style(pre-commit): various pre-commit based linting changes

Author: shinybrar

.release-please-manifest.json

@@ -1,3 +1,3 @@
 {
   ".": "0.25.0"
-}
+}

README.md

@@ -35,7 +35,7 @@ This project has been funded in part by:
 Skaha is a general purpose online platform for running science containers interactively.  It is part of the [CANFAR Science Platform](https://canfar.net).  In the architecture diagram below, skaha is the main API to the Science Platform.
 
 ![science-platform-architecture](docs/images/canfar-architecture-2024-04-08.png)
-The CANFAR Science Platform Architecture.  
+The CANFAR Science Platform Architecture.
 ![canfar-architecture](docs/images/canfar-architecture-1.0.png)
 Skaha is the API to the Science Platform box.
 
@@ -74,4 +74,4 @@ skaha relies on a number of other opencadc modules to operate.
 * access control (ac) web service (https://github.com/opencadc/ac) -- If the IdentityManager implementation is configured to use cadc-access-control-server for authentication an operational ac web service is required to be running.
 * credential delegation (cdp) web service (https://github.com/opencadc/cdp) -- The cdp service is used to obtain users' delegated proxy certificates.
 * cavern -- skaha is complimented by having the cavern VOSpace implementation mounted as a shared POSIX file system.  (https://github.com/opencadc/vos/tree/master/cavern).  cavern is a vospace implementation where both the data and metadata are based on the contents of a file system.  If the software-containers have access to the cavern file system the contents of that file system can be accessed and shared through the cavern web service.
-* posix/sssd -- Containers in skaha are always run _as the user_ and with the users' group memberships.  If skaha-desktop and software-containers are run with a SSSD configuration that points to the same LDAP instance as used by ac, the names of those uids and gids can be resolved.
+* posix/sssd -- Containers in skaha are always run _as the user_ and with the users' group memberships.  If skaha-desktop and software-containers are run with a SSSD configuration that points to the same LDAP instance as used by ac, the names of those uids and gids can be resolved.

image-cache/README.md

@@ -4,4 +4,4 @@ This builds a simple image with some formatting tools to support the image cachi
 to a running Redis cache.  See the [cache-images.sh script](https://github.com/opencadc/science-platform/blob/main/deployment/helm/skaha/image-cache/cache-images.sh) in
 Skaha, which is run from _within_ this Image.
 
-See also the [`CronJob` and initialization `Job`](https://github.com/opencadc/science-platform/blob/main/deployment/helm/skaha/templates/image-caching-cronjob.yaml) on how this image is used from a Skaha deployment.
+See also the [`CronJob` and initialization `Job`](https://github.com/opencadc/science-platform/blob/main/deployment/helm/skaha/templates/image-caching-cronjob.yaml) on how this image is used from a Skaha deployment.

release-please-config.json

@@ -22,4 +22,4 @@
       }
     },
     "$schema": "https://raw.githubusercontent.com/googleapis/release-please/main/schemas/config.json"
-}
+}

skaha/README.md

@@ -63,7 +63,7 @@ These two kubernetes job configuration files are templates used by skaha to run
 
 ## apply version tags
 ```bash
-. VERSION && echo "tags: $TAGS" 
+. VERSION && echo "tags: $TAGS"
 for t in $TAGS; do
    docker image tag images.canfar.net/skaha-system/skaha:latest images.canfar.net/skaha-system/skaha:$t
 done

skaha/gradle.properties

@@ -14,4 +14,4 @@ minorVersion = 25
 # x-release-please-end
 # x-release-please-start-patch
 patchVersion = 0
-# x-release-please-end
+# x-release-please-end

skaha/gradlew

@@ -144,15 +144,15 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac

skaha/src/main/webapp/WEB-INF/web.xml

@@ -2,7 +2,7 @@
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.2//EN" "http://java.sun.com/j2ee/dtds/web-app_2_2.dtd">
 <web-app>
     <display-name>skaha</display-name>
-    
+
     <servlet>
         <servlet-name>logControl</servlet-name>
         <servlet-class>ca.nrc.cadc.log.LogControlServlet</servlet-class>
@@ -21,18 +21,18 @@
         </init-param>
         <load-on-startup>1</load-on-startup>
     </servlet>
-    
+
      <servlet>
          <servlet-name>SessionServlet</servlet-name>
          <servlet-class>ca.nrc.cadc.rest.RestServlet</servlet-class>
          <init-param>
              <param-name>get</param-name>
-             <param-value>org.opencadc.skaha.session.GetAction</param-value> 
+             <param-value>org.opencadc.skaha.session.GetAction</param-value>
              <!-- <param-value>org.opencadc.platform.docker.DockerGet</param-value> -->
          </init-param>
          <init-param>
              <param-name>post</param-name>
-             <param-value>org.opencadc.skaha.session.PostAction</param-value> 
+             <param-value>org.opencadc.skaha.session.PostAction</param-value>
              <!-- <param-value>org.opencadc.platform.docker.DockerPost</param-value> -->
          </init-param>
          <init-param>
@@ -50,24 +50,24 @@
          </init-param>
          <load-on-startup>2</load-on-startup>
     </servlet>
-    
+
     <servlet>
          <servlet-name>ContextServlet</servlet-name>
          <servlet-class>ca.nrc.cadc.rest.RestServlet</servlet-class>
          <init-param>
              <param-name>get</param-name>
-             <param-value>org.opencadc.skaha.context.GetAction</param-value> 
+             <param-value>org.opencadc.skaha.context.GetAction</param-value>
              <!-- <param-value>org.opencadc.platform.docker.DockerGet</param-value> -->
          </init-param>
          <load-on-startup>2</load-on-startup>
     </servlet>
-    
+
     <servlet>
          <servlet-name>ImageServlet</servlet-name>
          <servlet-class>ca.nrc.cadc.rest.RestServlet</servlet-class>
          <init-param>
              <param-name>get</param-name>
-             <param-value>org.opencadc.skaha.image.GetAction</param-value> 
+             <param-value>org.opencadc.skaha.image.GetAction</param-value>
              <!-- <param-value>org.opencadc.platform.docker.DockerGet</param-value> -->
          </init-param>
          <load-on-startup>2</load-on-startup>
@@ -117,17 +117,17 @@
     </servlet>
 
     <!-- URL-to-servlet mapping -->
-    
+
     <servlet-mapping>
         <servlet-name>SessionServlet</servlet-name>
         <url-pattern>/v0/session/*</url-pattern>
     </servlet-mapping>
-    
+
     <servlet-mapping>
         <servlet-name>ContextServlet</servlet-name>
         <url-pattern>/v0/context/*</url-pattern>
     </servlet-mapping>
-    
+
     <servlet-mapping>
         <servlet-name>ImageServlet</servlet-name>
         <url-pattern>/v0/image/*</url-pattern>
@@ -137,23 +137,23 @@
         <servlet-name>ImageRepositoryServlet</servlet-name>
         <url-pattern>/v0/repository/*</url-pattern>
     </servlet-mapping>
-        
+
     <servlet-mapping>
         <servlet-name>CapabilitiesServlet</servlet-name>
         <url-pattern>/capabilities</url-pattern>
     </servlet-mapping>
-    
+
     <servlet-mapping>
         <servlet-name>AvailabilityServlet</servlet-name>
         <url-pattern>/availability</url-pattern>
     </servlet-mapping>
-    
+
       <!-- Log control servlet endpoint -->
     <servlet-mapping>
         <servlet-name>logControl</servlet-name>
         <url-pattern>/logControl</url-pattern>
     </servlet-mapping>
-    
+
     <welcome-file-list>
         <welcome-file>index.html</welcome-file>
     </welcome-file-list>

skaha/src/main/webapp/capabilities.xml

@@ -15,7 +15,7 @@
       <accessURL use="full">https://replace.me.com/skaha/availability</accessURL>
     </interface>
   </capability>
-  
+
   <capability standardID="vos://cadc.nrc.ca~vospace/CADC/std/Logging#control-1.0">
     <interface xsi:type="vs:ParamHTTP" role="std" version="1.0">
       <accessURL use="full">https://replace.me.com/skaha/logControl</accessURL>
@@ -38,4 +38,3 @@
   </capability>
 
 </vosi:capabilities>
-

skaha/src/main/webapp/service.yaml

@@ -53,7 +53,7 @@ paths:
           in: query
           type: string
           description: |
-              The name for the session (for user informational purposes only).  
+              The name for the session (for user informational purposes only).
           required: true
         - name: image
           in: query

skaha/src/obsolete/java/org/opencadc/arcade/docker/DockerDelete.java

@@ -73,13 +73,13 @@
 public class DockerDelete extends DeleteAction {
 
     private static final Logger log = Logger.getLogger(DockerDelete.class);
-    
+
     @Override
     public void stopSession(String userID, String sessionID) throws Exception {
         // kill the session specified by sessionID
         log.debug("Stopping VNC session");
         String[] stopVNCCmd = new String[] {"/scripts/docker/stop-desktop.sh", userID, sessionID};
         execute(stopVNCCmd);
     }
-    
+
 }

skaha/src/obsolete/java/org/opencadc/arcade/docker/DockerGet.java

@@ -76,15 +76,15 @@
 import ca.nrc.cadc.util.StringUtil;
 
 public class DockerGet extends GetAction {
-    
+
     private static final Logger log = Logger.getLogger(DockerGet.class);
-    
+
     @Override
     public void listSessions() throws Exception {
 
         String[] getVNCSessions = new String[] {"docker", "ps", "--format", "{{.Names}}\\t{{.Status}}", "--filter", "label=canfar-net-userid=" + userID};
         String vncSessions = execute(getVNCSessions);
-        
+
         if (StringUtil.hasLength(vncSessions)) {
             String[] lines = vncSessions.split("\n");
             if (lines.length > 0) {
@@ -120,21 +120,21 @@ public void listSessions() throws Exception {
         }
         log.debug("No container listing output");
     }
-    
+
     protected String parseCID(String vncName) {
         String[] parts = vncName.split("_");
         String sessionID = parts[parts.length - 2];
         return sessionID;
     }
-    
+
     protected String parseCURL(String vncName) throws IOException, InterruptedException {
         String sessionID = parseCID(vncName);
         String[] getIpCmd = new String[] {
                 "docker", "inspect", "--format", "{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}", vncName};
         String ipAddress = execute(getIpCmd);
         return getVNCURL(server, sessionID, ipAddress);
     }
-    
+
     protected String parseCName(String vncName) {
         String[] parts = vncName.split("_");
         return parts[parts.length - 1];

skaha/src/obsolete/java/org/opencadc/arcade/docker/DockerPost.java

@@ -79,9 +79,9 @@
 import ca.nrc.cadc.util.StringUtil;
 
 public class DockerPost extends PostAction {
-    
+
     private static final Logger log = Logger.getLogger(DockerPost.class);
-    
+
     @Override
     public void checkForExistingSession(String userid) throws Exception {
         String[] getVNCSessions = new String[] {"docker", "ps", "--format", "{{.Names}}\\t{{.Status}}", "--filter", "label=canfar-net-userid=" + userID};
@@ -93,48 +93,48 @@ public void checkForExistingSession(String userid) throws Exception {
             }
         }
     }
-    
+
     @Override
     public URL createSession(String sessionID, String name) throws Exception {
 
         String[] runNoVNCCmd = new String[] {"/scripts/docker/run-desktop.sh", userID, sessionID, name, homedir, scratchdir};
         String imageID = execute(runNoVNCCmd);
-        
+
         // insert the user's proxy cert on the container
         Subject subject = AuthenticationUtil.getCurrentSubject();
         //injectProxyCert("/home", subject, userID);
-        
+
         String[] getIpCmd = new String[] {
             "docker", "inspect", "--format", "{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}", imageID};
         String ipAddress = execute(getIpCmd);
-        
+
         // give vnc a few seconds to initialize
         try {
             log.debug("3 second wait for vnc initialization");
             Thread.sleep(2000);
         } catch (InterruptedException ignore) {
         }
         log.debug("wait over");
-        
+
         String redirectPath = super.getVNCURL(server, sessionID, ipAddress);
         return new URL(redirectPath);
     }
-    
+
     @Override
     public void attachSoftware(String software, List<String> params, String targetIP) throws Exception {
-        
+
         confirmSoftware(software);
-        
+
         // only one parameter supported for now
         String param = "xterm";
         if (params != null && params.size() > 0) {
             param = params.get(0);
         }
         log.debug("Using parameter: " + param);
-        
+
         String[] runAppCmd = new String[] {"/scripts/docker/software.sh", software, targetIP, userID, homedir, scratchdir,  param};
         String imageID = execute(runAppCmd);
-        
+
         // refresh the user's proxy cert
         Subject subject = AuthenticationUtil.getCurrentSubject();
         //injectProxyCert("/home", subject, userID);