Feature/company license (#1164)

* Modify company data schema to include licensing details (#1146)

* Added termination warning email button (#1151)

* Added endpoints to send company notification email (#1152)

* Bump elliptic from 6.5.2 to 6.5.7

Bumps [elliptic](https://github.com/indutny/elliptic) from 6.5.2 to 6.5.7.
- [Commits](indutny/elliptic@v6.5.2...v6.5.7)

---
updated-dependencies:
- dependency-name: elliptic
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>

* allow keypress events for textareas

* Fix data download (#1162)

* User is granted API access on approval (#1163)

* Added endpoints to send notification email

* Data version is now displayed (#1165)

* Addressed PR comments

* Updated Setup Java in Git Actions (#1166)

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Hongxin <[email protected]>
Co-authored-by: bprize15 <[email protected]>
Co-authored-by: bprize15 <[email protected]>
Co-authored-by: Calvin Lu <[email protected]>

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Hongxin <[email protected]>
Co-authored-by: bprize15 <[email protected]>
Co-authored-by: bprize15 <[email protected]>
Co-authored-by: Calvin Lu <[email protected]>

Author: 5 people

.jhipster/Company.json

@@ -42,6 +42,11 @@
     {
       "fieldName": "legalContact",
       "fieldType": "String"
+    },
+    {
+      "fieldName": "additionalInfo",
+      "fieldType": "byte[]",
+      "fieldTypeBlobContent": "text"
     }
   ],
   "relationships": [

jhipster-jdl.jdl

@@ -40,6 +40,7 @@ entity Company {
     licenseStatus LicenseStatus required,
     businessContact String,
     legalContact String,
+    additionalInfo TextBlob
 }
 
 entity CompanyDomain {

screenshot-test/__baseline_snapshots__/Company Details Page-snap.png

@@ -10,7 +10,18 @@
     "businessContact": "Representative",
     "legalContact": "override orchid reboot",
     "companyDomains": ["oncokb.org"],
-    "numberOfUsers": 0
+    "numberOfUsers": 0,
+    "additionalInfo": {
+      "license": {
+        "termination": {
+          "date": "2025-09-21",
+          "notes": "notes",
+          "notificationDays": 3433
+        },
+        "autoRenewal": false,
+        "activation": "2024-09-28"
+      }
+    }
   },
   {
     "id": 2,
@@ -23,6 +34,17 @@
     "businessContact": "Steel Configuration Designer",
     "legalContact": "system engine Australian Dollar",
     "companyDomains": ["mskcc.org"],
-    "numberOfUsers": 3
+    "numberOfUsers": 3,
+    "additionalInfo": {
+      "license": {
+        "termination": {
+          "date": "2025-09-21",
+          "notes": "notes",
+          "notificationDays": 3433
+        },
+        "autoRenewal": false,
+        "activation": "2024-09-28"
+      }
+    }
   }
 ]

screenshot-test/data/api-companies.json

@@ -9,5 +9,16 @@
   "businessContact": "Representative",
   "legalContact": "override orchid reboot",
   "companyDomains": ["oncokb.org"],
-  "numberOfUsers": 0
+  "numberOfUsers": 0,
+  "additionalInfo": {
+    "license": {
+      "termination": {
+        "date": "2024-09-21",
+        "notes": "notes",
+        "notificationDays": 3433
+      },
+      "autoRenewal": false,
+      "activation": "2024-09-28"
+    }
+  }
 }

screenshot-test/data/api-company-details.json

@@ -188,5 +188,4 @@ public RecaptchaProperties getRecaptcha() {
     public void setRecaptcha(RecaptchaProperties recaptcha) {
         this.recaptcha = recaptcha;
     }
-
 }

src/main/java/org/mskcc/cbio/oncokb/config/application/ApplicationProperties.java

@@ -66,6 +66,10 @@ public class Company implements Serializable {
     @Column(name = "legal_contact", length = 255)
     private String legalContact;
 
+    @Lob
+    @Column(name = "additional_info")
+    private String additionalInfo;
+
     @ManyToMany(fetch = FetchType.EAGER, cascade = {CascadeType.PERSIST, CascadeType.MERGE})
     @JoinTable(name = "company_company_domain",
                joinColumns = @JoinColumn(name = "company_id", referencedColumnName = "id"),
@@ -185,6 +189,19 @@ public void setLegalContact(String legalContact) {
         this.legalContact = legalContact;
     }
 
+    public String getAdditionalInfo() {
+        return additionalInfo;
+    }
+
+    public Company additionalInfo(String additionalInfo) {
+        this.additionalInfo = additionalInfo;
+        return this;
+    }
+
+    public void setAdditionalInfo(String additionalInfo) {
+        this.additionalInfo = additionalInfo;
+    }
+
     public Set<CompanyDomain> getCompanyDomains() {
         return companyDomains;
     }
@@ -240,6 +257,7 @@ public String toString() {
             ", licenseStatus='" + getLicenseStatus() + "'" +
             ", businessContact='" + getBusinessContact() + "'" +
             ", legalContact='" + getLegalContact() + "'" +
+            ", additionalInfo='" + getAdditionalInfo() + "'" +
             "}";
     }
 }

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

@@ -119,6 +119,9 @@ public enum MailType {
     , LIST_OF_UNAPPROVED_USERS(new MailTypeBuilder()
         .templateName("listOfUnapprovedUsers")
         .description("List of unapproved users"))
+    , TERMINATION_NOTIFICATION_EMAIL(new MailTypeBuilder()
+        .templateName("terminationNotificationEmail")
+        .description("Notifies admins about companies with licenses about to expire"))
     , TEST(new MailTypeBuilder()
         .templateName("testEmail")
         .description("Test"))

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

@@ -24,4 +24,7 @@ public interface CompanyRepository extends JpaRepository<Company, Long> {
 
     @Cacheable(cacheResolver = "companyCacheResolver")
     Optional<Company> findOneByNameIgnoreCase(String name);
+
+    @Query("select c from Company c where c.id in ?1")
+    List<Company> findCompaniesByIds(List<Long> ids);
 }

src/main/java/org/mskcc/cbio/oncokb/repository/CompanyRepository.java

@@ -1,5 +1,6 @@
 package org.mskcc.cbio.oncokb.service;
 
+import org.mskcc.cbio.oncokb.domain.Company;
 import org.mskcc.cbio.oncokb.domain.enumeration.LicenseStatus;
 import org.mskcc.cbio.oncokb.service.dto.CompanyDTO;
 import org.mskcc.cbio.oncokb.web.rest.vm.CompanyVM;
@@ -58,4 +59,7 @@ public interface CompanyService {
      * @param id the id of the entity.
      */
     void delete(Long id);
+
+
+    List<CompanyDTO> findCompaniesByIds(List<Long> ids);
 }

src/main/java/org/mskcc/cbio/oncokb/service/CompanyService.java

@@ -10,6 +10,7 @@
 import org.mskcc.cbio.oncokb.domain.Company;
 import org.mskcc.cbio.oncokb.domain.UserMessagePair;
 import org.mskcc.cbio.oncokb.domain.enumeration.MailType;
+import org.mskcc.cbio.oncokb.service.dto.TerminationEmailDTO;
 import org.mskcc.cbio.oncokb.service.dto.UserDTO;
 import org.mskcc.cbio.oncokb.service.dto.UserMailsDTO;
 import org.mskcc.cbio.oncokb.web.rest.vm.ExposedToken;
@@ -85,6 +86,20 @@ private UnknownMailTypeException() {
         }
     }
 
+    public void sendEmail(TerminationEmailDTO dto) throws MessagingException {
+        log.debug("Send email to company ID '{}' with subject '{}' and content={}",
+            dto.getCompanyId(),  dto.getSubject(), dto.getContent());
+
+        MimeMessage mimeMessage = javaMailSender.createMimeMessage();
+        MimeMessageHelper message = new MimeMessageHelper(mimeMessage, false, StandardCharsets.UTF_8.name());
+        message.setFrom(dto.getFrom());
+        message.setBcc(dto.getBcc().split(";"));
+        message.setCc(dto.getCc().split(";"));
+        message.setSubject(dto.getSubject());
+        message.setText(dto.getContent(), false);
+        javaMailSender.send(mimeMessage);
+    }
+
     @Async
     public void sendEmail(String to, String from, String cc, String subject, String content, List<String> attachmentFilesNames, boolean isMultipart, boolean isHtml) throws MessagingException {
         log.debug("Send email[multipart '{}' and html '{}'] to '{}' with subject '{}' and content={}",
@@ -236,6 +251,21 @@ public void sendEmailFromTemplate(UserDTO user, MailType mailType, String subjec
         }
     }
 
+    public void sendInternalEmailFromTemplate(MailType mailType, String subject, String to, Context additionalContext) {
+        Context context = new Context(Locale.ENGLISH);
+
+        if (additionalContext != null)
+            additionalContext.getVariableNames().forEach(name -> context.setVariable(name, additionalContext.getVariable(name)));
+
+        String from = jHipsterProperties.getMail().getFrom();
+        String content = templateEngine.process("mail/" + mailType.getTemplateName(), context);
+        try {
+            sendEmail(to, from, null, subject, content, null, false, true);
+        } catch (MailException | MessagingException e) {
+            log.warn("Internal email could not be sent to '{}'", to, e);
+        }
+    }
+
     @Async
     public void sendActivationEmail(UserDTO user) {
         log.debug("Sending activation email to '{}'", user.getEmail());

src/main/java/org/mskcc/cbio/oncokb/service/MailService.java

@@ -7,14 +7,15 @@
 import javax.persistence.Lob;
 import org.mskcc.cbio.oncokb.domain.enumeration.CompanyType;
 import org.mskcc.cbio.oncokb.domain.enumeration.LicenseType;
+import org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo.CompanyAdditionalInfoDTO;
 import org.mskcc.cbio.oncokb.domain.enumeration.LicenseModel;
 import org.mskcc.cbio.oncokb.domain.enumeration.LicenseStatus;
 
 /**
  * A DTO for the {@link org.mskcc.cbio.oncokb.domain.Company} entity.
  */
 public class CompanyDTO implements Serializable {
-    
+
     private Long id;
 
     @NotNull
@@ -42,8 +43,11 @@ public class CompanyDTO implements Serializable {
     @NotEmpty
     private Set<String> companyDomains = new HashSet<>();
 
+    @Lob
+    private CompanyAdditionalInfoDTO additionalInfo;
+
     private Integer numberOfUsers;
-    
+
     public Long getId() {
         return id;
     }
@@ -124,6 +128,14 @@ public void setCompanyDomains(Set<String> companyDomains) {
         this.companyDomains = companyDomains;
     }
 
+    public CompanyAdditionalInfoDTO getAdditionalInfo() {
+        return additionalInfo;
+    }
+
+    public void setAdditionalInfo(CompanyAdditionalInfoDTO additionalInfo) {
+        this.additionalInfo = additionalInfo;
+    }
+
     public Integer getNumberOfUsers() {
         return this.numberOfUsers;
     }
@@ -162,6 +174,7 @@ public String toString() {
             ", licenseStatus='" + getLicenseStatus() + "'" +
             ", businessContact='" + getBusinessContact() + "'" +
             ", legalContact='" + getLegalContact() + "'" +
+            ", additionalInfo='" + getAdditionalInfo() + "'" +
             ", companyDomains='" + getCompanyDomains() + "'" +
             ", numberOfUsers='" + getNumberOfUsers() + "'" +
             "}";

src/main/java/org/mskcc/cbio/oncokb/service/dto/CompanyDTO.java

@@ -0,0 +1,61 @@
+package org.mskcc.cbio.oncokb.service.dto;
+
+import java.io.Serializable;
+
+public class TerminationEmailDTO  implements Serializable {
+    private String subject;
+    private String from;
+    private String bcc;
+    private String cc;
+    private String content;
+    private Long companyId;
+
+    public String getSubject() {
+        return subject;
+    }
+
+    public void setSubject(String subject) {
+        this.subject = subject;
+    }
+
+
+    public String getFrom() {
+        return from;
+    }
+
+    public void setFrom(String from) {
+        this.from = from;
+    }
+
+    public String getBcc() {
+        return bcc;
+    }
+
+    public void setBcc(String bcc) {
+        this.bcc = bcc;
+    }
+
+    public String getCc() {
+        return cc;
+    }
+
+    public void setCc(String cc) {
+        this.cc = cc;
+    }
+
+    public String getContent() {
+        return content;
+    }
+
+    public void setContent(String content) {
+        this.content = content;
+    }
+
+    public Long getCompanyId() {
+        return companyId;
+    }
+
+    public void setCompanyId(Long companyId) {
+        this.companyId = companyId;
+    }
+}

src/main/java/org/mskcc/cbio/oncokb/service/dto/TerminationEmailDTO.java

@@ -0,0 +1,15 @@
+package org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo;
+
+import java.io.Serializable;
+
+public class CompanyAdditionalInfoDTO implements Serializable {
+  private CompanyLicense license;
+
+  public CompanyLicense getLicense() {
+    return license;
+  }
+
+  public void setLicense(CompanyLicense license) {
+    this.license = license;
+  }
+}

src/main/java/org/mskcc/cbio/oncokb/service/dto/companyadditionalinfo/CompanyAdditionalInfoDTO.java

@@ -0,0 +1,34 @@
+package org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo;
+
+import java.io.Serializable;
+import java.time.Instant;
+
+public class CompanyLicense implements Serializable {
+  private Instant activation;
+  private boolean autoRenewal;
+  private CompanyTermination termination;
+
+  public Instant getActivation() {
+    return activation;
+  }
+
+  public void setActivation(Instant activation) {
+    this.activation = activation;
+  }
+
+  public boolean isAutoRenewal() {
+    return autoRenewal;
+  }
+
+  public void setAutoRenewal(boolean autoRenewal) {
+    this.autoRenewal = autoRenewal;
+  }
+
+  public CompanyTermination getTermination() {
+    return termination;
+  }
+
+  public void setTermination(CompanyTermination termination) {
+    this.termination = termination;
+  }
+}