Merge pull request #172 from TheJacksonLaboratory/develop

Develop

.github/workflows/documentation.yaml

@@ -21,6 +21,5 @@ jobs:
       - run: pip install mkdocs-material
       - run: pip install mkdocs-material[imaging]
       - run: pip install pillow cairosvg
-      - run: pip install mkdocs-material-extensions
       - run: pip install mkdocstrings[python]
       - run: mkdocs gh-deploy --force

docs/index.md

@@ -5,7 +5,7 @@ made by the [isopret expectation maximization algorithm](https://pubmed.ncbi.nlm
 to perform gene-level  and isoform-level GO overrepresentation analysis.
 
 ## Background: Gene Ontology
-[Gene Ontology](http://geneontology.org/) traditionally has provided
+[Gene Ontology](http://geneontology.org/){:target="\_blank"}. traditionally has provided
 annotations for genes rather than for specific isoforms. However, in
 some cases, the functions of the individual isoforms of a gene are
 differ with respect to one or more of the gene's function. In this project,
@@ -18,13 +18,12 @@ expressed genes or the differentially spliced isoforms.
 ## Background: HBA-DEALS
 Isopret requires as input a file that has the fold changes and p-values
 for genes and isoforms in a case-control cohort that has been studied
-by RNA-seq. We have previously published [HBA-DEALS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6),
+by RNA-seq. We have previously published [HBA-DEALS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6){:target="\_blank"}.,
 a hierarchical Bayesian algorithm that performs such an analysis, and this
 is the recommended input file.
 Isopret uses the analysis (output) file of
 [HBA-DEALS](https://pubmed.ncbi.nlm.nih.gov/32660516/){:target="_blank"}.
 
-TODO -- point to tutorial amd also mention EDGER
 
 HBA-DEALS analyzes RNA-Seq data to determine differentially expression and differential splicing simultaneous. Isopret then performs Gene Ontology analysis using an updated implementation of code from the [Ontologizer](https://pubmed.ncbi.nlm.nih.gov/18511468/){:target="_blank"}.
 

docs/setup.md

@@ -2,7 +2,7 @@
 
 
 isopret-gui is a desktop Java application. You can download precompiled executable
-JAR files from the [Releases page](https://github.com/TheJacksonLaboratory/isopret/releases).
+JAR files from the [Releases page](https://github.com/TheJacksonLaboratory/isopret/releases){:target="\_blank"}..
 of the GitHub site. Later, we will generate stand-alone Windows and Mac native apps.
 This is currently the recommended way of using isopret-gui.
 
@@ -15,13 +15,13 @@ Additionally, the following text describes how to build isopret-gui from source.
 
 isopret-gui was written with Java version 17. If you want to
 build isopret-gui from source, then the build process described below requires
-[Git](https://git-scm.com/book/en/v2) and [maven](https://maven.apache.org/install.html). (version 3.5.3 or higher).
+[Git](https://git-scm.com/book/en/v2){:target="\_blank"}. and [maven](https://maven.apache.org/install.html){:target="\_blank"}.. (version 3.5.3 or higher).
 
 
 ### Installation
 
 
-Go the GitHub page of [isopretGO](https://github.com/TheJacksonLaboratory/isopretGO), and clone the project.
+Go the GitHub page of [isopretGO](https://github.com/TheJacksonLaboratory/isopretGO){:target="\_blank"}., and clone the project.
 Build the executable from source with maven, and then test the build.
 
 ```bash
@@ -46,9 +46,9 @@ java -jar target/isopret.jar
 
 ## Set up documentation
 
-This step is not needed to run the application, but rather describes the code we use to 
+This step is not needed to run the application, but rather describes the code we use to
 generate the isopretGO documentation.
-Enter the following code to install mkdocs and run a server with the documentation locally. 
+Enter the following code to install mkdocs and run a server with the documentation locally.
 The GitHub action will create a comparable site online.
 
 ```
@@ -63,7 +63,13 @@ pip install mkdocstrings[python]
 mkdocs serve
 ```
 
+Note that on an M! Mac we have encountered a difficulty with mkdocs not finding the cairo library. This can be solved
+by running
 
+```
+export DYLD_FALLBACK_LIBRARY_PATH=/opt/homebrew/lib
+```
+before running mkdocs serve.
 
 
 

isopret-cli/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.1</version>
     </parent>
 
     <artifactId>isopret-cli</artifactId>

isopret-core/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.1</version>
     </parent>
 
     <artifactId>isopret-core</artifactId>

isopret-core/src/main/java/org/jax/isopret/core/analysis/IsopretStats.java

@@ -107,6 +107,10 @@ public Map<String,String> getAllEntries() {
         return all;
     }
 
+    public void addInfo(String inputFile, String basename) {
+        this.info.put(inputFile, basename);
+    }
+
     /**
      * Convenient way of collecting data about the current run.
      */

isopret-core/src/main/java/org/jax/isopret/core/impl/go/IsopretAssociationContainer.java

@@ -76,6 +76,7 @@ public Map<TermId, List<TermId>> getOntologyTermToDomainItemsMap() {
     //  in interface AssociationContainer<T> after PR merged to only use Interface in client code
     public Set<TermId> getDomainItemsAnnotatedByGoTerm(TermId goTermId) {
         Set<TermId> domainItemSet = new HashSet<>();
+        //ontology.graph().getDescendants(goTermId, )
         Set<TermId> descendentSet = OntologyAlgorithm.getDescendents(this.ontology, goTermId);
         for (Map.Entry<TermId, IsopretAnnotations> entry : associationMap.entrySet()) {
             TermId gene = entry.getKey();

isopret-data/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.1</version>
     </parent>
 
     <artifactId>isopret-data</artifactId>
@@ -35,12 +35,7 @@
             <artifactId>svart</artifactId>
             <version>${svart.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.jax.isopret</groupId>
-            <artifactId>isopret-exception</artifactId>
-            <version>1.2.0</version>
-            <scope>compile</scope>
-        </dependency>
+
     </dependencies>
 
 </project>

isopret-exception/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.1</version>
     </parent>
 
     <artifactId>isopret-exception</artifactId>

isopret-gui/pom.xml

@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.1</version>
     </parent>
 
     <artifactId>isopret-gui</artifactId>

isopret-gui/src/main/java/org/jax/isopret/gui/controller/HbaGeneController.java

@@ -17,6 +17,7 @@
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 import org.apache.commons.io.IOUtils;
+import org.jax.isopret.gui.widgets.GoTableGeneratorPopup;
 import org.jax.isopret.visualization.*;
 import org.jax.isopret.gui.service.HostServicesWrapper;
 import org.jax.isopret.gui.service.IsopretService;
@@ -365,5 +366,22 @@ private void saveToPdf(String contents, File pdfFile) {
         PopupFactory.showInfoMessage( "Successfully created " + pdfFile.getAbsolutePath(), "Info");
     }
 
+    /**
+     * Export a TSV file with isopret annotations for this gene
+     */
+    @FXML
+    public void goAnnotExport(ActionEvent e) {
+        e.consume();
+        Optional<String> opt = service.getGoReportDefaultFilename();
+        String baseName;
+        if (opt.isPresent()) {
+            baseName = opt.get().replace(".tsv", "");
+            baseName = String.format("%s-%s", baseName, visualizable.getGeneSymbol());
+        } else {
+            baseName = visualizable.getGeneSymbol();
+        }
+        GoAnnotationMatrix goMatrix = visualizable.getGoAnnotationMatrix();
+        GoTableGeneratorPopup popup = new GoTableGeneratorPopup(goMatrix, baseName);
 
+    }
 }

isopret-gui/src/main/java/org/jax/isopret/gui/controller/MainController.java

@@ -262,7 +262,7 @@ private void isopretAnalysis(ActionEvent actionEvent) {
                 interproTab = new Tab("Interpro");
                 interproTab.setClosable(false);
             } catch (IOException e) {
-                e.printStackTrace();
+                LOGGER.error(e.getMessage());
             }
             // Now the same for DAS
             try {
@@ -283,7 +283,7 @@ private void isopretAnalysis(ActionEvent actionEvent) {
                 GeneOntologyController gc2 = loader.getController();
                 gc2.refreshGeneOntologyTable();
             } catch (IOException e) {
-                e.printStackTrace();
+                LOGGER.error(e.getMessage());
             }
 
             // now for interpro
@@ -311,13 +311,12 @@ private void isopretAnalysis(ActionEvent actionEvent) {
                 interproController.refreshTable();
 
             }catch (IOException e) {
-                e.printStackTrace();
+                LOGGER.error(e.getMessage());
             }
         });
         task.setOnFailed(eh -> {
             Exception exc = (Exception)eh.getSource().getException();
-            eh.getSource().getException().printStackTrace();
-            //eh.getSource().getException().toString()
+            LOGGER.error(eh.getSource().getException().getMessage());
             PopupFactory.displayException("Error",
                     "Exception encountered while attempting to perform isopret analysis",
                     exc);