Merge pull request #78 from Open-MBEE/release/4.0.19

Release/4.0.19

Author: HuiJun

build.gradle

@@ -44,11 +44,39 @@ dependencies {
             "org.springframework.boot:spring-boot-starter-web",
             "org.springframework.boot:spring-boot-starter-actuator",
             "org.postgresql:postgresql:42.2.27",
-            "org.springdoc:springdoc-openapi-ui:1.5.4",
-            "org.springdoc:springdoc-openapi-webmvc-core:1.5.4",
-            "org.springdoc:springdoc-openapi-security:1.5.4",
             "org.zalando:logbook-spring-boot-starter:2.2.1",
-            "ch.qos.logback:logback-classic:1.2.11"
+            "ch.qos.logback:logback-classic:1.2.11",
+//            below was commented out due to changes to spring 2.6.7 > 2.7.x upgrade
+            //change the opanapi version from 1.5.4 to 1.6.9
+            'org.springdoc:springdoc-openapi-ui:1.6.9',
+            "org.springdoc:springdoc-openapi-webmvc-core:1.6.9",
+            "org.springdoc:springdoc-openapi-security:1.6.9",
+            //resolve https://nvd.nist.gov/vuln/detail/CVE-2022-1471
+            "org.yaml:snakeyaml:2.0",
+            //https://nvd.nist.gov/vuln/detail/CVE-2022-46364
+            "org.apache.cxf:cxf-core:3.5.5",
+
+            // https://nvd.nist.gov/vuln/detail/CVE-2023-34034
+            "org.springframework.security:spring-security-core:5.6.12",
+            "org.springframework.security:spring-security-config:5.6.12",
+
+//        RESOLVE HIGH VULNERABILITIES
+        "org.apache.tomcat.embed:tomcat-embed-core:9.0.75",
+        "org.springframework.boot:spring-boot-autoconfigure:2.7.12",
+        "org.jsoup:jsoup:1.15.3",
+        "org.bouncycastle:bcprov-jdk15on:1.67",
+        "org.apache.lucene:lucene-core:8.10.0",
+        "org.apache.commons:commons-compress:1.21",
+        "com.amazonaws:aws-java-sdk-s3:1.12.261",
+        "com.fasterxml.jackson.core:jackson-core:2.15.0",
+        "com.github.junrar:junrar:7.4.1",
+        // https://mvnrepository.com/artifact/com.google.guava/guava
+        "com.google.guava:guava:32.0.1-jre",
+        "com.google.protobuf:protobuf-java:3.16.3",
+
+
+
+
     )
     testImplementation(
             'org.springframework.boot:spring-boot-starter-test'

docs/conf.py

@@ -19,14 +19,14 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'Model Management System Reference Implementation'
+project = 'Model Management System (MMS 4) Reference Implementation'
 copyright = '2020, OpenMBEE'
 author = 'OpenMBEE'
 
 master_doc = 'index'
 
 # The full version, including alpha/beta/rc tags
-release = '4.0.9'
+release = '4.0.19'
 
 
 # -- General configuration ---------------------------------------------------

docs/configuration.rst

@@ -16,7 +16,7 @@ Configuration Options
   mms.stream.batch.size
     The limit to use when processing stream data.
 
-    | `Default: 100000`
+    | `Default: 5000`
 
   rdb.project.prefix
     The prefix to use for project database creation.
@@ -124,10 +124,12 @@ LDAP Configuration
   ldap.user.dn.pattern
     The dn pattern for the user. Can accept multiple patterns for separate branches, delimited by ';'. Required.
 
+    | `Default: uid={0}`
+
   ldap.user.attributes.username
     The attribute to use for the username. Optional.
 
-    | `Default: uid={0}`
+    | `Default: uid`
 
   ldap.user.attributes.email
     The attribute to use for the email address. Optional.
@@ -155,6 +157,9 @@ Storage Configuration
 
 If aws s3 environment is used and s3.access_key and s3.secret_key are not defined, credentials will be taken according to the `aws default credential provider chain <https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/credentials.html>`_.
 
+  s3.endpoint
+    Endpoint of S3 compliant storage service
+
   s3.access_key
     This is the access key for the S3 bucket. Required (Optional if using AWS).
 

docs/docker.rst

@@ -49,7 +49,7 @@ Running MMS
     First, create a container from an MMS image. In the example below, the container is using the host network for simplicity.
     ::
 
-      docker create --name=mms --network="host" -e "SPRING_CONFIG_LOCATION=/mms.properties" openmbee/mms:4.0.0-b5
+      docker create --name=mms --network="host" -e "SPRING_CONFIG_LOCATION=/mms.properties" openmbee/mms:4.0.19
 
   Copy properties
     If using the above command, copy the properties file to the defined spring config location.

docs/overview.rst

@@ -2,8 +2,6 @@
 Overview
 ========
 
-The Model Management System (MMS) provide services for managing models and is a version control system for structured data. It exposes model information through RESTful web services that can be used for CRUD operations, branching, and tagging of the model repository.
-
-The MMS also provides web services for storing and searching Jupyter Lab notebooks.
+The Model Management System (MMS 4) provide services for managing models and is a version control system for structured data. It exposes model information through RESTful web services that can be used for CRUD operations, branching, and tagging of the model repository.
 
 This Reference Implementation provides a generic build with basic features aimed at the end user.

gradle.properties

@@ -1,5 +1,5 @@
-version=4.0.18
+version=4.0.19
 group=org.openmbee.mms
 
-mmsVersion=4.0.18
-springBootVersion=2.6.7
+mmsVersion=4.0.19
+springBootVersion=2.7.11

openapi/api-docs.yaml

@@ -5,7 +5,7 @@ info:
   license:
     name: Apache 2.0
     url: http://www.apache.org/licenses/LICENSE-2.0.txt
-  version: 4.0.18
+  version: 4.0.19
   contact:
     name: OpenMBEE
     url: http://openmbee.org
@@ -1917,6 +1917,9 @@ components:
           items:
             type: string
             nullable: true
+        commitId:
+          type: string
+          nullable: true
         rejected:
           type: array
           nullable: true

openapi/doc-config.json

@@ -3,5 +3,5 @@
     "invokerPackage": "org.openmbee.mms",
     "groupId": "org.openmbee.mms",
     "artifactId": "mms-client",
-    "artifactVersion": "4.0.17"
+    "artifactVersion": "4.0.19"
 }

openapi/java-config.json

@@ -1,7 +1,7 @@
 {
     "groupId": "org.openmbee.mms",
     "artifactId": "mms-java-client",
-    "artifactVersion": "4.0.17",
+    "artifactVersion": "4.0.19",
     "artifactUrl": "https://github.com/Open-MBEE/mms",
     "artifactDescription": "Java OpenAPI Client for MMS",
     "library": "jersey2",

openapi/python-config.json

@@ -1,5 +1,5 @@
 {
     "packageName": "mms_python_client",
     "projectName": "mms-python-client",
-    "packageVersion": "4.0.17"
+    "packageVersion": "4.0.19"
 }

src/main/java/org/openmbee/mms/mmsri/MMSRIApplication.java

@@ -13,7 +13,7 @@
 @OpenAPIDefinition(
     info = @Info(
         title = "MMS Reference Implementation API",
-        version = "4.0.18",
+        version = "4.0.19",
         description = "Documentation for MMS API",
         license = @License(name = "Apache 2.0", url = "http://www.apache.org/licenses/LICENSE-2.0.txt")
     ),