update token model and db to support github token format

.jhipster/Token.json

@@ -36,6 +36,10 @@
       "fieldName": "renewable",
       "fieldType": "Boolean",
       "fieldValidateRules": ["required"]
+    },
+    {
+      "fieldName": "newToken",
+      "fieldType": "String"
     }
   ],
   "changelogDate": "20190823204705",

jhipster-jdl.jdl

@@ -4,7 +4,8 @@ entity Token {
     expiration Instant,
     usageLimit Integer,
     currentUsage Integer required,
-    renewable Boolean required
+    renewable Boolean required,
+    newToken String
 }
 
 entity TokenStats {

src/main/java/org/mskcc/cbio/oncokb/domain/Token.java

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import org.hibernate.annotations.Type;
+import org.mskcc.cbio.oncokb.domain.enumeration.TokenType;
 
 import javax.persistence.*;
 import javax.validation.constraints.*;
@@ -44,6 +45,10 @@ public class Token implements Serializable {
     @Column(name = "renewable", nullable = false)
     private Boolean renewable = true;
 
+    @Convert(converter = TokenKeyConverter.class)
+    @Column(name = "new_token")
+    private TokenKey newToken;
+
     @ManyToOne
     @JsonIgnoreProperties(value = "tokens", allowSetters = true)
     private User user;
@@ -135,6 +140,19 @@ public void setRenewable(Boolean renewable) {
         this.renewable = renewable;
     }
 
+    public TokenKey getNewToken() {
+        return newToken;
+    }
+
+    public Token newToken(TokenKey newToken) {
+        this.newToken = newToken;
+        return this;
+    }
+
+    public void setNewToken(TokenKey newToken) {
+        this.newToken = newToken;
+    }
+
     public User getUser() {
         return user;
     }
@@ -176,6 +194,54 @@ public String toString() {
             ", usageLimit=" + getUsageLimit() +
             ", currentUsage=" + getCurrentUsage() +
             ", renewable='" + isRenewable() + "'" +
+            ", newToken='" + getNewToken() + "'" +
             "}";
     }
 }
+
+class TokenKeyConverter implements AttributeConverter<TokenKey, String> {
+    @Override
+    public String convertToDatabaseColumn(TokenKey tokenKey) {
+        if (tokenKey.getTokenType() == null || tokenKey.getToken() == null || tokenKey.getChecksum() == null) {
+            return null;
+        }
+        if (tokenKey.getToken().length() != TokenKey.TOKEN_CHAR_LENGTH || tokenKey.getChecksum().length() != TokenKey.CHECKSUM_CHAR_LENGTH) {
+            return null;
+        }
+        return tokenKey.getTokenType().getType() + "_" + tokenKey.getToken() + tokenKey.getChecksum();
+    }
+
+    @Override
+    public TokenKey convertToEntityAttribute(String dbData) {
+        if (dbData == null) {
+            return null;
+        }
+        String[] parts = dbData.split("_");
+        if (parts.length != 2) {
+            return null;
+        }
+
+
+        TokenKey tokenKey = new TokenKey();
+        String type = parts[0];
+        if (type.equals(TokenType.SERVICE.getType())) {
+            tokenKey.setTokenType(TokenType.SERVICE);
+        } else if (type.equals(TokenType.USER.getType())) {
+            tokenKey.setTokenType(TokenType.USER);
+        } else {
+            return null;
+        }
+
+        String tokenAndChecksum = parts[1];
+        if (tokenAndChecksum.length() == TokenKey.TOKEN_CHAR_LENGTH + TokenKey.CHECKSUM_CHAR_LENGTH) {
+            String token = tokenAndChecksum.substring(0, TokenKey.TOKEN_CHAR_LENGTH);
+            String checksum = tokenAndChecksum.substring(TokenKey.TOKEN_CHAR_LENGTH);
+            tokenKey.setToken(token);
+            tokenKey.setChecksum(checksum);  
+        } else {
+            return null;
+        }
+
+        return tokenKey;
+    }
+}

src/main/java/org/mskcc/cbio/oncokb/domain/TokenKey.java

@@ -0,0 +1,84 @@
+package org.mskcc.cbio.oncokb.domain;
+
+import java.io.Serializable;
+import java.security.SecureRandom;
+import java.util.zip.CRC32;
+
+import org.apache.commons.lang3.StringUtils;
+import org.mskcc.cbio.oncokb.domain.enumeration.TokenType;
+
+public class TokenKey implements Serializable {
+    public static int TOKEN_CHAR_LENGTH = 30;
+
+    public static int CHECKSUM_CHAR_LENGTH = 6;
+
+    private static String BASE62_CHARS = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
+
+    private TokenType tokenType;
+
+    private String token;
+
+    private String checksum;
+
+    public static TokenKey generate(TokenType type) {
+        TokenKey tokenKey = new TokenKey();
+        tokenKey.setTokenType(type);
+
+        CRC32 crc32 = new CRC32();
+
+        String token = generateToken();
+        tokenKey.setToken(token);
+
+        crc32.update(token.getBytes());
+        String base62Checksum = toBase62(crc32.getValue());
+        if (base62Checksum.length() < CHECKSUM_CHAR_LENGTH) {
+            base62Checksum = StringUtils.repeat('0', CHECKSUM_CHAR_LENGTH - base62Checksum.length());
+        }
+        tokenKey.setChecksum(base62Checksum);
+
+        return tokenKey;
+    }
+
+    private static String generateToken() {
+        SecureRandom secureRandom = new SecureRandom();
+        StringBuilder token = new StringBuilder();
+        for (int i = 0; i < TOKEN_CHAR_LENGTH; i++) {
+            token.append(BASE62_CHARS.charAt(secureRandom.nextInt(BASE62_CHARS.length())));
+        }
+        return token.toString();
+    }
+
+    public static String toBase62(long val) {
+        StringBuffer sb = new StringBuffer();
+        while(val > 0) {
+            int remainder = (int) (val % 62);
+            val = val / 62;
+            sb.insert(0, BASE62_CHARS.charAt((int) remainder));
+        }
+        return sb.toString();
+    }
+
+    public TokenType getTokenType() {
+        return tokenType;
+    }
+
+    public void setTokenType(TokenType tokenType) {
+        this.tokenType = tokenType;
+    }
+
+    public String getToken() {
+        return token;
+    }
+
+    public void setToken(String token) {
+        this.token = token;
+    }
+
+    public String getChecksum() {
+        return checksum;
+    }
+
+    public void setChecksum(String checksum) {
+        this.checksum = checksum;
+    }
+}

src/main/java/org/mskcc/cbio/oncokb/domain/enumeration/TokenType.java

@@ -0,0 +1,16 @@
+package org.mskcc.cbio.oncokb.domain.enumeration;
+
+public enum TokenType {
+    USER("ocku"),
+    SERVICE("okbs");
+
+    String type;
+
+    TokenType(String type) {
+        this.type = type;
+    }
+
+    public String getType() {
+        return this.type;
+    }
+}

src/main/java/org/mskcc/cbio/oncokb/security/uuid/TokenProvider.java

@@ -2,7 +2,9 @@
 
 import org.mskcc.cbio.oncokb.domain.Authority;
 import org.mskcc.cbio.oncokb.domain.Token;
+import org.mskcc.cbio.oncokb.domain.TokenKey;
 import org.mskcc.cbio.oncokb.domain.User;
+import org.mskcc.cbio.oncokb.domain.enumeration.TokenType;
 import org.mskcc.cbio.oncokb.repository.UserRepository;
 import org.mskcc.cbio.oncokb.security.AuthoritiesConstants;
 import org.mskcc.cbio.oncokb.security.SecurityUtils;
@@ -74,6 +76,7 @@ private Token getNewToken(Set<Authority> authorities, Optional<Instant> definedE
             token.setExpiration(expirationTime);
         }
         token.setToken(UUID.randomUUID());
+        token.setNewToken(TokenKey.generate(TokenType.USER));
         return token;
     }
 

src/main/resources/config/liquibase/changelog/20241118184124_added_field_newToken_to_Token.xml

@@ -0,0 +1,8 @@
+<?xml version="1.1" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:pro="http://www.liquibase.org/xml/ns/pro" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog-ext http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-ext.xsd http://www.liquibase.org/xml/ns/pro http://www.liquibase.org/xml/ns/pro/liquibase-pro-3.9.xsd http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.9.xsd">
+    <changeSet author="preiserb (generated)" id="1731955350576-1">
+        <addColumn tableName="token">
+            <column name="new_token" type="varchar(255)"/>
+        </addColumn>
+    </changeSet>
+</databaseChangeLog>

src/main/resources/config/liquibase/master.xml

@@ -27,6 +27,7 @@
     <include file="config/liquibase/changelog/20191230201137_added_entity_constraints_UserMails.xml" relativeToChangelogFile="false"/>
     <include file="config/liquibase/changelog/20210927165533_added_entity_constraints_CompanyDomain.xml" relativeToChangelogFile="false"/>
     <include file="config/liquibase/changelog/20210927165433_added_entity_constraints_Company.xml" relativeToChangelogFile="false"/>
+    <include file="config/liquibase/changelog/20241118184124_added_field_newToken_to_Token.xml" relativeToChangelogFile="false"/>
     <!-- jhipster-needle-liquibase-add-constraints-changelog - JHipster will add liquibase constraints changelogs here -->
     <!-- jhipster-needle-liquibase-add-incremental-changelog - JHipster will add incremental liquibase changelogs here -->
 </databaseChangeLog>

src/test/java/org/mskcc/cbio/oncokb/domain/TokenKeyTest.java

@@ -0,0 +1,31 @@
+package org.mskcc.cbio.oncokb.domain;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.nio.ByteBuffer;
+
+import org.apache.commons.lang3.StringUtils;
+import org.junit.Test;
+
+public class TokenKeyTest {
+    @Test
+    public void toBase62() {
+        String test = "d";
+        assertThat(TokenKey.toBase62(stringToLong(test))).isEqualTo("1c");
+
+        test = "hello";
+        assertThat(TokenKey.toBase62(stringToLong(test))).isEqualTo("7tQLFHz");
+
+        test = "oncokb";
+        assertThat(TokenKey.toBase62(122519905332066L)).isEqualTo("Yn1xclvu");
+    }
+
+    private long stringToLong(String str) {
+        if (str.length() < Long.BYTES) {
+            str = StringUtils.repeat('\0', Long.BYTES - str.length()) + str;
+        }
+
+        ByteBuffer buffer = ByteBuffer.wrap(str.getBytes());
+        return buffer.getLong(0);
+    }
+}