[publication] Add columns to publications

SQL/0000-00-00-schema.sql

@@ -890,7 +890,7 @@ CREATE TABLE `mri_violations_log` (
   PRIMARY KEY (`LogID`),
   CONSTRAINT `FK_tarchive_mriViolationsLog_1`
     FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` (`TarchiveID`),
-  CONSTRAINT `FK_mri_checks_group_1` 
+  CONSTRAINT `FK_mri_checks_group_1`
     FOREIGN KEY (`MriProtocolChecksGroupID`) REFERENCES `mri_protocol_checks_group` (`MriProtocolChecksGroupID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
@@ -2156,6 +2156,13 @@ CREATE TABLE `publication` (
     `Title` varchar(255) NOT NULL,
     `RejectedReason` varchar(255) default NULL,
     `Description` text NOT NULL,
+    `journal` varchar(255) DEFAULT NULL,
+    `doi` text DEFAULT NULL,
+    `datePublication` date DEFAULT NULL,
+    `link` varchar(255) DEFAULT NULL,
+    `publishingStatus` enum('In Progress','Published') DEFAULT NULL,
+    `project` int(10) unsigned DEFAULT NULL,
+    CONSTRAINT `FK_publication_project` FOREIGN KEY (project) REFERENCES Project(ProjectID),
     CONSTRAINT `PK_publication` PRIMARY KEY(`PublicationID`),
     CONSTRAINT `FK_publication_UserID` FOREIGN KEY(`UserID`) REFERENCES `users` (`ID`),
     CONSTRAINT `FK_publication_RatedBy` FOREIGN KEY(`RatedBy`) REFERENCES `users` (`ID`),

SQL/Cleanup_patches/2021-03-01-publication-add-columns.sql

@@ -0,0 +1,9 @@
+ALTER TABLE publication
+    ADD COLUMN journal varchar(255) DEFAULT NULL,
+    ADD COLUMN doi text DEFAULT NULL,
+    ADD COLUMN datePublication date DEFAULT NULL,
+    ADD COLUMN link varchar(255) DEFAULT NULL,
+    ADD COLUMN publishingStatus enum('In Progress','Published') DEFAULT NULL,
+    ADD COLUMN project int(10) unsigned DEFAULT NULL,
+    ADD CONSTRAINT `FK_publication_project`
+    FOREIGN KEY (project) REFERENCES Project(ProjectID);

modules/publication/ajax/FileUpload.php

@@ -57,8 +57,14 @@ function uploadPublication() : void
     if ($exists) {
         showPublicationError('Submitted title already exists', 400);
     }
-    $desc            = $_POST['description'] ?? null;
-    $leadInvest      = $_POST['leadInvestigator'] ?? null;
+    $desc    = $_POST['description'] ?? null;
+    $project = $_POST['project'] ?? null;
+    $publishingStatus = $_POST['publishingStatus'] ?? null;
+    $datePublication  = $_POST['datePublication'] ?? null;
+    $journal          = $_POST['journal'] ?? null;
+    $doi        = $_POST['doi'] ?? null;
+    $link       = $_POST['link'] ?? null;
+    $leadInvest = $_POST['leadInvestigator'] ?? null;
     $leadInvestEmail = $_POST['leadInvestigatorEmail'] ?? null;
 
     // check if lead investigator already exists in collaborator table
@@ -68,8 +74,8 @@ function uploadPublication() : void
         'FROM publication_collaborator '.
         'WHERE Name = :n OR Email = :e',
         [
-            'n' => $leadInvest,
             'e' => $leadInvestEmail,
+            'n' => $leadInvest,
         ]
     );
     if (empty($leadInvID)) {
@@ -94,6 +100,12 @@ function uploadPublication() : void
         'UserID'             => $uid,
         'Title'              => $title,
         'Description'        => $desc,
+        'project'            => $project,
+        'publishingStatus'   => $publishingStatus,
+        'datePublication'    => $datePublication,
+        'journal'            => $journal,
+        'doi'                => $doi,
+        'link'               => $link,
         'LeadInvestigatorID' => $leadInvID,
         'DateProposed'       => $today,
     ];
@@ -513,7 +525,13 @@ function editProject() : void
     $statusID         = $_POST['status'] ?? null;
     $rejectedReason   = $_POST['rejectedReason'] ?? null;
     $description      = $_POST['description'] ?? null;
-    $leadInvestigator = $_POST['leadInvestigator'] ?? null;
+    $project          = $_POST['project'] ?? null;
+    $publishingStatus = $_POST['publishingStatus'] ?? null;
+    $datePublication  = $_POST['datePublication'] ?? null;
+    $journal          = $_POST['journal'] ?? null;
+    $doi  = $_POST['doi'] ?? null;
+    $link = $_POST['link'] ?? null;
+    $leadInvestigator      = $_POST['leadInvestigator'] ?? null;
     $leadInvestigatorEmail = $_POST['leadInvestigatorEmail'] ?? null;
 
     $pubData = $db->pselectRow(
@@ -546,6 +564,24 @@ function editProject() : void
     if ($pubData['Description'] !== $description) {
         $toUpdate['Description'] = $description;
     }
+    if ($pubData['project'] !== $project) {
+        $toUpdate['project'] = $project;
+    }
+    if ($pubData['publishingStatus'] !== $publishingStatus) {
+        $toUpdate['publishingStatus'] = $publishingStatus;
+    }
+    if ($pubData['datePublication'] !== $datePublication) {
+        $toUpdate['datePublication'] = $datePublication;
+    }
+    if ($pubData['journal'] !== $journal) {
+        $toUpdate['journal'] = $journal;
+    }
+    if ($pubData['doi'] !== $doi) {
+        $toUpdate['doi'] = $doi;
+    }
+    if ($pubData['link'] !== $link) {
+        $toUpdate['link'] = $link;
+    }
     if ($pubData['LeadInvestigator'] !== $leadInvestigator) {
         $leadInvToUpdate['Name'] = $leadInvestigator;
     }

modules/publication/ajax/getData.php

@@ -65,6 +65,16 @@ function getData($db) : array
         []
     );
 
+    $rawProject = $db->pselect(
+        'SELECT ProjectID, Name FROM Project',
+        []
+    );
+
+    $projectOptions = [];
+    foreach ($rawProject as $dataProject) {
+        $projectOptions[$dataProject['ProjectID']] = $dataProject['Name'];
+    }
+
     // merge variables and test names into one array
     $bvlVOIs = array_merge(
         array_column($bvlVOIs, 'Name'),
@@ -78,11 +88,11 @@ function getData($db) : array
 
     // imaging VoIs -- filter out non-human readable DICOM tags
     $imgVOIs = $db->pselectCol(
-        "SELECT DISTINCT p.Name FROM parameter_type p 
-         JOIN parameter_type_category_rel ptcr 
-         ON p.ParameterTypeID=ptcr.ParameterTypeID 
-         JOIN parameter_type_category ptc 
-         ON ptc.ParameterTypeCategoryID=ptcr.ParameterTypeCategoryID 
+        "SELECT DISTINCT p.Name FROM parameter_type p
+         JOIN parameter_type_category_rel ptcr
+         ON p.ParameterTypeID=ptcr.ParameterTypeID
+         JOIN parameter_type_category ptc
+         ON ptc.ParameterTypeCategoryID=ptcr.ParameterTypeCategoryID
          WHERE ptc.Name='MRI Variables'",
         []
     );
@@ -112,6 +122,7 @@ function getData($db) : array
     );
     $collabs = array_combine($collabs, $collabs);
 
+    $data['projectOptions'] = $projectOptions;
     $data['users']          = $users;
     $data['uploadTypes']    = getUploadTypes();
     $data['existingTitles'] = $titles;
@@ -132,12 +143,15 @@ function getData($db) : array
  */
 function getProjectData($db, $user, $id) : array
 {
-    $query  = 'SELECT Title, Description, DateProposed, '.
+    $query  = 'SELECT Title, Description, pr.Name as project, datePublication, '.
+        'journal, link, publishingStatus, DateProposed, '.
         'pc.Name as LeadInvestigator, pc.Email as LeadInvestigatorEmail, '.
         'PublicationStatusID, UserID, RejectedReason  '.
         'FROM publication p '.
         'LEFT JOIN publication_collaborator pc '.
         'ON p.LeadInvestigatorID = pc.PublicationCollaboratorID '.
+        'LEFT JOIN Project pr '.
+        'ON p.project = pr.ProjectID '.
         'WHERE p.PublicationID=:pid ';
     $result = $db->pselectRow(
         $query,
@@ -167,13 +181,22 @@ function getProjectData($db, $user, $id) : array
 
         $usersWithEditPerm = $userIDs;
 
-        $title          = htmlspecialchars_decode($result['Title']);
-        $description    = htmlspecialchars_decode($result['Description']);
-        $rejectedReason = htmlspecialchars_decode($result['RejectedReason']);
+        $title           = htmlspecialchars_decode($result['Title']);
+        $description     = htmlspecialchars_decode($result['Description']);
+        $datePublication = htmlspecialchars_decode($result['datePublication']);
+        $journal         = htmlspecialchars_decode($result['journal']);
+        $link            = htmlspecialchars_decode($result['link']);
+        $publishingStatus = htmlspecialchars_decode($result['publishingStatus']);
+        $rejectedReason   = htmlspecialchars_decode($result['RejectedReason']);
 
         $pubData = [
             'title'                 => $title,
             'description'           => $description,
+            'project'               => $result['project'],
+            'datePublication'       => $datePublication,
+            'journal'               => $journal,
+            'link'                  => $link,
+            'publishingStatus'      => $publishingStatus,
             'leadInvestigator'      => $result['LeadInvestigator'],
             'leadInvestigatorEmail' => $result['LeadInvestigatorEmail'],
             'status'                => $result['PublicationStatusID'],

modules/publication/jsx/projectFields.js

@@ -381,6 +381,11 @@ class ProjectFormFields extends React.Component {
       Imaging: 'Imaging',
     };
 
+    const publishingStatusOptions = {
+      'In Progress': 'In progress',
+      'Published': 'Published',
+    };
+
     const allVOIs = this.props.allVOIs;
     let voiOptions = {};
     let type = this.props.formData.voiType;
@@ -392,6 +397,8 @@ class ProjectFormFields extends React.Component {
       voiOptions = Object.assign(bvlCopy, allVOIs.Imaging);
     }
 
+    const published = this.props.formData.publishingStatus==='Published';
+
     return (
       <div>
         <TextareaElement
@@ -401,6 +408,56 @@ class ProjectFormFields extends React.Component {
           required={true}
           value={this.props.formData.description}
         />
+        <SelectElement
+          name="project"
+          label="Project"
+          options={this.props.projectOptions}
+          onUserInput={this.props.setFormData}
+          required={true}
+          value={this.props.formData.project}
+          emptyOption={true}
+        />
+        <SelectElement
+          name="publishingStatus"
+          label="Publishing status"
+          options={publishingStatusOptions}
+          onUserInput={this.props.setFormData}
+          required={true}
+          value={this.props.formData.publishingStatus}
+          emptyOption={true}
+        />
+        <DateElement
+          name="datePublication"
+          label="Date published"
+          onUserInput={this.props.setFormData}
+          required={published}
+          value={this.props.formData.datePublication}
+          disabled={!published}
+        />
+        <TextboxElement
+          name="journal"
+          label="Journal"
+          onUserInput={this.props.setFormData}
+          required={published}
+          value={this.props.formData.journal}
+          disabled={!published}
+        />
+        <TextboxElement
+          name="doi"
+          label="DOI"
+          onUserInput={this.props.setFormData}
+          required={false}
+          value={this.props.formData.doi}
+          disabled={!published}
+        />
+        <TextboxElement
+          name="link"
+          label="Link"
+          onUserInput={this.props.setFormData}
+          required={published}
+          value={this.props.formData.link}
+          disabled={!published}
+        />
         <TextboxElement
           name="leadInvestigator"
           label="Lead Investigator"

modules/publication/jsx/uploadForm.js

@@ -266,6 +266,7 @@ class PublicationUploadForm extends React.Component {
               removeListItem={this.removeListItem}
               toggleEmailNotify={this.toggleEmailNotify}
               uploadTypes={this.state.Data.uploadTypes}
+              projectOptions={this.state.Data.projectOptions}
               users={this.state.Data.users}
               allVOIs={this.state.Data.allVOIs}
               allKWs={this.state.Data.allKWs}

modules/publication/jsx/viewProject.js

@@ -100,6 +100,11 @@ class ViewProject extends React.Component {
           let formData = {
             title: data.title,
             description: data.description,
+            project: data.project,
+            publishingStatus: data.publishingStatus,
+            datePublication: data.datePublication,
+            journal: data.journal,
+            link: data.link,
             leadInvestigator: data.leadInvestigator,
             leadInvestigatorEmail: data.leadInvestigatorEmail,
             notifyLead: false,
@@ -131,6 +136,7 @@ class ViewProject extends React.Component {
 
           this.setState({
             formData: formData,
+            projectOptions: data.projectOptions,
             users: data.users,
             statusOpts: data.statusOpts,
             userCanEdit: data.userCanEdit,
@@ -283,6 +289,31 @@ class ViewProject extends React.Component {
           label="Description"
           text={this.state.formData.description}
         />
+        <StaticElement
+          name="project"
+          label="Project"
+          text={this.state.formData.project}
+        />
+        <StaticElement
+          name="publishingStatus"
+          label="Publishing status"
+          text={this.state.formData.publishingStatus}
+        />
+        <StaticElement
+          name="datePublication"
+          label="Date published"
+          text={this.state.formData.datePublication}
+        />
+        <StaticElement
+          name="journal"
+          label="Journal"
+          text={this.state.formData.journal}
+        />
+        <StaticElement
+          name="link"
+          label="Link"
+          text={this.state.formData.link}
+        />
         <StaticElement
           name="leadInvestigator"
           label="Lead Investigator"
@@ -319,6 +350,7 @@ class ViewProject extends React.Component {
           removeListItem={this.removeListItem}
           toggleEmailNotify={this.toggleEmailNotify}
           uploadTypes={this.state.uploadTypes}
+          projectOptions={this.state.projectOptions}
           users={this.state.users}
           allVOIs={this.state.allVOIs}
           allKWs={this.state.allKWs}