Updated dependencies to fix git security warnings

Author: u0028003

TestResources/Json/GQueryAPI/queryOptions.json

@@ -48,7 +48,7 @@
     true,
     false
    ],
-   "description": "For vcf input queries, require that vcf records match chr, pos, ref, and at least one alt. Will set 'fetchData' = true. Be sure to vt normalize and decompose_blocksub your vcf input, see https://github.com/atks/vt.",
+   "description": "For vcf queries, require intersecting vcf records match chr, pos, ref, and at least one alt. Will set 'fetchData' = true. Be sure to vt normalize your vcf input, see https://github.com/atks/vt.",
    "defaultOption": false
   },
   {
@@ -81,6 +81,14 @@
    "name": "regExDataLine",
    "description": "Require each record data line to match these java regular expressions, semicolon delimited. Note, a .* is added to both ends of each regEx. Will set 'fetchData' = true."
   },
+  {
+   "examples": [
+    "Benign",
+    "FailsQC"
+   ],
+   "name": "regExDataLineExclude",
+   "description": "Exclude record data lines that match any of these java regular expressions, semicolon delimited. Note, a .* is added to both ends of each regEx. Will set 'fetchData' = true."
+  },
   {
    "name": "matchAllDirPathRegEx",
    "options": [

TestResources/Json/GQueryCLI/optionsTest.json

@@ -50,7 +50,7 @@
             true,
             false
          ],
-         "description": "For vcf input queries, require that vcf records match chr, pos, ref, and at least one alt. Will set 'fetchData' = true. Be sure to vt normalize and decompose_blocksub your vcf input, see https://github.com/atks/vt.",
+         "description": "For vcf queries, require intersecting vcf records match chr, pos, ref, and at least one alt. Will set 'fetchData' = true. Be sure to vt normalize your vcf input, see https://github.com/atks/vt.",
          "defaultOption": false
       },
       {
@@ -83,6 +83,14 @@
          "name": "regExDataLine",
          "description": "Require each record data line to match these java regular expressions, semicolon delimited. Note, a .* is added to both ends of each regEx. Will set 'fetchData' = true."
       },
+      {
+         "examples": [
+            "Benign",
+            "FailsQC"
+         ],
+         "name": "regExDataLineExclude",
+         "description": "Exclude record data lines that match any of these java regular expressions, semicolon delimited. Note, a .* is added to both ends of each regEx. Will set 'fetchData' = true."
+      },
       {
          "name": "matchAllDirPathRegEx",
          "options": [
@@ -113,16 +121,16 @@
       {
          "searchableFiles": [
             "Data/B38/clinvar_B38_chr21.vcf.gz",
-            "Data/B37/TCGA/CU/CU_Test.maf.txt.gz",
             "Data/B37/Thor/3994-7.mt2.pass.vcf.gz",
+            "Data/B37/TCGA/CU/CU_Test.maf.txt.gz",
             "Data/B37/TCGA/AP/AP_Test.maf.txt.gz",
             "Data/B37/GVCFs/wgSeq_chr22.g.vcf.gz",
             "Data/B37/VCFData/chr20-21TRF037738.vcf.gz",
             "Data/B37/VCFData/chr20_cosmic.vcf.gz",
             "Data/B37/VCFData/chr20_1_3Mut2.vcf.gz",
-            "Data/Hg19/chr20-22Ribo.bed.gz",
             "Data/B37/BedData/chr20-21_Exome_UniObRC.bedGraph.gz",
-            "Data/B37/BedData/b37EnsGenes_ExonsChr20-21.bed.gz"
+            "Data/B37/BedData/b37EnsGenes_ExonsChr20-21.bed.gz",
+            "Data/Hg19/chr20-22Ribo.bed.gz"
          ],
          "name": "dataSources",
          "userDirPathRegEx": [".+"],

WebContent/WEB-INF/web.xml

@@ -68,7 +68,7 @@
   <context-param>
     <description>Boolean indicating whether authorization is enabled.  If true, complete the userGroup param.</description>
     <param-name>authorizationEnabled</param-name>
-    <param-value>false</param-value>
+    <param-value>true</param-value>
   </context-param>
   <context-param>
     <description>If using authorization, provide a full path to the userGroup file. This parent dir will also be used to store the encryption key so keep it secure.</description>

pom.xml

@@ -2,7 +2,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>GQuery</groupId>
   <artifactId>GQuery</artifactId>
-  <version>0.0.1-SNAPSHOT</version>
+  <version>0.1</version>
   <packaging>war</packaging>
   <build>
     <sourceDirectory>src</sourceDirectory>
@@ -64,7 +64,7 @@
   	<dependency>
     	<groupId>org.apache.logging.log4j</groupId>
     	<artifactId>log4j-core</artifactId>
-    	<version>2.13.0</version>
+    	<version>2.13.2</version>
   	</dependency>
   	  	<dependency>
   		<groupId>javax.servlet</groupId>
@@ -74,7 +74,7 @@
   	<dependency>
   		<groupId>junit</groupId>
   		<artifactId>junit</artifactId>
-  		<version>4.12</version>
+  		<version>4.13.1</version>
   	</dependency>
   	<dependency>
   		<groupId>com.github.samtools</groupId>