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Accounted for newly added role, allowing to create DBs
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@GuilhemSempere
GuilhemSempere committed Dec 20, 2024
1 parent 22fea54 commit 92ae770
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Showing 2 changed files with 13 additions and 9 deletions.
11 changes: 6 additions & 5 deletions src/main/java/fr/cirad/web/controller/gigwa/GigwaRestController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1851,6 +1851,7 @@ else if (filesByExtension.containsKey(fileExtension))
progress.setError("Uploaded data is larger than your allowed maximum (" + maxUploadSize + " Mb).");

boolean fAdminImporter = auth.getAuthorities().contains(new SimpleGrantedAuthority(IRoleDefinition.ROLE_ADMIN));
boolean fDbCreatorImporter = auth.getAuthorities().contains(new SimpleGrantedAuthority(IRoleDefinition.ROLE_DB_CREATOR));
boolean fAnonymousImporter = auth == null || "anonymousUser".equals(auth.getName());
if (progress.getError() == null) {
for (String uri : Arrays.asList(dataUri1, dataUri2, dataUri3))
Expand Down Expand Up @@ -2051,7 +2052,7 @@ else if (!writableDBs.contains(sNormalizedModule))
progress.moveToNextStep();

try { // create it
if (!fAdminImporter) { // only administrators may create permanent databases
if (!fAdminImporter && !fDbCreatorImporter) { // only administrators and DB creators may create permanent databases
expiryDate = System.currentTimeMillis() + 1000 * 60 * 60 * 24 /* 1 day */;
// expiryDate = System.currentTimeMillis() + 1000*60*5 /* 5 mn */;

Expand All @@ -2070,7 +2071,7 @@ else if (sHost == null || sHost.trim().length() == 0 && !MongoTemplateManager.ge
if (sHost == null || sHost.trim().length() == 0)
throw new Exception("No host was specified!");

if (MongoTemplateManager.saveOrUpdateDataSource(MongoTemplateManager.ModuleAction.CREATE, sNormalizedModule, !fAdminImporter, !fAdminImporter, sHost, ncbiTaxonIdNameAndSpecies, expiryDate)) {
if (MongoTemplateManager.saveOrUpdateDataSource(MongoTemplateManager.ModuleAction.CREATE, sNormalizedModule, !fAdminImporter && !fDbCreatorImporter, !fAdminImporter, sHost, ncbiTaxonIdNameAndSpecies, expiryDate)) {
LOG.info("Adding database " + sNormalizedModule + " to host " + sHost);
fDatasourceExists = true;
}
Expand Down Expand Up @@ -2294,8 +2295,8 @@ else if (MongoTemplateManager.removeDataSource(sNormalizedModule, true))
else if (!fDatasourceAlreadyExisted.get() && !fAnonymousImporter && !fAdminImporter) // a new permanent database was created so we give this user supervisor role on it
try {
UserWithMethod owner = (UserWithMethod) userDao.loadUserByUsername(auth.getName());
if (owner.getAuthorities() != null && (owner.getAuthorities().contains(new SimpleGrantedAuthority(IRoleDefinition.ROLE_ADMIN))))
return; // no need to grant any role to administrators
// if (owner.getAuthorities() != null && (owner.getAuthorities().contains(new SimpleGrantedAuthority(IRoleDefinition.ROLE_ADMIN))))
// return; // no need to grant any role to administrators

SimpleGrantedAuthority role = new SimpleGrantedAuthority(sModule + UserPermissionController.ROLE_STRING_SEPARATOR + IRoleDefinition.ROLE_DB_SUPERVISOR);
if (!owner.getAuthorities().contains(role)) {
Expand All @@ -2309,7 +2310,7 @@ else if (!fDatasourceAlreadyExisted.get() && !fAnonymousImporter && !fAdminImpor
tokenManager.reloadUserPermissions(securityContext);
}
catch (IOException e) {
LOG.error("Unable to give manager role to importer of project " + createdProjectId + " in database " + sModule);
LOG.error("Unable to give manager role to importer of project " + createdProjectId + " in database " + sModule, e);
}

if (scanner != null)
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11 changes: 7 additions & 4 deletions src/main/webapp/WEB-INF/jsp/import.jsp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
* Public License V3.
--%>
<!DOCTYPE html>
<%@ page language="java" contentType="text/html; charset=utf-8" import="fr.cirad.web.controller.ga4gh.Ga4ghRestController,fr.cirad.security.base.IRoleDefinition,fr.cirad.web.controller.gigwa.GigwaRestController,fr.cirad.io.brapi.BrapiService,org.brapi.v2.api.ServerinfoApi,org.brapi.v2.api.SamplesApi" %>
<%@ page language="java" contentType="text/html; charset=utf-8" import="fr.cirad.web.controller.ga4gh.Ga4ghRestController,fr.cirad.security.base.IRoleDefinition,org.springframework.security.core.context.SecurityContextHolder,fr.cirad.web.controller.gigwa.GigwaRestController,fr.cirad.io.brapi.BrapiService,org.brapi.v2.api.ServerinfoApi,org.brapi.v2.api.SamplesApi" %>
<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>
<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags" %>
Expand All @@ -28,6 +28,9 @@
<c:set var="appVersionNumber" value='<%= splittedAppVersion[0] %>' />
<c:set var="appVersionType" value='<%= splittedAppVersion.length > 1 ? splittedAppVersion[1] : "" %>' />
<c:set var="supervisorRoleSuffix" value='<%= "$" + IRoleDefinition.ROLE_DB_SUPERVISOR %>' />
<c:set var="loggedUser" value="<%=SecurityContextHolder.getContext().getAuthentication().getPrincipal()%>" />
<c:set var='dbCreatorRole' value='<%= IRoleDefinition.ROLE_DB_CREATOR %>' />
<c:set var="hasDbCreatorRole" value="false" /><c:forEach var="authority" items="${loggedUser.authorities}"><c:if test="${authority == dbCreatorRole}"><c:set var="hasDbCreatorRole" value="true" /></c:if></c:forEach>
<sec:authorize access="hasRole('ROLE_ADMIN')" var="isAdmin"/>
<sec:authorize access="hasRole('ROLE_ANONYMOUS')" var="isAnonymous"/>

Expand Down Expand Up @@ -75,7 +78,7 @@
var brapiGenotypesToken, distinctBrapiMetadataURLs;
var extRefIdField = "<%= BrapiService.BRAPI_FIELD_externalReferenceId %>";
var extRefSrcField = "<%= BrapiService.BRAPI_FIELD_externalReferenceSource %>";
var isAnonymous = ${isAnonymous}, isAdmin = ${isAdmin};
var isAnonymous = ${isAnonymous}, isAdmin = ${isAdmin}, hasDbCreatorRole = ${hasDbCreatorRole};
var supervisedModules = [];
<c:if test="${!isAnonymous}">
<sec:authentication property="principal.authorities" var="authorities" />
Expand Down Expand Up @@ -140,7 +143,7 @@
<input id="ploidy" name="ploidy" class="form-control text-input input-sm" type='number' step="1" min="1" placeholder="ploidy" title="Specifying ploidy is recommended for HapMap and Flapjack formats (if left blank, guessing will be attempted and import will take longer)">
</div>
<div class="col-md-3" id="newModuleDiv">
<input id="moduleToImport" name="module" class="form-control text-input input-sm" type='<c:choose><c:when test="${isAdmin}">text</c:when><c:otherwise>hidden</c:otherwise></c:choose>' placeholder="New database name">
<input id="moduleToImport" name="module" class="form-control text-input input-sm" type='<c:choose><c:when test="${isAdmin || hasDbCreatorRole}">text</c:when><c:otherwise>hidden</c:otherwise></c:choose>' placeholder="New database name">
</div>
</div>
</div>
Expand All @@ -152,7 +155,7 @@
<div class="col-md-3" id="hostDiv">
<select class="selectpicker" id="host" name="host" data-actions-box="true" data-width="100%" data-live-search="true"></select>
</div>
<c:if test="${!isAdmin}">
<c:if test="${!isAdmin && !hasDbCreatorRole}">
<div class="col-md-3 text-red row">
<div class="col-md-1 glyphicon glyphicon-warning-sign" style="font-size:20px;"></div>
<div class="col-md-10" style="font-size:10px; margin-top:-1px;">You may only create temporary databases</div>
Expand Down

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