Squashed commit of the following:

commit 67584a843c18b8d7fb8ea2d83d28fdd6bea350fe Merge: 986d24e 7627037 Author: Emily McMullan <[email protected]> Date: Mon Sep 18 17:07:41 2023 -0400 Merge branch 'main' of https://github.com/konveyor-ecosystem/kantra into json-output commit 986d24ef68f228615e6c2f3d742e4777d761f61c Author: Emily McMullan <[email protected]> Date: Mon Sep 18 16:56:57 2023 -0400 Squashed commit of the following: commit 70c4efd Author: Shawn Hurley <[email protected]> Date: Mon Sep 18 08:11:39 2023 -0400 :bug: fixing ci with latest analyzer-lsp (#68) Signed-off-by: Shawn Hurley <[email protected]> Signed-off-by: Emily McMullan <[email protected]> commit 4ae7388 Author: Pranav Gaikwad <[email protected]> Date: Thu Sep 14 16:07:46 2023 -0400 :ghost: script to replace name & image (#64) Signed-off-by: Pranav Gaikwad <[email protected]> Signed-off-by: Emily McMullan <[email protected]> commit 55ba073 Author: Emily McMullan <[email protected]> Date: Thu Sep 14 16:07:37 2023 -0400 add examples to readme (#66) Signed-off-by: Emily McMullan <[email protected]> commit d26973c Author: Savitha Raghunathan <[email protected]> Date: Thu Sep 14 08:28:19 2023 -0400 Create bug.yaml (#65) Signed-off-by: Emily McMullan <[email protected]> commit 5f87ca9 Author: Emily McMullan <[email protected]> Date: Wed Sep 13 13:31:30 2023 -0400 add json output flag Signed-off-by: Emily McMullan <[email protected]> commit 7627037 Author: Shawn Hurley <[email protected]> Date: Mon Sep 18 08:11:39 2023 -0400 :bug: fixing ci with latest analyzer-lsp (#68) Signed-off-by: Shawn Hurley <[email protected]> commit 437a34a Author: Pranav Gaikwad <[email protected]> Date: Thu Sep 14 16:07:46 2023 -0400 :ghost: script to replace name & image (#64) Signed-off-by: Pranav Gaikwad <[email protected]> commit 423beaa Author: Emily McMullan <[email protected]> Date: Thu Sep 14 16:07:37 2023 -0400 add examples to readme (#66)
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diff --git a/README.md b/README.md
@@ -3,9 +3,9 @@
 Kantra is an experimental CLI that unifies analysis and transformation capabilities of Konveyor.
 
 ## Installation
-### Linux
+The easiest way to install Kantra is to get it via the container image. To download latest container image, run:
 
-Easiest way to install Kantra is to get it via the container image. To download latest container image, run:
+### Linux
 
 ```sh
 podman pull quay.io/konveyor/kantra:latest && podman run --name kantra-download quay.io/konveyor/kantra:latest 1> /dev/null 2> /dev/null && podman cp kantra-download:/usr/local/bin/kantra . && podman rm kantra-download
@@ -25,12 +25,19 @@ Ensure that we use the connection to the VM `<vm_name>` we created earlier by de
 podman system connection default <vm_name>
 ```
 
-
 ```sh
 podman pull quay.io/konveyor/kantra:latest && podman run --name kantra-download quay.io/konveyor/kantra:latest 1> /dev/null 2> /dev/null && podman cp kantra-download:/usr/local/bin/darwin-kantra kantra && podman rm kantra-download
 ```
 
-This will copy the binary into your current working directory. To make it available system-wide, run:
+### Windows
+
+```sh
+podman pull quay.io/konveyor/kantra:latest && podman run --name kantra-download quay.io/konveyor/kantra:latest 1> /dev/null 2> /dev/null && podman cp kantra-download:/usr/local/bin/windows-kantra kantra && podman rm kantra-download
+```
+
+---
+
+The above will copy the binary into your current directory. Move it to PATH for system-wide use:
 
 ```sh
 sudo mv ./kantra /usr/local/bin/
@@ -70,7 +77,7 @@ Use "kantra [command] --help" for more information about a command.
 
 ### Analyze
 
-Analyze allows running source code and binary analysis using analyzer-lsp.
+Analyze allows running source code and binary analysis using [analyzer-lsp](https://github.com/konveyor/analyzer-lsp)
 
 To run analysis on application source code, run:
 
@@ -90,6 +97,7 @@ Flags:
       --analyze-known-libraries   analyze known open-source libraries
   -h, --help                      help for analyze
   -i, --input string              path to application source code or a binary
+      --json-output               create analysis and dependency output as json
       --list-sources              list rules for available migration sources
       --list-targets              list rules for available migration targets
   -m, --mode string               analysis mode. Must be one of 'full' or 'source-only' (default "full")
@@ -129,7 +137,7 @@ Use "kantra transform [command] --help" for more information about a command.
 
 #### OpenRewrite
 
-`openrewrite` subcommand allows running OpenRewrite recipes on source code.
+`openrewrite` subcommand allows running [OpenRewrite](https://docs.openrewrite.org/) recipes on source code.
 
 
 ```sh
@@ -157,7 +165,7 @@ kantra transform openrewrite --input=<path/to/source/code> --target=<exactly_one
 
 #### Rules
 
-`rules` subcommand allows converting Windup XML rules to analyzer-lsp YAML rules.
+`rules` subcommand allows converting Windup XML rules to analyzer-lsp YAML rules using [windup-shim](https://github.com/konveyor/windup-shim)
 
 ```sh
 Convert XML rules to YAML
@@ -180,6 +188,50 @@ To run `transform rules` on application source code, run:
 kantra transform rules --input=<path/to/xmlrules> --output=<path/to/output/dir>
 ```
 
+## Quick Demos
+
+Once you have kantra installed, these examples will help you run both an 
+analyze and a transform command.
+
+### Analyze
+
+- Get the example application to run analysis on  
+`git clone https://github.com/konveyor/example-applications`
+
+- List available target technologies  
+`kantra analyze --list-targets`
+
+- Run analysis with a specified target technology  
+`kantra analyze --input=<path-to/example-applications/example-1> --output=<path-to-output-dir> --target=cloud-readiness`
+
+- Several analysis reports will have been created in your specified output path:
+
+```sh
+$ ls ./output/ -1
+analysis.log
+dependencies.yaml
+dependency.log
+output.yaml
+static-report
+```
+
+`output.yaml` is the file that contains issues report.   
+`static-report` contains the static HTML report.  
+`dependencies.yaml`contains a dependencies report.  
+
+### Transform
+
+- Get the example application to transform source code  
+`git clone https://github.com/ivargrimstad/jakartaee-duke`
+
+- View available OpenRewrite recipes  
+`kantra transform openrewrite --list-targets` 
+
+- Run a recipe on the example application  
+`kantra transform openrewrite --input=<path-to/jakartaee-duke> --target=jakarta-imports`
+
+- Inspect the `jakartaee-duke` application source code diff to see the transformation  
+
 
 ## Code of Conduct
 Refer to Konveyor's Code of Conduct [here](https://github.com/konveyor/community/blob/main/CODE_OF_CONDUCT.md).
diff --git a/cmd/analyze.go b/cmd/analyze.go
@@ -46,6 +46,7 @@ type analyzeCommand struct {
 	listTargets           bool
 	skipStaticReport      bool
 	analyzeKnownLibraries bool
+	jsonOutput            bool
 	mavenSettingsFile     string
 	sources               []string
 	targets               []string
@@ -106,6 +107,11 @@ func NewAnalyzeCmd(log logr.Logger) *cobra.Command {
 				log.Error(err, "failed to run analysis")
 				return err
 			}
+			err = analyzeCmd.CreateJSONOutput()
+			if err != nil {
+				log.Error(err, "failed to create json output file")
+				return err
+			}
 			err = analyzeCmd.GenerateStaticReport(cmd.Context())
 			if err != nil {
 				log.Error(err, "failed to generate static report")
@@ -136,6 +142,7 @@ func NewAnalyzeCmd(log logr.Logger) *cobra.Command {
 	analyzeCommand.Flags().BoolVar(&analyzeCmd.analyzeKnownLibraries, "analyze-known-libraries", false, "analyze known open-source libraries")
 	analyzeCommand.Flags().StringVar(&analyzeCmd.mavenSettingsFile, "maven-settings", "", "path to a custom maven settings file to use")
 	analyzeCommand.Flags().StringVarP(&analyzeCmd.mode, "mode", "m", string(provider.FullAnalysisMode), "analysis mode. Must be one of 'full' or 'source-only'")
+	analyzeCommand.Flags().BoolVar(&analyzeCmd.jsonOutput, "json-output", false, "create analysis and dependency output as json")
 
 	return analyzeCommand
 }
@@ -580,6 +587,60 @@ func (a *analyzeCommand) RunAnalysis(ctx context.Context, xmlOutputDir string) e
 	return nil
 }
 
+func (a *analyzeCommand) CreateJSONOutput() error {
+	if !a.jsonOutput {
+		return nil
+	}
+	outputPath := filepath.Join(a.output, "output.yaml")
+	depPath := filepath.Join(a.output, "dependencies.yaml")
+
+	data, err := ioutil.ReadFile(outputPath)
+	if err != nil {
+		return err
+	}
+	ruleOutput := &[]outputv1.RuleSet{}
+	err = yaml.Unmarshal(data, ruleOutput)
+	if err != nil {
+		a.log.V(1).Error(err, "failed to unmarshal output yaml")
+		return err
+	}
+
+	jsonData, err := json.MarshalIndent(ruleOutput, "", "	")
+	if err != nil {
+		a.log.V(1).Error(err, "failed to marshal output file to json")
+		return err
+	}
+	err = ioutil.WriteFile(filepath.Join(a.output, "output.json"), jsonData, os.ModePerm)
+	if err != nil {
+		a.log.V(1).Error(err, "failed to write json output", "dir", a.output, "file", "output.json")
+		return err
+	}
+
+	depData, err := ioutil.ReadFile(depPath)
+	if err != nil {
+		return err
+	}
+	depOutput := &[]outputv1.DepsFlatItem{}
+	err = yaml.Unmarshal(depData, depOutput)
+	if err != nil {
+		a.log.V(1).Error(err, "failed to unmarshal dependencies yaml")
+		return err
+	}
+
+	jsonDataDep, err := json.MarshalIndent(depOutput, "", "	")
+	if err != nil {
+		a.log.V(1).Error(err, "failed to marshal dependencies file to json")
+		return err
+	}
+	err = ioutil.WriteFile(filepath.Join(a.output, "dependencies.json"), jsonDataDep, os.ModePerm)
+	if err != nil {
+		a.log.V(1).Error(err, "failed to write json dependencies output", "dir", a.output, "file", "dependencies.json")
+		return err
+	}
+
+	return nil
+}
+
 func (a *analyzeCommand) GenerateStaticReport(ctx context.Context) error {
 	if a.skipStaticReport {
 		return nil

diff --git a/go.sum b/go.sum
@@ -33,6 +33,7 @@ github.com/go-openapi/jsonpointer v0.19.5 h1:gZr+CIYByUqjcgeLXnQu2gHYQC9o73G2XUe
 github.com/go-openapi/jsonpointer v0.19.5/go.mod h1:Pl9vOtqEWErmShwVjC8pYs9cog34VGT37dQOVbmoatg=
 github.com/go-openapi/swag v0.19.5 h1:lTz6Ys4CmqqCQmZPBlbQENR1/GucA2bzYTE12Pw4tFY=
 github.com/go-openapi/swag v0.19.5/go.mod h1:POnQmlKehdgb5mhVOsnJFsivZCEZ/vjK9gh66Z9tfKk=
+github.com/golang/groupcache v0.0.0-20200121045136-8c9f03a8e57e/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc=
 github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
 github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
 github.com/golang/protobuf v1.5.0/go.mod h1:FsONVRAS9T7sI+LIUmWTfcYkHO4aIWwzhcaSAoJOfIk=
@@ -142,6 +143,7 @@ golang.org/x/text v0.8.0 h1:57P1ETyNKtuIjB4SRd15iJxuhj8Gc416Y78H3qgMh68=
 golang.org/x/text v0.8.0/go.mod h1:e1OnstbJyHTd6l/uOt8jFFHp6TRDWZR/bV3emEE/zU8=
 golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
+google.golang.org/appengine v1.6.7/go.mod h1:8WjMMxjGQR8xUklV/ARdw2HLXBOI7O7uCIDZVag1xfc=
 google.golang.org/genproto v0.0.0-20230110181048-76db0878b65f h1:BWUVssLB0HVOSY78gIdvk1dTVYtT1y8SBWtPYuTJ/6w=
 google.golang.org/genproto v0.0.0-20230110181048-76db0878b65f/go.mod h1:RGgjbofJ8xD9Sq1VVhDM1Vok1vRONV+rg+CjzG4SZKM=
 google.golang.org/grpc v1.54.0 h1:EhTqbhiYeixwWQtAEZAxmV9MGqcjEU2mFx52xCzNyag=

diff --git a/hack/update-settings.sh b/hack/update-settings.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+# Set IMAGE and NAME environment variables, and run the script in root dir:
+# $ IMAGE=quay.io/konveyor/kantra NAME=kantra ./hack/update-settings.sh
+
+image="${IMAGE:-quay.io/konveyor/kantra}"
+name="${NAME:-kantra}"
+
+sed -i \
+    -e "s,\(RootCommandName *string.*default:\"\)[^\"]*\",\1$name\"," \
+    -e "s,\(RunnerImage *string.*default:\"\)[^\"]*\",\1$image\"," \
+    ./cmd/settings.go
diff --git a/test-data/analysis-output.yaml b/test-data/analysis-output.yaml
@@ -138,8 +138,10 @@
       labels:
       - konveyor.io/target=cloud-readiness
       - discovery
+      - konveyor.io/source
+      - konveyor.io/target
       incidents:
-      - uri: file:///opt/input/source/target/classes/persistence.properties
+      - uri: file:///opt/input/source/src/main/resources/persistence.properties
         message: When migrating environments, hard-coded IP addresses may need to be modified or eliminated.
         codeSnip: |2
             1  jdbc.driverClassName=oracle.jdbc.driver.OracleDriver
@@ -151,7 +153,7 @@
         lineNumber: 2
         variables:
           matchingText: 169.60.225.216
-      - uri: file:///opt/input/source/src/main/resources/persistence.properties
+      - uri: file:///opt/input/source/target/classes/persistence.properties
         message: When migrating environments, hard-coded IP addresses may need to be modified or eliminated.
         codeSnip: |2
             1  jdbc.driverClassName=oracle.jdbc.driver.OracleDriver
@@ -163,7 +165,6 @@
         lineNumber: 2
         variables:
           matchingText: 169.60.225.216
-      extras: []
       effort: 1
   unmatched:
   - discover-license
@@ -1446,28 +1447,27 @@
       - konveyor.io/source
       - jni
       incidents:
-      - uri: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
+      - uri: file:///root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/io/konveyor/demo/config/ApplicationConfiguration.java
         message: Java native libraries might not run in a cloud or container environment.. Recommendations. * Review the purpose of the native library in your application.. * Check whether the native library is compatible with a cloud environment.. * Reuse or embed the native library or application in a cloud environment, for example, in a JBoss module.. * Replace, remove, or rewrite the native library or application using a cloud-compatible equivalent.
         codeSnip: "  1  package io.konveyor.demo.config;\n  2  \n  3  import java.io.FileInputStream;\n  4  import java.io.InputStream;\n  5  import java.util.Properties;\n  6  \n  7  public class ApplicationConfiguration {\n  8  \n  9  \tprivate Properties config;\n 10  \n 11  \tpublic ApplicationConfiguration() {\n 12  \t\tsuper();\n 13  \t\tthis.config = loadProperties();\n 14  \n 15  \t}\n 16  \n 17  \tprivate Properties loadProperties() {\n 18  \t\tProperties properties = new Properties();\n 19  \n 20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n 21  \n 22  \t\t\tproperties.load(inputStream);\n 23  \n 24  \t\t} catch (Exception e) {\n 25  \t\t\tSystem.out.println(\"Exception: \" + e);\n 26  \t\t}\n 27  \n 28  \t\treturn properties;\n 29  \t}\n 30  \n 31  \tpublic String getProperty (String name) {\n 32  \t\treturn config.getProperty(name);\n 33  \t}\n 34  \n 35  \n 36  \n 37  }\n"
         lineNumber: 12
         variables:
-          file: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
+          file: file:///root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/io/konveyor/demo/config/ApplicationConfiguration.java
           kind: Constructor
           name: ApplicationConfiguration
-      - uri: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
+      - uri: file:///root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/io/konveyor/demo/config/ApplicationConfiguration.java
         message: Java native libraries might not run in a cloud or container environment.. Recommendations. * Review the purpose of the native library in your application.. * Check whether the native library is compatible with a cloud environment.. * Reuse or embed the native library or application in a cloud environment, for example, in a JBoss module.. * Replace, remove, or rewrite the native library or application using a cloud-compatible equivalent.
         codeSnip: "  1  package io.konveyor.demo.config;\n  2  \n  3  import java.io.FileInputStream;\n  4  import java.io.InputStream;\n  5  import java.util.Properties;\n  6  \n  7  public class ApplicationConfiguration {\n  8  \n  9  \tprivate Properties config;\n 10  \n 11  \tpublic ApplicationConfiguration() {\n 12  \t\tsuper();\n 13  \t\tthis.config = loadProperties();\n 14  \n 15  \t}\n 16  \n 17  \tprivate Properties loadProperties() {\n 18  \t\tProperties properties = new Properties();\n 19  \n 20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n 21  \n 22  \t\t\tproperties.load(inputStream);\n 23  \n 24  \t\t} catch (Exception e) {\n 25  \t\t\tSystem.out.println(\"Exception: \" + e);\n 26  \t\t}\n 27  \n 28  \t\treturn properties;\n 29  \t}\n 30  \n 31  \tpublic String getProperty (String name) {\n 32  \t\treturn config.getProperty(name);\n 33  \t}\n 34  \n 35  \n 36  \n 37  }\n"
         lineNumber: 21
         variables:
-          file: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
+          file: file:///root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/io/konveyor/demo/config/ApplicationConfiguration.java
           kind: Method
           name: loadProperties
       links:
       - url: https://access.redhat.com/solutions/229443
         title: How to load native libraries and access them via JNI in EAP (with or without a module)
       - url: https://access.redhat.com/solutions/1444643
         title: Is it supported to compile the JNI code as 32-bit shared libraries and use it in 64-bit compiled Java code ?
-      extras: []
       effort: 7
     local-storage-00001:
       description: |-
@@ -1479,12 +1479,12 @@
       - konveyor.io/source
       - storage
       incidents:
-      - uri: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
+      - uri: file:///root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/io/konveyor/demo/config/ApplicationConfiguration.java
         message: 'An application running inside a container could lose access to a file in local storage.. Recommendations. The following recommendations depend on the function of the file in local storage:. * Logging: Log to standard output and use a centralized log collector to analyze the logs.. * Caching: Use a cache backing service.. * Configuration: Store configuration settings in environment variables so that they can be updated without code changes.. * Data storage: Use a database backing service for relational data or use a persistent data storage system.. * Temporary data storage: Use the file system of a running container as a brief, single-transaction cache.'
         codeSnip: "  1  package io.konveyor.demo.config;\n  2  \n  3  import java.io.FileInputStream;\n  4  import java.io.InputStream;\n  5  import java.util.Properties;\n  6  \n  7  public class ApplicationConfiguration {\n  8  \n  9  \tprivate Properties config;\n 10  \n 11  \tpublic ApplicationConfiguration() {\n 12  \t\tsuper();\n 13  \t\tthis.config = loadProperties();\n 14  \n 15  \t}\n 16  \n 17  \tprivate Properties loadProperties() {\n 18  \t\tProperties properties = new Properties();\n 19  \n 20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n 21  \n 22  \t\t\tproperties.load(inputStream);\n 23  \n 24  \t\t} catch (Exception e) {\n 25  \t\t\tSystem.out.println(\"Exception: \" + e);\n 26  \t\t}\n 27  \n 28  \t\treturn properties;\n 29  \t}\n 30  \n 31  \tpublic String getProperty (String name) {\n 32  \t\treturn config.getProperty(name);\n 33  \t}\n 34  \n 35  \n 36  \n 37  }\n"
         lineNumber: 19
         variables:
-          file: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
+          file: file:///root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/io/konveyor/demo/config/ApplicationConfiguration.java
           kind: Constructor
           name: loadProperties
       links:
@@ -1500,7 +1500,6 @@
         title: 'OpenShift Container Platform: Input secrets and ConfigMaps'
       - url: https://docs.openshift.com/container-platform/4.5/storage/understanding-persistent-storage.html
         title: 'OpenShift Container Platform: Understanding persistent storage'
-      extras: []
       effort: 1
   unmatched:
   - embedded-cache-libraries-01000
@@ -1521,18 +1520,18 @@
   - logging-0000
   - logging-0001
   - jca-00000
-  - local-storage-00003
   - local-storage-00004
+  - local-storage-00003
   - session-00000
   - java-rmi-00000
   - logging-0001
-  - java-rpc-00000
   - logging-0000
+  - java-rpc-00000
   - socket-communication-00001
   - mail-00000
+  - local-storage-00005
   - session-00001
   - local-storage-00002
-  - local-storage-00005
   - socket-communication-00000
 - name: os/windows
   description: This is a ruleset for Windows operating system specific rules while migrating to Linux operating system.