRecipe>> toolNames = new ConcurrentHashMap<>();
 
diff --git a/registry-pipelines/src/main/java/pro/biocontainers/pipelines/jobs/ImportContainersFromDockerHubJob.java b/registry-pipelines/src/main/java/pro/biocontainers/pipelines/jobs/ImportContainersFromDockerHubJob.java
@@ -1,4 +1,4 @@
-package pro.biocontainers.pipelines.jobs.registries.dockerhub;
+package pro.biocontainers.pipelines.jobs;
 
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.batch.core.Job;
diff --git a/registry-pipelines/src/main/resources/application.properties b/registry-pipelines/src/main/resources/application.properties
@@ -21,7 +21,7 @@ github.docker-containers-recipes=https://github.com/BioContainers/containers/mas
 github.bioconda-containers-recipes=https://github.com/bioconda/bioconda-recipes/master/recipes/%%software_tool_version%%/meta.yaml
 
 github.docker-api-containers-urls=https://api.github.com/repos/biocontainers/containers/git/trees/master?recursive=2
-githug.conda-api-containers-urls=https://api.github.com/repositories/42372094/git/trees/master?recursive=2
+github.conda-api-containers-urls=https://api.github.com/repositories/42372094/git/trees/master?recursive=2
 
 
 
diff --git a/registry-pipelines/src/test/java/pro/biocontainers/pipelines/jobs/registries/AnnotateToolFromContainerVersionsJobTest.java b/registry-pipelines/src/test/java/pro/biocontainers/pipelines/jobs/registries/AnnotateToolFromContainerVersionsJobTest.java
@@ -12,10 +12,7 @@
 import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import pro.biocontainers.pipelines.configs.JobRunnerTestConfiguration;
-import pro.biocontainers.pipelines.jobs.registries.dockerhub.ImportContainersFromDockerHubJob;
-
-import static org.junit.Assert.*;
-
+import pro.biocontainers.pipelines.jobs.AnnotateToolFromContainerVersionsJob;
 
 
 @RunWith(SpringJUnit4ClassRunner.class)
diff --git a/registry-pipelines/src/test/java/pro/biocontainers/pipelines/jobs/registries/bioconda/ImportContainersFromCondaJobTest.java b/registry-pipelines/src/test/java/pro/biocontainers/pipelines/jobs/registries/bioconda/ImportContainersFromCondaJobTest.java
@@ -12,6 +12,7 @@
 import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import pro.biocontainers.pipelines.configs.JobRunnerTestConfiguration;
+import pro.biocontainers.pipelines.jobs.ImportContainersFromCondaJob;
 
 /**
  * This code is licensed under the Apache License, Version 2.0 (the
diff --git a/registry-pipelines/src/test/java/pro/biocontainers/pipelines/jobs/registries/dockerhub/ImportContainersFromDockerHubJobTest.java b/registry-pipelines/src/test/java/pro/biocontainers/pipelines/jobs/registries/dockerhub/ImportContainersFromDockerHubJobTest.java
@@ -12,6 +12,7 @@
 import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import pro.biocontainers.pipelines.configs.JobRunnerTestConfiguration;
+import pro.biocontainers.pipelines.jobs.ImportContainersFromDockerHubJob;
 
 /**
  * This code is licensed under the Apache License, Version 2.0 (the

Original file line number	Diff line number	Diff line change
`@@ -19,7 +19,7 @@ public class GitHubConfiguration {`
`19`	`19`	`@Value("${github.docker-api-containers-urls}")`
`20`	`20`	`String gitHubAPIDockerFiles;`
`21`	`21`
`22`		`- @Value("${githug.conda-api-containers-urls}")`
	`22`	`+ @Value("${github.conda-api-containers-urls}")`
`23`	`23`	`String gitHubAPICondaFiles;`
`24`	`24`
`25`	`25`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-package pro.biocontainers.pipelines.jobs.registries;`
	`1`	`+package pro.biocontainers.pipelines.jobs;`
`2`	`2`
`3`	`3`	`/**`
`4`	`4`	`* This code is licensed under the Apache License, Version 2.0 (the`