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]>
oncokb · Oct 11, 2024 · 16532d6 · 16532d6
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diff --git a/.github/workflows/after-master-commit.yml b/.github/workflows/after-master-commit.yml
@@ -62,9 +62,10 @@ jobs:
           version: ${{ steps.previoustag.outputs.tag }}
 
       - name: 'Setup Java'
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v4
         with:
-          java-version: 8
+          distribution: 'temurin'
+          java-version: 11
 
       - name: 'Get Current Version Level'
         id: 'version-level'

diff --git a/.github/workflows/docker-sentry-release.yml b/.github/workflows/docker-sentry-release.yml
@@ -17,10 +17,10 @@ jobs:
       - uses: actions/setup-node@v2
         with:
           node-version: 12.16.1
-      - uses: actions/setup-java@v2
+      - uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: 11
       - name: Install node.js packages
         run: yarn install
       - name: Package application with Jib

diff --git a/.github/workflows/github-ci.yml b/.github/workflows/github-ci.yml
@@ -15,10 +15,10 @@ jobs:
             - uses: actions/setup-node@v2
               with:
                   node-version: 12.16.1
-            - uses: actions/setup-java@v2
+            - uses: actions/setup-java@v4
               with:
-                  distribution: 'adopt'
-                  java-version: '11'
+                  distribution: 'temurin'
+                  java-version: 11
             - name: Stop MySQL server
               run: sudo /etc/init.d/mysql stop
             - name: Install node.js packages

diff --git a/src/main/java/org/mskcc/cbio/oncokb/domain/enumeration/MailType.java b/src/main/java/org/mskcc/cbio/oncokb/domain/enumeration/MailType.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"))

diff --git a/src/main/java/org/mskcc/cbio/oncokb/repository/CompanyRepository.java b/src/main/java/org/mskcc/cbio/oncokb/repository/CompanyRepository.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);
 }
diff --git a/src/main/java/org/mskcc/cbio/oncokb/service/CompanyService.java b/src/main/java/org/mskcc/cbio/oncokb/service/CompanyService.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);
 }
diff --git a/src/main/java/org/mskcc/cbio/oncokb/service/MailService.java b/src/main/java/org/mskcc/cbio/oncokb/service/MailService.java
@@ -251,6 +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());

diff --git a/...main/java/org/mskcc/cbio/oncokb/service/dto/companyadditionalinfo/CompanyTermination.java b/...main/java/org/mskcc/cbio/oncokb/service/dto/companyadditionalinfo/CompanyTermination.java
@@ -7,6 +7,7 @@ public class CompanyTermination implements Serializable {
   private Integer notificationDays;
   private Instant date;
   private String notes;
+  private Boolean hasBeenNotified;
 
   public Integer getNotificationDays() {
     return notificationDays;
@@ -31,4 +32,12 @@ public String getNotes() {
   public void setNotes(String note) {
     this.notes = note;
   }
+
+  public Boolean getHasBeenNotified() {
+    return hasBeenNotified;
+  }
+
+  public void setHasBeenNotified(Boolean hasBeenNotified) {
+    this.hasBeenNotified = hasBeenNotified;
+  }
 }
diff --git a/src/main/java/org/mskcc/cbio/oncokb/service/impl/CompanyServiceImpl.java b/src/main/java/org/mskcc/cbio/oncokb/service/impl/CompanyServiceImpl.java
@@ -25,6 +25,7 @@
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
+import java.util.ArrayList;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Objects;
@@ -214,4 +215,14 @@ private void clearCompanyCaches(Company company) {
         Objects.requireNonNull(cacheManager.getCache(this.cacheNameResolver.getCacheName(COMPANIES_BY_NAME_CACHE))).evict(company.getName());
     }
 
+    @Override
+    @Transactional(readOnly = true)
+    public List<CompanyDTO> findCompaniesByIds(List<Long> ids) {
+        log.debug("Request to get Company : {}", ids);
+        return companyRepository.findCompaniesByIds(ids)
+            .stream()
+            .map(companyMapper::toDto)
+            .collect(Collectors.toCollection(ArrayList::new));
+    }
+
 }
diff --git a/src/main/java/org/mskcc/cbio/oncokb/web/rest/CompanyResource.java b/src/main/java/org/mskcc/cbio/oncokb/web/rest/CompanyResource.java
@@ -16,6 +16,9 @@
 import org.mskcc.cbio.oncokb.web.rest.vm.VerifyCompanyNameVM;
 import org.mskcc.cbio.oncokb.service.dto.CompanyDTO;
 import org.mskcc.cbio.oncokb.service.dto.UserDTO;
+import org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo.CompanyAdditionalInfoDTO;
+import org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo.CompanyLicense;
+import org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo.CompanyTermination;
 
 import io.github.jhipster.web.util.ResponseUtil;
 import org.slf4j.Logger;
@@ -28,6 +31,9 @@
 import javax.validation.Valid;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.time.Instant;
+import java.time.temporal.ChronoUnit;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
@@ -195,4 +201,32 @@ public ResponseEntity<Void> deleteCompany(@PathVariable Long id) {
         companyService.delete(id);
         return ResponseEntity.ok().build();
     }
+
+    @GetMapping("/companies/licenses-about-to-expire-pending-notification")
+    public List<Long> getLicensesAboutToExpirePendingNotification() {
+        log.debug("Request to get Company license is about to expire");
+        Instant now = Instant.now();
+        ArrayList<Long> companies = new ArrayList<>();
+        for (CompanyDTO company : companyService.findAll()) {
+           Optional<CompanyTermination> optionalTermination = Optional.ofNullable(company.getAdditionalInfo())
+               .map(CompanyAdditionalInfoDTO::getLicense)
+               .map(CompanyLicense::getTermination);
+           if (optionalTermination.isPresent()) {
+               CompanyTermination termination = optionalTermination.get();
+               Boolean hasBeenNotified = termination.getHasBeenNotified();
+               if (hasBeenNotified == null) {
+                   hasBeenNotified = false;
+               }
+               Integer notificationDays = termination.getNotificationDays();
+               Instant terminationDate = termination.getDate();
+               if (!hasBeenNotified && notificationDays != null && terminationDate != null) {
+                   Instant start = terminationDate.minus(notificationDays, ChronoUnit.DAYS);
+                   if (now.isAfter(start) && now.isBefore(terminationDate)) {
+                       companies.add(company.getId());
+                   }
+               }
+           }
+        }
+        return companies;
+    }
 }
diff --git a/src/main/java/org/mskcc/cbio/oncokb/web/rest/MailsController.java b/src/main/java/org/mskcc/cbio/oncokb/web/rest/MailsController.java
@@ -26,8 +26,12 @@
 import org.mskcc.cbio.oncokb.service.dto.CompanyDTO;
 import org.mskcc.cbio.oncokb.service.dto.TerminationEmailDTO;
 import org.mskcc.cbio.oncokb.service.dto.UserDTO;
+import org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo.CompanyAdditionalInfoDTO;
+import org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo.CompanyLicense;
+import org.mskcc.cbio.oncokb.service.dto.companyadditionalinfo.CompanyTermination;
 import org.mskcc.cbio.oncokb.service.mapper.UserMapper;
 import org.mskcc.cbio.oncokb.web.rest.errors.BadRequestAlertException;
+import org.mskcc.cbio.oncokb.web.rest.vm.CompanyVM;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.http.HttpStatus;
@@ -40,7 +44,9 @@
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.server.ResponseStatusException;
+import org.springframework.web.servlet.support.ServletUriComponentsBuilder;
 import org.mskcc.cbio.oncokb.config.Constants;
+import org.thymeleaf.context.Context;
 
 /**
  * REST controller for managing mails.
@@ -179,8 +185,58 @@ public TerminationEmailDTO getTerminationWarningEmail(@PathVariable Long company
         return dto;
     }
 
-    @PostMapping("mails/termination-warning")
+    @PostMapping("mails/company-termination-warning")
     public void sendTerminationWarningEmail(@Valid @RequestBody TerminationEmailDTO terminationEmailDTO) throws MessagingException {
         this.mailService.sendEmail(terminationEmailDTO);
     }
+
+    @PostMapping("mails/company-termination-notification")
+    public void sendTerminationNotificationEmail(@Valid @RequestBody List<Long> companyIds) throws MessagingException {
+        List<CompanyDTO> companiesToNotify =  companyService.findCompaniesByIds(companyIds);
+        EmailAddresses addresses = this.applicationProperties.getEmailAddresses();
+        Context context = new Context();
+        final String baseUrl = ServletUriComponentsBuilder.fromCurrentContextPath().build().toUriString();
+        context.setVariable("baseUrl", baseUrl);
+        context.setVariable("companies", companiesToNotify);
+        String to = addresses.getLicenseAddress();
+        mailService.sendInternalEmailFromTemplate(MailType.TERMINATION_NOTIFICATION_EMAIL, "Licenses are about to expire.", to, context);
+
+        for (CompanyDTO company : companiesToNotify) {
+            if (company.getAdditionalInfo() == null) {
+                company.setAdditionalInfo(new CompanyAdditionalInfoDTO());
+            }
+
+            CompanyAdditionalInfoDTO additionalInfoDTO = company.getAdditionalInfo();
+
+            if (additionalInfoDTO.getLicense() == null) {
+                additionalInfoDTO.setLicense(new CompanyLicense());
+            }
+
+            CompanyLicense license = additionalInfoDTO.getLicense();
+
+            if (license.getTermination() == null) {
+                license.setTermination(new CompanyTermination());
+            }
+
+            CompanyTermination termination = license.getTermination();
+
+            termination.setHasBeenNotified(true);
+
+            CompanyVM companyVM = new CompanyVM();
+            companyVM.setId(company.getId());
+            companyVM.setName(company.getName());
+            companyVM.setDescription(company.getDescription());
+            companyVM.setCompanyType(company.getCompanyType());
+            companyVM.setLicenseType(company.getLicenseType());
+            companyVM.setLicenseModel(company.getLicenseModel());
+            companyVM.setLicenseStatus(company.getLicenseStatus());
+            companyVM.setBusinessContact(company.getBusinessContact());
+            companyVM.setLegalContact(company.getLegalContact());
+            companyVM.setCompanyDomains(company.getCompanyDomains());
+            companyVM.setAdditionalInfo(company.getAdditionalInfo());
+
+            companyService.updateCompany(companyVM);
+        }
+
+    }
 }
diff --git a/src/main/resources/templates/mail/terminationNotificationEmail.html b/src/main/resources/templates/mail/terminationNotificationEmail.html
@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html xmlns:th="http://www.thymeleaf.org" lang="en">
+<head>
+  <title>Termination Notification Email</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+</head>
+<body>
+  <p>The following companies licenses are about to expire.</p>
+  <table>
+    <thead>
+    <tr style="text-align: left">
+      <th>Name</th>
+      <th>Link to Company Page</th>
+    </tr>
+    </thead>
+    <tbody>
+    <tr th:each="company : ${companies}">
+      <td th:text="${company.name}"/>
+      <td>
+        <a th:with="url=(@{|${baseUrl}/companies/${company.id}|})" th:href="${url}">Company Page</a>
+      </td>
+    </tr>
+    </tbody>
+  </table>
+</body>
+</html>
diff --git a/src/main/webapp/app/components/newCompanyForm/NewCompanyForm.tsx b/src/main/webapp/app/components/newCompanyForm/NewCompanyForm.tsx
@@ -138,7 +138,7 @@ export class NewCompanyForm extends React.Component<INewCompanyFormProps> {
       <AvForm
         onValidSubmit={this.handleValidSubmit}
         onKeyPress={(event: any) => {
-          if (event.which === 13) {
+          if (event.which === 13 && event.target.type !== 'textarea') {
             event.preventDefault();
           }
         }}

diff --git a/src/main/webapp/app/config/constants.tsx b/src/main/webapp/app/config/constants.tsx
@@ -821,7 +821,7 @@ export type DataRelease = {
 };
 
 export const DATA_RELEASES: DataRelease[] = [
-  { date: '09192024', version: 'v4.21' },
+  { date: '09252024', version: 'v4.21' },
   { date: '08152024', version: 'v4.20' },
   { date: '07042024', version: 'v4.19' },
   { date: '07022024', version: 'v4.18' },

diff --git a/src/main/webapp/app/pages/apiAccessGroup/APIAccessPage.tsx b/src/main/webapp/app/pages/apiAccessGroup/APIAccessPage.tsx
@@ -30,7 +30,6 @@ import AuthenticationStore from 'app/store/AuthenticationStore';
 import { Linkout } from 'app/shared/links/Linkout';
 import { If, Then, Else } from 'react-if';
 import { getPageTitle } from 'app/shared/utils/Utils';
-import { has } from 'app/shared/utils/LodashUtils';
 import { Helmet } from 'react-helmet-async';
 
 type DownloadAvailabilityWithDate = DataRelease & DownloadAvailability;
@@ -109,7 +108,7 @@ export default class APIAccessPage extends React.Component<{
       // do not provide data on version 1
       return DATA_RELEASES.filter(
         release =>
-          has(availableVersions, release.version) &&
+          availableVersions[release.version] &&
           !release.version.startsWith('v1')
       ).reduce((acc, next) => {
         const currentVersionData: DownloadAvailability =

diff --git a/src/main/webapp/app/pages/companyPage/CompanyAdditionalInfo.tsx b/src/main/webapp/app/pages/companyPage/CompanyAdditionalInfo.tsx
@@ -111,6 +111,7 @@ export default function CompanyAdditionalInfo({
                       ...additionalInfo?.license,
                       termination: {
                         ...additionalInfo?.license?.termination,
+                        hasBeenNotified: false,
                         date: terminationDate?.toISOString(),
                         notificationDays:
                           additionalInfo?.license?.termination
@@ -145,6 +146,7 @@ export default function CompanyAdditionalInfo({
                           ...additionalInfo?.license,
                           termination: {
                             ...additionalInfo?.license?.termination,
+                            hasBeenNotified: false,
                             notificationDays: value
                               ? +value
                               : ((undefined as unknown) as number),

diff --git a/src/main/webapp/app/pages/companyPage/CompanyPage.tsx b/src/main/webapp/app/pages/companyPage/CompanyPage.tsx
@@ -670,7 +670,7 @@ export default class CompanyPage extends React.Component<ICompanyPage> {
                             this.editAllModeEnabled = false;
                             client
                               .getTerminationWarningEmailUsingGET({
-                                id: this.company.id,
+                                companyId: this.company.id,
                               })
                               .then(x => {
                                 this.sendTerminationNoticePayload = x;
@@ -698,7 +698,10 @@ export default class CompanyPage extends React.Component<ICompanyPage> {
                   <AvForm
                     onValidSubmit={this.onValidFormSubmit}
                     onKeyPress={(event: any) => {
-                      if (event.which === 13) {
+                      if (
+                        event.which === 13 &&
+                        event.target.type !== 'textarea'
+                      ) {
                         event.preventDefault();
                       }
                     }}