[EEG] EEG uploader module

SQL/0000-00-01-Modules.sql

@@ -51,5 +51,6 @@ INSERT INTO modules (Name, Active) VALUES ('timepoint_list', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('user_accounts', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('electrophysiology_browser', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('dqt', 'Y');
+INSERT INTO modules (Name, Active) VALUES ('electrophysiology_uploader', 'Y');
 
 ALTER TABLE issues ADD CONSTRAINT `fk_issues_7` FOREIGN KEY (`module`) REFERENCES `modules` (`ID`);

SQL/0000-00-03-ConfigTables.sql

@@ -78,6 +78,8 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MINCToolsPath', 'Path to the MINC tools', 1, 0, 'web_path', ID, 'Path to the MINC tools', 12 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'documentRepositoryPath', 'Path to uploaded document repository files', 1, 0, 'web_path', ID, 'Document Repository Upload Path', 13 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataReleasePath', 'Path to uploaded data release files', 1, 0, 'web_path', ID, 'Data release Upload Path', 14 FROM ConfigSettings WHERE Name="paths";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EEGUploadIncomingPath', 'Path to the upload directory for incoming EEG studies', 1, 0, 'text', ID, 'EEG Incoming Directory', 7 FROM ConfigSettings WHERE Name="paths";
+
 
 
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('gui', 'Settings related to the overall display of LORIS', 1, 0, 'GUI', 3);
@@ -289,4 +291,4 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, ''  FROM ConfigSettings WHERE Na
 INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_dataset_authors';
 INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_acknowledgments_text';
 INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_readme_text';
-INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_validator_options_to_ignore';
+INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_validator_options_to_ignore';

SQL/0000-00-05-ElectrophysiologyTables.sql

@@ -481,6 +481,21 @@ CREATE TABLE `physiological_annotation_rel` (
         REFERENCES `physiological_annotation_file` (`AnnotationFileID`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
+-- Create EEG upload table
+CREATE TABLE `electrophysiology_uploader` (
+    `UploadID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+    `UploadedBy` varchar(255) NOT NULL DEFAULT '',
+    `UploadDate` DateTime DEFAULT NULL,
+    `UploadLocation` varchar(255) NOT NULL DEFAULT '',
+    `Status` enum('Not Started', 'In Progress', 'Complete', 'Failed') DEFAULT 'Not Started',
+    `SessionID` int(10) unsigned NOT NULL default '0',
+    `MetaData` TEXT default NULL,
+    PRIMARY KEY (`UploadID`),
+    KEY (`SessionID`),
+    CONSTRAINT `FK_eegupload_SessionID`
+        FOREIGN KEY (`SessionID`) REFERENCES `session` (`ID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
 -- Insert into physiological_output_type
 INSERT INTO physiological_output_type
   (`OutputTypeName`, `OutputTypeDescription`)

SQL/New_patches/2023-02-24-electrophysiology_uploader.sql

@@ -0,0 +1,21 @@
+-- Create EEG upload table
+CREATE TABLE `electrophysiology_uploader` (
+    `UploadID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+    `UploadedBy` varchar(255) NOT NULL DEFAULT '',
+    `UploadDate` DateTime DEFAULT NULL,
+    `UploadLocation` varchar(255) NOT NULL DEFAULT '',
+    `Status` enum('Not Started', 'In Progress', 'Complete', 'Failed') DEFAULT 'Not Started',
+    `SessionID` int(10) unsigned NOT NULL default '0',
+    `MetaData` TEXT default NULL,
+    PRIMARY KEY (`UploadID`),
+    KEY (`SessionID`),
+    CONSTRAINT `FK_eegupload_SessionID`
+        FOREIGN KEY (`SessionID`) REFERENCES `session` (`ID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+-- Add to module table
+INSERT INTO modules (Name, Active) VALUES ('electrophysiology_uploader', 'Y');
+
+-- Add new configurations for eeg uploader
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'EEGUploadIncomingPath', 'Path to the upload directory for incoming EEG studies', 1, 0, 'text', ID, 'EEG Incoming Directory', 7 FROM ConfigSettings WHERE Name="paths";
+

modules/electrophysiology_uploader/.gitignore

@@ -0,0 +1 @@
+js/*

modules/electrophysiology_uploader/jsx/ElectrophysiologyUploader.js

@@ -0,0 +1,92 @@
+import {useState, useEffect} from 'react';
+import PropTypes from 'prop-types';
+import Loader from 'jsx/Loader';
+import {TabPane, Tabs} from 'jsx/Tabs';
+import UploadForm from './UploadForm';
+import UploadViewer from './UploadViewer';
+import {createRoot} from 'react-dom/client';
+
+/**
+ * UploadViewer
+ *
+ * @param {array} props
+ * @return {JSX}
+ */
+export default function ElectrophysiologyUploader(props) {
+  const [isLoaded, setIsLoaded] = useState(false);
+  const [data, setData] = useState({});
+
+  /**
+   * Called by React when the component has been rendered on the page.
+   */
+  useEffect(() => {
+    fetchData();
+  }, []);
+
+  /**
+   * Retrive data from the provided URL and save it in state
+   * Additionaly add hiddenHeaders to global loris vairable
+   * for easy access by columnFormatter.
+   */
+  const fetchData = () => {
+    fetch(`${props.DataURL}/?format=json`, {
+      method: 'GET',
+    }).then((response) => {
+      if (!response.ok) {
+        console.error(response.status + ': ' + response.statusText);
+        return;
+      }
+
+      response.json().then((data) => {
+        setData(data);
+        setIsLoaded(true);
+      });
+    }).catch((error) => {
+      console.error(error);
+    });
+  };
+
+  if (!isLoaded) {
+    return <Loader />;
+  }
+
+  const tabList = [
+    {id: 'browse', label: 'Browse'},
+    {id: 'upload', label: 'Upload'},
+  ];
+
+  return (
+    <Tabs tabs={tabList} defaultTab='browse' updateURL={true}>
+      <TabPane TabId={tabList[0].id}>
+        <UploadViewer
+          data={data.Data}
+          fieldOptions={data.fieldOptions}
+        />
+      </TabPane>
+      <TabPane TabId={tabList[1].id}>
+        <UploadForm
+          uploadURL={`${props.DataURL}/upload`}
+        />
+      </TabPane>
+    </Tabs>
+  );
+}
+
+ElectrophysiologyUploader.propTypes = {
+  DataURL: PropTypes.string.isRequired,
+};
+
+/**
+ * Render imaging_uploader on page load
+ */
+document.addEventListener('DOMContentLoaded', function() {
+  const root = createRoot(
+    document.getElementById('lorisworkspace')
+  );
+  root.render(
+    <ElectrophysiologyUploader
+      Module='imaging_uploader'
+      DataURL={loris.BaseURL + '/electrophysiology_uploader'}
+    />
+  );
+});