Merge pull request #1675 from jjgao/master

release 1.2.5

.github/PULL_REQUEST_TEMPLATE.md

@@ -20,8 +20,14 @@ If this is a new visual feature please add a before/after screenshot or gif
 here with e.g. [GifGrabber](http://www.gifgrabber.com/).
 
 # Notify reviewers
-If your pull request involves changes to an existing file, one or more of the
-people that edited before you might be good candidates to review it. Please use
-`git blame <filename>` to determine that and notify them here. Otherwise notify
-everybody in the core team:
-@cBioPortal/core-developers
+Read our [Pull request merging
+policy](../CONTRIBUTING.md#pull-request-merging-policy). If you are part of the
+cBioPortal organization, notify the approprate team (remove inappropriate):
+
+@cBioPortal/frontend
+@cBioPortal/backend
+@cBioPortal/devops
+
+If you are not part of the cBioPortal organization look at who worked on the
+file before you. Please use `git blame <filename>` to determine that
+and notify them here:

.gitignore

@@ -77,3 +77,5 @@ nbactions.xml
 */.project
 dependency-reduced-pom.xml
 /core/nbactions-private.xml
+.profile.d/
+Procfile

CONTRIBUTING.md

@@ -86,6 +86,67 @@ Once you downloaded the images you do the following for each screenshot:
 - If the change in the screenshot is **desired**, add the screenshot to the
   repo, commit it and push it to your PR's branch.
 
+## Pull Request Merging Policy
+Pull Requests (PRs) are reviewed by the
+[backend](https://github.com/orgs/cBioPortal/teams/backend),
+[frontend](https://github.com/orgs/cBioPortal/teams/frontend) and
+[devops](https://github.com/orgs/cBioPortal/teams/devops) teams of cBioPortal.
+For each PR the submitter should propose what team(s) is/are appropriate to
+review it. This is the current merging policy:
+
+- A documentation change needs one **Approve**
+- A simple bugfix to rc or hotfix requires one **Approve**
+- A new feature requires two **Approve**. One from someone at MSKCC and one from
+  another institution.
+
+If these requirements are met, any person with merge rights can merge to rc or
+hotfix.
+
+## Pull Request Reviewers Guide
+Here we describe the guidelines for the reviewer. Always follow the checks in
+general, then follow the other checks that apply:
+
+### General
+- Double check all the things in the **Checks** section of the Pull Request.
+  Remind the submitter if any of them are not fulfilled
+- Are the test cases spanning a decent amount of scenarios? It is the
+  submitters as well as the reviewers responsibility to not let any errors
+  sneak into the portal.
+
+Bug fixes:
+
+- Should the bug that causes the issue be added as a test case?
+
+New features:
+
+- If this is a new feature make sure the proposed changes are in line with the
+  current planning of cBioPortal e.g. is the right API used, is this in line
+  with current refactoring efforts.
+
+### Backend
+New features:
+
+- Is the new persistence stack used?
+
+### Frontend
+New features:
+
+- What APIs are used to get the data? Is the REST API used?
+- Should this be a separate library in a separate repo or should it be part of cBioPortal?
+- Are dependencies properly listed? Ideally in a package.json
+- How is the package included in cBioPortal?
+
+### Devops
+New features:
+
+- Does the configuration style follow the config guidelines? That is compile
+  (Maven) config goes in the appriopriate `pom.xml` (root, `scripts/`, `portal/`, `core/`).
+  Runtime (Spring) goes in `portal.properties`. Default values should be in `GlobalProperties.java`.
+- Non-stable configuration should be done through war overlays.
+- Is the configuration tested as part of Travis CI? It's not a necessity but be
+  aware that untested configuration will be tough to maintain.
+- Is there documentation on the proposed changes?
+
 ## Additional Resources
 
 * [cBioPortal Issue Tracker](https://github.com/cBioPortal/cbioportal/issues)

business/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.2.4</version>
+    <version>1.2.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>business</artifactId>

core/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.2.4</version>
+    <version>1.2.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>core</artifactId>

core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java

@@ -255,6 +255,14 @@ public String getOncotatorUniprotName() {
             return oncotatorUniprotName;
         }
 
+        /**
+         * Set the UniprotKB name (formerly known as ID) of the protein record.
+         *
+         * @param oncotatorUniprotName the UniprotKB name
+         * @deprecated set the accession with
+         *             {@link #setOncotatorUniprotAccession(String)} instead
+         */
+        @Deprecated
         public void setOncotatorUniprotName(String oncotatorUniprotName) {
             this.oncotatorUniprotName = oncotatorUniprotName;
         }
@@ -835,6 +843,14 @@ public String getOncotatorUniprotName()
         return event.getOncotatorUniprotName();
     }
 
+    /**
+     * Set the UniprotKB name (formerly known as ID) of the protein record.
+     *
+     * @param oncotatorUniprotName the UniprotKB name
+     * @deprecated set the accession with
+     *             {@link #setOncotatorUniprotAccession(String)} instead
+     */
+    @Deprecated
     public void setOncotatorUniprotName(String oncotatorUniprotName)
     {
         event.setOncotatorUniprotName(oncotatorUniprotName);

core/src/main/java/org/mskcc/cbio/portal/model/GeneticProfile.java

@@ -32,6 +32,8 @@
 
 package org.mskcc.cbio.portal.model;
 
+import java.util.Properties;
+
 import org.apache.commons.lang.builder.ToStringBuilder;
 
 /**
@@ -47,14 +49,15 @@ public class GeneticProfile {
     private String profileDescription;
     private String targetLine;
     private boolean showProfileInAnalysisTab;
+    private Properties otherMetadataFields;
 
     public GeneticProfile() {
       super();
    }
 
    public GeneticProfile(String stableId, int cancerStudyId, GeneticAlterationType geneticAlterationType,
 						 String datatype, String profileName, String profileDescription, boolean showProfileInAnalysisTab) {
-      super();
+      this();
       this.stableId = stableId;
       this.cancerStudyId = cancerStudyId;
       this.geneticAlterationType = geneticAlterationType;
@@ -64,6 +67,26 @@ public GeneticProfile(String stableId, int cancerStudyId, GeneticAlterationType
       this.showProfileInAnalysisTab = showProfileInAnalysisTab;
    }
 
+
+   /**
+    * Constructs a new genetic profile object with the same attributes as the one given as an argument.
+    *
+    * @param template  the object to copy
+    */
+   public GeneticProfile(GeneticProfile template) {
+       this(
+               template.getStableId(),
+               template.getCancerStudyId(),
+               template.getGeneticAlterationType(),
+               template.getDatatype(),
+               template.getProfileName(),
+               template.getProfileDescription(),
+               template.showProfileInAnalysisTab());
+       this.setGeneticProfileId(template.geneticProfileId);
+       this.setTargetLine(template.getTargetLine());
+       this.setOtherMetadataFields(template.getAllOtherMetadataFields());
+   }
+
    public int getGeneticProfileId() {
         return geneticProfileId;
     }
@@ -135,10 +158,42 @@ public boolean showProfileInAnalysisTab() {
     public void setShowProfileInAnalysisTab(boolean showProfileInAnalysisTab) {
         this.showProfileInAnalysisTab = showProfileInAnalysisTab;
     }
-
+
+    /**
+     * Stores metadata fields only recognized in particular data file types.
+     *
+     * @param fields  a properties instance holding the keys and values
+     */
+    public void setOtherMetadataFields(Properties fields) {
+        this.otherMetadataFields = fields;
+    }
+
+    /**
+     * Returns all file-specific metadata fields as a Properties object.
+     *
+     * @return  a properties instance holding the keys and values or null
+     */
+    public Properties getAllOtherMetadataFields() {
+        return this.otherMetadataFields;
+    }
+
+    /**
+     * Retrieves metadata fields specific to certain data file types.
+     *
+     * @param fieldname  the name of the field to retrieve
+     * @return  the value of the field or null
+     */
+    public String getOtherMetaDataField(String fieldname) {
+        if (otherMetadataFields == null) {
+            return null;
+        } else {
+            return otherMetadataFields.getProperty(fieldname);
+        }
+    }
+
     @Override
     public String toString() {
        return ToStringBuilder.reflectionToString(this);
     }
-    
+
 }

core/src/main/java/org/mskcc/cbio/portal/scripts/FetchPfamGraphicsData.java

@@ -48,7 +48,7 @@
  */
 public class FetchPfamGraphicsData
 {
-	public static final String URL_PREFIX = "http://pfam.sanger.ac.uk/protein/";
+	public static final String URL_PREFIX = "http://pfam.xfam.org/protein/";
 	public static final String URL_SUFFIX = "/graphic";
 
 	/**