fix frontendproperties readFile() to work with classpath and update download_custom_buttons_json reference

docs/deployment/customization/application.properties-Reference.md

@@ -800,9 +800,9 @@ enable_study_tags=true|false
 ```
 
 # Add Custom Buttons to data tables
-Custom Buttons can be defined which will conditionally appear in all group comparison data tables (with CopyDownloadControls) to launch a custom URL. This can be used, for example, to launch a software application (that is installed on the user's system) with the data. This configuration can also customize new elements on the Visualize page. It points to a JSON file on the classpath. (See [download_custom_buttons reference](download_custom_buttons-Reference.md)).
+Custom Buttons can be defined which will conditionally appear in all group comparison data tables (with CopyDownloadControls) to launch a custom URL. This can be used, for example, to launch a software application (that is installed on the user's system) with the data. This configuration can also customize new elements on the Visualize page. It points to a JSON file. (See [download_custom_buttons reference](download_custom_buttons-Reference.md)). 
 
 
 ```
-download_custom_buttons_json=classpath:/custom_buttons/download_custom_button_avm.json
+download_custom_buttons_json=classpath:custom_buttons/download_custom_button_avm.json
 ```

docs/deployment/customization/download_custom_buttons-Reference.md

@@ -4,8 +4,7 @@ Custom Buttons can be defined which will conditionally appear in all group compa
 
 ## Configuration File
 
-The Custom Buttons are defined in a JSON file in the classpath. Set `download_custom_buttons_json` to refer to the file in the 
-`application.properties` (See [application.properties reference](application.properties-Reference.md#add-custom-buttons-to-data-tables)).
+The Custom Buttons are defined in a JSON file on the classpath. Set `download_custom_buttons_json` to refer to the file (see [application.properties reference](application.properties-Reference.md#add-custom-buttons-to-data-tables)).
 
 ## JSON format
 
@@ -67,6 +66,4 @@ To modify software to leverage this:
 
 - Modify your software to read data from clipboard.
 - Modify your software or installer to register a URL protocol to launch.
-- Modify your software or installer to install a custom font.
-
-
+- Modify your software or installer to install a custom font.

src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java

@@ -8,6 +8,10 @@
 import org.springframework.stereotype.Service;
 
 import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Paths;
@@ -291,18 +295,63 @@ private Map<String,String> cloneProperties() {
  );
  }
 
- private String readFile(String fileName) {
- if (fileName != null && !fileName.isEmpty()) {
- try (BufferedReader br = Files.newBufferedReader(Paths.get(fileName))) {
- return br.lines().map(String::trim).collect(Collectors.joining(""));
- } catch (Exception e) {
- log.error("Error reading frontend config file: {}", e.getMessage());
- return null;
+ /**
+ * Read the file and return the content as a single-line string. This works for:
+ * 1) loose files given absolute path
+ * 2) loose files relative to PORTAL_HOME
+ * 3) "classpath:..."" in the app.jar (relative to PORTAL_HOME)
+ * @propertiesFileName: the file path 
+ * REF: based on getResourceStream() in WebServletContextListener.java
+ */
+ private String readFile(String propertiesFileName) {
+ if (propertiesFileName == null || propertiesFileName.isEmpty()) {
+ return null;
+ }
+
+ InputStream inputStream = null;
+
+ // strip off classpath prefix and always check ClassLoader and file system, with latter taking precedence
+ String filePath = propertiesFileName.startsWith("classpath:") 
+ ? propertiesFileName.substring("classpath:".length()) 
+ : propertiesFileName;
+
+ try {
+ String home = System.getenv("PORTAL_HOME");
+
+ // try absolute or relative to working directory
+ File file = new File(filePath);
+ if (file.exists()) {
+ inputStream = new FileInputStream(file);
+ } else if (home != null) {
+ // try relative to PORTAL_HOME
+ file = new File(Paths.get(home, filePath).toString());
+ if (file.exists()) {
+ inputStream = new FileInputStream(file);
+ }
+ } 
+
+ if (inputStream != null) {
+ log.info("Reading frontend config file: {}", file.getAbsolutePath());
+ } else {
+ // try resource (e.g. app.jar)
+ inputStream = this.getClass().getClassLoader().getResourceAsStream(filePath);
+ if (inputStream != null) {
+ log.info("Reading frontend config resource: {}", filePath);
+ } else {
+ throw new Exception("File not found in system or classpath: " + filePath);
+ }
  }
+
+ // read the file and return the content as a single-line string
+ // PRE: inputStream != null
+ BufferedReader br = new BufferedReader(new InputStreamReader(inputStream));
+ return br.lines().map(String::trim).collect(Collectors.joining("")); 
+ } catch (Exception e) {
+ log.error("Error reading frontend config file: {}", e.getMessage());
+ return null;
  }
- return null;
  }
-  
+
  public String getFrontendUrl(String propertyValue) {
  String frontendUrlRuntime = env.getProperty("frontend.url.runtime", "");
  if (frontendUrlRuntime.length() > 0) {

src/main/resources/application.properties.EXAMPLE

@@ -427,7 +427,7 @@ spring.devtools.restart.enabled=false
 #enable_study_tags=true|false
 
 ## Custom Buttons
-# download_custom_buttons_json=classpath:/custom_buttons/download_custom_button_avm.json
+# download_custom_buttons_json=classpath:custom_buttons/download_custom_button_avm.json
 
 # EOL - Do not delete the following lines