Repackage by feature instead of layer

Mark Robinson · Mark Robinson · commit f46a67a67ee2 · 2017-03-11T19:14:58.000Z
diff --git a/src/main/java/org/commonwl/viewer/PageController.java b/src/main/java/org/commonwl/viewer/PageController.java
@@ -17,9 +17,9 @@
  * under the License.
  */
 
-package org.commonwl.viewer.web;
+package org.commonwl.viewer;
 
-import org.commonwl.viewer.domain.WorkflowForm;
+import org.commonwl.viewer.workflow.WorkflowForm;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.GetMapping;
diff --git a/src/main/java/org/commonwl/viewer/cwl/CWLElement.java b/src/main/java/org/commonwl/viewer/cwl/CWLElement.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain.cwl;
+package org.commonwl.viewer.cwl;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/src/main/java/org/commonwl/viewer/cwl/CWLProcess.java b/src/main/java/org/commonwl/viewer/cwl/CWLProcess.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain.cwl;
+package org.commonwl.viewer.cwl;
 
 /**
  * Enum for possible CWL processes
diff --git a/src/main/java/org/commonwl/viewer/cwl/CWLService.java b/src/main/java/org/commonwl/viewer/cwl/CWLService.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.services;
+package org.commonwl.viewer.cwl;
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -26,11 +26,10 @@
 import com.fasterxml.jackson.databind.node.TextNode;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
-import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.domain.Workflow;
-import org.commonwl.viewer.domain.cwl.CWLElement;
-import org.commonwl.viewer.domain.cwl.CWLProcess;
-import org.commonwl.viewer.domain.cwl.CWLStep;
+import org.commonwl.viewer.docker.DockerService;
+import org.commonwl.viewer.github.GitHubService;
+import org.commonwl.viewer.github.GithubDetails;
+import org.commonwl.viewer.workflow.Workflow;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
diff --git a/src/main/java/org/commonwl/viewer/cwl/CWLStep.java b/src/main/java/org/commonwl/viewer/cwl/CWLStep.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain.cwl;
+package org.commonwl.viewer.cwl;
 
 import java.util.Map;
 
diff --git a/src/main/java/org/commonwl/viewer/docker/DockerService.java b/src/main/java/org/commonwl/viewer/docker/DockerService.java
@@ -1,4 +1,4 @@
-package org.commonwl.viewer.services;
+package org.commonwl.viewer.docker;
 
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
diff --git a/src/main/java/org/commonwl/viewer/github/GitHubService.java b/src/main/java/org/commonwl/viewer/github/GitHubService.java
@@ -17,11 +17,10 @@
  * under the License.
  */
 
-package org.commonwl.viewer.services;
+package org.commonwl.viewer.github;
 
 import org.apache.commons.io.IOUtils;
-import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.domain.researchobject.HashableAgent;
+import org.commonwl.viewer.researchobject.HashableAgent;
 import org.eclipse.egit.github.core.*;
 import org.eclipse.egit.github.core.client.GitHubClient;
 import org.eclipse.egit.github.core.service.CommitService;
@@ -43,6 +42,7 @@
 
 /**
  * Handles Github related functionality including API usage
+ * Is mainly a wrapper for org.eclipse.egit.github.core
  */
 @Service
 public class GitHubService {
diff --git a/src/main/java/org/commonwl/viewer/github/GithubDetails.java b/src/main/java/org/commonwl/viewer/github/GithubDetails.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.github;
 
 import java.io.Serializable;
 
diff --git a/src/main/java/org/commonwl/viewer/graphviz/DotWriter.java b/src/main/java/org/commonwl/viewer/graphviz/DotWriter.java
@@ -17,12 +17,12 @@
  * under the License.
  */
 
-package org.commonwl.viewer.services;
+package org.commonwl.viewer.graphviz;
 
-import org.commonwl.viewer.domain.Workflow;
-import org.commonwl.viewer.domain.cwl.CWLElement;
-import org.commonwl.viewer.domain.cwl.CWLProcess;
-import org.commonwl.viewer.domain.cwl.CWLStep;
+import org.commonwl.viewer.cwl.CWLElement;
+import org.commonwl.viewer.cwl.CWLProcess;
+import org.commonwl.viewer.cwl.CWLStep;
+import org.commonwl.viewer.workflow.Workflow;
 
 import java.io.IOException;
 import java.io.Writer;
diff --git a/src/main/java/org/commonwl/viewer/graphviz/GraphVizService.java b/src/main/java/org/commonwl/viewer/graphviz/GraphVizService.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.services;
+package org.commonwl.viewer.graphviz;
 
 import com.github.jabbalaci.graphviz.GraphViz;
 import org.springframework.beans.factory.annotation.Autowired;
diff --git a/src/main/java/org/commonwl/viewer/researchobject/HashableAgent.java b/src/main/java/org/commonwl/viewer/researchobject/HashableAgent.java
@@ -1,4 +1,4 @@
-package org.commonwl.viewer.domain.researchobject;
+package org.commonwl.viewer.researchobject;
 
 import org.apache.taverna.robundle.manifest.Agent;
 
diff --git a/src/main/java/org/commonwl/viewer/researchobject/ROBundle.java b/src/main/java/org/commonwl/viewer/researchobject/ROBundle.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain.researchobject;
+package org.commonwl.viewer.researchobject;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
@@ -26,8 +26,8 @@
 import org.apache.taverna.robundle.manifest.Agent;
 import org.apache.taverna.robundle.manifest.Manifest;
 import org.apache.taverna.robundle.manifest.PathMetadata;
-import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.services.GitHubService;
+import org.commonwl.viewer.github.GitHubService;
+import org.commonwl.viewer.github.GithubDetails;
 import org.eclipse.egit.github.core.RepositoryContents;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
diff --git a/src/main/java/org/commonwl/viewer/researchobject/ROBundleFactory.java b/src/main/java/org/commonwl/viewer/researchobject/ROBundleFactory.java
@@ -17,11 +17,12 @@
  * under the License.
  */
 
-package org.commonwl.viewer.services;
+package org.commonwl.viewer.researchobject;
 
-import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.domain.Workflow;
-import org.commonwl.viewer.domain.researchobject.ROBundle;
+import org.commonwl.viewer.github.GitHubService;
+import org.commonwl.viewer.github.GithubDetails;
+import org.commonwl.viewer.workflow.Workflow;
+import org.commonwl.viewer.workflow.WorkflowRepository;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -72,7 +73,7 @@ public ROBundleFactory(@Value("${applicationName}") String applicationName,
      * @throws IOException Any API errors which may have occurred
      */
     @Async
-    void workflowROFromGithub(GitHubService githubService, GithubDetails githubInfo, String commitSha)
+    public void workflowROFromGithub(GitHubService githubService, GithubDetails githubInfo, String commitSha)
             throws IOException, InterruptedException {
         logger.info("Creating Research Object Bundle");
 
diff --git a/src/main/java/org/commonwl/viewer/researchobject/ROBundleNotFoundException.java b/src/main/java/org/commonwl/viewer/researchobject/ROBundleNotFoundException.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.web;
+package org.commonwl.viewer.researchobject;
 
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ResponseStatus;
diff --git a/src/main/java/org/commonwl/viewer/workflow/Workflow.java b/src/main/java/org/commonwl/viewer/workflow/Workflow.java
@@ -17,11 +17,12 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.workflow;
 
-import org.commonwl.viewer.domain.cwl.CWLElement;
-import org.commonwl.viewer.domain.cwl.CWLStep;
-import org.commonwl.viewer.services.DotWriter;
+import org.commonwl.viewer.cwl.CWLElement;
+import org.commonwl.viewer.cwl.CWLStep;
+import org.commonwl.viewer.github.GithubDetails;
+import org.commonwl.viewer.graphviz.DotWriter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.data.annotation.Id;
diff --git a/src/main/java/org/commonwl/viewer/workflow/WorkflowController.java b/src/main/java/org/commonwl/viewer/workflow/WorkflowController.java
@@ -17,15 +17,11 @@
  * under the License.
  */
 
-package org.commonwl.viewer.web;
+package org.commonwl.viewer.workflow;
 
 import org.apache.commons.lang.StringUtils;
-import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.domain.Workflow;
-import org.commonwl.viewer.domain.WorkflowForm;
-import org.commonwl.viewer.services.GraphVizService;
-import org.commonwl.viewer.services.WorkflowFormValidator;
-import org.commonwl.viewer.services.WorkflowService;
+import org.commonwl.viewer.github.GithubDetails;
+import org.commonwl.viewer.graphviz.GraphVizService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
diff --git a/src/main/java/org/commonwl/viewer/workflow/WorkflowForm.java b/src/main/java/org/commonwl/viewer/workflow/WorkflowForm.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.viewer.workflow;
 
 /**
  * Represents the submission form on the main page to create a new workflow
diff --git a/src/main/java/org/commonwl/viewer/workflow/WorkflowFormValidator.java b/src/main/java/org/commonwl/viewer/workflow/WorkflowFormValidator.java
@@ -17,10 +17,10 @@
  * under the License.
  */
 
-package org.commonwl.viewer.services;
+package org.commonwl.viewer.workflow;
 
-import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.domain.WorkflowForm;
+import org.commonwl.viewer.github.GitHubService;
+import org.commonwl.viewer.github.GithubDetails;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
diff --git a/src/main/java/org/commonwl/viewer/workflow/WorkflowNotFoundException.java b/src/main/java/org/commonwl/viewer/workflow/WorkflowNotFoundException.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.web;
+package org.commonwl.viewer.workflow;
 
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ResponseStatus;
diff --git a/src/main/java/org/commonwl/viewer/workflow/WorkflowRepository.java b/src/main/java/org/commonwl/viewer/workflow/WorkflowRepository.java
@@ -17,10 +17,9 @@
  * under the License.
  */
 
-package org.commonwl.viewer.services;
+package org.commonwl.viewer.workflow;
 
-import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.domain.Workflow;
+import org.commonwl.viewer.github.GithubDetails;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.repository.PagingAndSortingRepository;
diff --git a/src/main/java/org/commonwl/viewer/workflow/WorkflowService.java b/src/main/java/org/commonwl/viewer/workflow/WorkflowService.java
@@ -17,11 +17,14 @@
  * under the License.
  */
 
-package org.commonwl.viewer.services;
-
-import org.commonwl.viewer.domain.GithubDetails;
-import org.commonwl.viewer.domain.Workflow;
-import org.commonwl.viewer.web.ROBundleNotFoundException;
+package org.commonwl.viewer.workflow;
+
+import org.commonwl.viewer.cwl.CWLService;
+import org.commonwl.viewer.github.GitHubService;
+import org.commonwl.viewer.github.GithubDetails;
+import org.commonwl.viewer.graphviz.GraphVizService;
+import org.commonwl.viewer.researchobject.ROBundleFactory;
+import org.commonwl.viewer.researchobject.ROBundleNotFoundException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -42,7 +45,7 @@ public class WorkflowService {
     private final GitHubService githubService;
     private final CWLService cwlService;
     private final WorkflowRepository workflowRepository;
-    private final ROBundleFactory ROBundleFactory;
+    private final org.commonwl.viewer.researchobject.ROBundleFactory ROBundleFactory;
     private final GraphVizService graphVizService;
     private final int cacheDays;
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-package org.commonwl.viewer.services;`
	`1`	`+package org.commonwl.viewer.docker;`
`2`	`2`
`3`	`3`	`import java.util.regex.Matcher;`
`4`	`4`	`import java.util.regex.Pattern;`