Merge branch 'idc-test' of https://github.com/ImagingDataCommons/IDC-WebApp into idc-prod-sp

s-paquette · s-paquette · commit cb51848daafa · 2025-09-04T10:56:10.000-07:00
diff --git a/idc/settings.py b/idc/settings.py
@@ -159,12 +159,16 @@
             print("[ERROR] While trying to set local/developer git version: ")
             print(e)
             VERSION = "{}.{}.{}".format("local-dev", datetime.datetime.now().strftime('%Y%m%d%H%M'), "unavailable")
+    else:
+        print("[ERROR] Application version file not found for non-dev deployment! Exiting...")
+        exit(1)
 
 APP_VERSION = os.environ.get("APP_VERSION", VERSION)
 
 DEV_TIER = bool(DEBUG or re.search(r'^local-dev\.', APP_VERSION))
 
 print("[STATUS] DEV_TIER setting is {}".format(DEV_TIER))
+print("[STATUS] Application version is {}".format(APP_VERSION))
 
 # If this is a GAE-Flex deployment, we don't need to specify SSL; the proxy will take
 # care of that for us
diff --git a/shell/install-deps.sh b/shell/install-deps.sh
@@ -1,5 +1,5 @@
 if [ -n "$CI" ]; then
-    echo "Check our Python and Ubuntu versions since they keep getting updated without warning..."
+    echo "[STATUS] Check our Python and OS versions since they keep getting updated without warning..."
 
     ls -l /usr/bin/python3*
     cat /etc/os-release
@@ -14,7 +14,7 @@ if [ -n "$CI" ]; then
     elif [[ ${CIRCLE_BRANCH} == "expr" ]]; then
         COMMON_BRANCH=expr
     fi
-    echo "Cloning IDC-Common branch ${COMMON_BRANCH}..."
+    echo "[STATUS] Cloning IDC-Common branch ${COMMON_BRANCH}..."
     git clone -b ${COMMON_BRANCH} https://github.com/ImagingDataCommons/IDC-Common.git
 else
     if ( "/home/vagrant/www/shell/get_env.sh" ) ; then
@@ -35,7 +35,7 @@ find . -type f -name '*.pyc' -delete
 apt-get update -qq
 
 # Install and update apt-get info
-echo "Preparing System..."
+echo "[STATUS] Preparing System..."
 apt-get -y --force-yes install software-properties-common ca-certificates gnupg
 apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv B7B3B788A8D3785C
 wget "https://repo.mysql.com/mysql-apt-config_0.8.30-1_all.deb" -P /tmp
@@ -46,48 +46,48 @@ apt-get update -qq
 apt-get install mysql-client
 
 # Install apt-get dependencies
-echo "Installing Dependencies..."
+echo "[STATUS] Installing Dependencies..."
 apt-get install -y --force-yes unzip libffi-dev libssl-dev git g++ curl dos2unix pkg-config
 apt-get install -y --force-yes python3-distutils python3-mysqldb libmysqlclient-dev libpython3-dev build-essential
 apt-get install -y --force-yes python3-pip
 
-echo "Dependencies Installed"
+echo "[STATUS] Dependencies Installed"
 
 # If this is local development, clean out lib for a re-structuring 
 if [ -z "${CI}" ]; then
     # Clean out lib to prevent confusion over multiple builds in local development
     # and prep for local install
-    echo "Emptying out ${HOMEROOT}/lib/ ..."
+    echo "[STATUS] Emptying out ${HOMEROOT}/lib/ ..."
     rm -rf "${HOMEROOT}/lib/"
-    echo "Confirming clearance of lib:"
+    echo "[STATUS] Confirming clearance of lib:"
     ls ${HOMEROOT}/lib/
 fi
 
 # Install PIP + Dependencies
-echo "Installing pip3..."
+echo "[STATUS] Installing pip3..."
 curl --silent https://bootstrap.pypa.io/get-pip.py | python3
 
 # Install our primary python libraries
 # If we're not on CircleCI, or we are but the lib directory isn't there (cache miss), install lib
 if [ -z "${CI}" ] || [ ! -d "lib" ]; then
-    echo "Installing Python Libraries..."
+    echo "[STATUS] Installing Python Libraries..."
     pip install -r ${HOMEROOT}/requirements.txt -t ${HOMEROOT}/lib --upgrade --only-binary all
 else
-    echo "Using restored cache for Python Libraries"
+    echo "[STATUS] Using restored cache for Python Libraries"
 fi
 
 if [ -z "${CI}" ]; then
-    echo "Installing responses library for unit tests, but not for deployment..."
+    echo "[STATUS] Installing responses library for unit tests, but not for deployment..."
     pip install -q responses -t ${HOMEROOT}/lib --only-binary all
 fi
 
 if [ "$DEBUG" = "True" ] && [ "$DEBUG_TOOLBAR" = "True" ]; then
-    echo "Installing Django Debug Toolbar for local dev..."
+    echo "[STATUS] Installing Django Debug Toolbar for local dev..."
     pip install -q django-debug-toolbar==3.2.4 -t ${HOMEROOT}/lib --only-binary all
 fi
 
 if [ "$IS_DEV" = "True" ]; then
-    echo "Installing GitPython for local dev version display..."
+    echo "[STATUS] Installing GitPython for local dev version display..."
     pip install -q gitpython -t ${HOMEROOT}/lib --only-binary all
 fi
 
@@ -96,22 +96,22 @@ echo "Libraries Installed"
 # Install Google Cloud SDK
 # If we're not on CircleCI or we are but google-cloud-sdk isn't there, install it
 if [ -z "${CI}" ] || [ ! -d "/usr/lib/google-cloud-sdk" ]; then
-    echo "Installing Google Cloud SDK..."
+    echo "[STATUS] Installing Google Cloud SDK..."
     export CLOUDSDK_CORE_DISABLE_PROMPTS=1
     echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" | sudo tee -a /etc/apt/sources.list.d/google-cloud-sdk.list
     apt-get -y install apt-transport-https ca-certificates
     curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key --keyring /usr/share/keyrings/cloud.google.gpg add -
     apt-get update -qq
     apt-get -y install google-cloud-sdk
     apt-get -y install google-cloud-sdk-app-engine-python
-    echo "Google Cloud SDK Installed"
+    echo "[STATUS] Google Cloud SDK Installed"
 fi
 
 # Run dos2unix on the files in shell/ because of line terminator shenanigans with Windows
-echo "Running dos2unix on shell/*.sh..."
+echo "[STATUS] Running dos2unix on shell/*.sh..."
 dos2unix ${HOMEROOT}/shell/*.sh
 
-echo "Loading Git Hooks"
+echo "[STATUS] Loading Git Hooks"
 if [ -z "${CI}" ] && [ -d "${HOMEROOT}/git-hooks/" ]; then
     cp -r ${HOMEROOT}/git-hooks/* ${HOMEROOT}/.git/hooks/
 fi
@@ -123,5 +123,7 @@ if [ -n "${CI}" ]; then
     else
         TIER=${DEPLOYMENT_TIER,,}
     fi
-    echo "APP_VERSION=${TIER}.$(date '+%Y%m%d%H%M').${APP_SHA}" > ${HOMEROOT}/version.env
+    VERSION="${TIER}.$(date '+%Y%m%d%H%M').${APP_SHA}"
+    echo "[STATUS] Application version set to ${VERSION}"
+    echo "APP_VERSION=${VERSION}" > ${HOMEROOT}/version.env
 fi
diff --git a/static/css/search.css b/static/css/search.css
@@ -423,6 +423,14 @@ tr {
     width: 23.75%;
     word-wrap: break-word; }
 
+#cases_table td.narrow, #cases_table_head th.narrow {
+    width: 15%;
+    word-wrap: break-word; }
+
+#cases_table td.wide, #cases_table_head th.wide {
+    width: 28%;
+    word-wrap: break-word; }
+
 #studies_table_head th, #studies_table td {
     word-break: break-word; }
 
@@ -463,8 +471,11 @@ tr {
 }
 
 #studies_table_head th.download-col,
-#studies_table td.download-col {
+#studies_table td.download-col, #cases_table_head th.download-col,
+#cases_table td.download-col, #series_table_head th.download-col,
+#series_table td.download-col {
     width:6%;
+    min-width: 80px;
 }
 
 #series_table_head th, #series_table td {
diff --git a/static/css/style.css b/static/css/style.css
@@ -4522,6 +4522,11 @@ d-topics-list iframe {
   cursor: pointer;
 }
 
+.download-all-disabled {
+  cursor: not-allowed;
+  color: gray;
+}
+
 #floating-message {
   position: fixed;
   bottom: 50px;
diff --git a/static/js/downloader.js b/static/js/downloader.js
@@ -16,7 +16,7 @@
  *
  */
 
-// by @pieper 6/25/25
+// initial design by @pieper 6/25/25
 require.config({
     baseUrl: STATIC_FILES_URL + 'js/',
     paths: {
@@ -29,13 +29,20 @@ require([
     'base', 'jquery'
 ], function (base, $) {
 
-    const byte_level = {
+    const byte_level = Object.freeze({
         1: "KB",
         2: "MB",
         3: "GB",
         4: "TB",
         5: "PB"
-    };
+    });
+
+    const REQ_TYPE = Object.freeze({
+        COLLECTION: 1,
+        CASE: 2,
+        STUDY: 3,
+        SERIES: 4
+    });
 
     function size_display_string(size) {
         if(size <= 0) {
@@ -99,6 +106,7 @@ require([
     }
 
     class DownloadRequest {
+        request_type = REQ_TYPE.SERIES;
         region = "us-east-1";
 
         constructor(request) {
@@ -111,6 +119,20 @@ require([
             this.crdc_series_id = request['crdc_series_id'];
             this.directory = request['directory'];
             this.total_size = parseFloat(request['series_size']);
+
+            if(this.series_id) {
+                this.request_type = REQ_TYPE.SERIES;
+            } else if(this.study_id) {
+                this.request_type = REQ_TYPE.STUDY;
+            } else if(this.patient_id) {
+                this.request_type = REQ_TYPE.CASE;
+            } else {
+                this.request_type = REQ_TYPE.COLLECTION;
+            }
+        }
+
+        get request_type() {
+            return
         }
 
         async getAllS3ObjectKeys() {
@@ -181,7 +203,7 @@ require([
 
     class DownloadQueueManager {
         WORKING_QUEUE_LIMIT = 2000;
-        HOPPER_LIMIT = 500;
+        HOPPER_LIMIT = 4000;
 
         hopper = [];
         working_queue = [];
@@ -249,6 +271,7 @@ require([
         async _update_queue() {
             if(this.working_queue.length < this.WORKING_QUEUE_LIMIT && this.hopper.length > 0) {
                 let request = this.hopper.pop();
+                if(request)
                 await request.loadAllKeys().then(keys => {
                     this.working_queue.push(...keys);
                 });
diff --git a/static/js/tables.js b/static/js/tables.js
@@ -491,10 +491,10 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
             {className: "ckbx studyview","targets": [0]},
             {className: "ckbx shopping-cart-holder", "targets": [1]},
             {className: "ckbx cartnumholder", "targets":[2]},
-            {className: "col1 project-name", "targets": [3]},
+            {className: "col1 project-name wide", "targets": [3]},
             {className: "col1 case-id", "targets": [4]},
-            {className: "col1 numrows", "targets": [5]},
-            {className: "col1 numseries", "targets": [6]},
+            {className: "col1 numrows narrow", "targets": [5]},
+            {className: "col1 numseries narrow", "targets": [6]},
             {className: "col1 download-case download-col", "targets": [7]}];
     };
 
@@ -864,7 +864,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                     {className: "col1 numrows", "targets": [7]},
                     {className: "ohif open-viewer", "targets": [8]},
                     {className: "manifest-col", "targets": [9]},
-                    {className: "download-col", "targets": [10]},
+                    {className: "download-col download-study", "targets": [10]},
                 ],
                 "columns": [
                     {
@@ -1244,7 +1244,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                     {className: "series-description", "targets": [6]},
                     {className: "ohif open-viewer", "targets": [7]},
                     {className: "manifest-col", "targets": [8]},
-                    {className: "download-col", "targets": [9]}
+                    {className: "download-col download-series", "targets": [9]}
                  ],
                   "columns": [
                       {"type": "html", "orderable": false, render: function () {
diff --git a/templates/base.html b/templates/base.html
@@ -94,9 +94,6 @@
                 </div>
                 <div id="floating-message" style="display: none;">
                         <div class="alert alert-info alert-dismissible">
-                            <button type="button" class="close" data-dismiss="alert">
-                                <span aria-hidden="true">&times;</span><span class="sr-only">Close</span>
-                            </button>
                             <p class="floating-messages floating-message-header"></p>
                             <p><span class="floating-messages floating-message-content"></span>
                                 <i class="floating-message-icon floating-message-icon-download fa-solid fa-atom fa-spin"
diff --git a/templates/idc/explore.html b/templates/idc/explore.html
@@ -55,19 +55,6 @@
                     </div>
                 </div>
             </div>
-            <div class="row">
-                <div class="alert alert-warning alert-dismissible special-announcement">
-                    <button type="button" class="close" data-dismiss="alert">
-                        <span aria-hidden="true">&times;</span><span class="sr-only">Close</span>
-                    </button>
-                    We have removed user accounts from our system. If you would like to provide feedback on this
-                    decision or need help accessing your previously saved cohorts, please visit us at our
-                    <a class="external-link" href="" url="https://discourse.canceridc.dev/t/idc-portal-sign-in-feature-deprecation/723"
-                         title="IDC Discourse Forum" data-toggle="modal" data-target="#external-web-warning">
-                        Discourse topic <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                    </a>.
-                </div>
-            </div>
             <h3 class="pull-left" role="heading" aria-level="1">Explore Image Data </h3>
 {#            {% if request.user.is_authenticated %}#}
 {#            <button id="save-cohort-btn" class="btn btn-special pull-right" data-toggle="modal"#}
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
@@ -864,11 +864,11 @@ <h4 class="panel-title">
                                             </th>
                                             <th class="ckbx cart-info"><i class="fa-solid fa-info-circle cart-info-icon"></i></th>
                                             <th class="ckbx cartnumholder"># of Series in Cart</th>
-                                            <th class="text_data">Collection Name</th>
+                                            <th class="text_data wide">Collection Name</th>
                                             <th class="text_data">Case ID <i class="fas fa-info-circle case-info"></i></th>
-                                            <th class="numeric_data">Total # of Studies</th>
-                                            <th class="numeric_data">Total # of Series</th>
-                                            <th class="download-case"></th>
+                                            <th class="numeric_data narrow">Total # of Studies</th>
+                                            <th class="numeric_data narrow">Total # of Series</th>
+                                            <th class="download-case download-col"></th>
                                         </tr>
                                         </thead>
                                     </table>
@@ -895,7 +895,7 @@ <h4 class="panel-title">
                                             <th class="col1 numrows numeric_data table-count"># of Series</th>
                                             <th class="ohif text_data open-viewer">View</th>
                                             <th class="manifest-col"></th>
-                                            <th class="download-col"></th>
+                                            <th class="download-col download-study"></th>
                                         </tr>
                                         </thead>
                                     </table>
@@ -917,9 +917,8 @@ <h4 class="panel-title">
                                             <th class="body-part-examined">Body Part Examined</th>
                                             <th class="series-description">Series Description</th>
                                             <th class="open-viewer text_data">View</th>
-                                            <th class="series-citations"></th>
                                             <th class="download-manifest"></th>
-                                            <th class="download-files"></th>
+                                            <th class="download-files dowbload-series download-col"></th>
                                         </tr>
                                         </thead>
                                     </table>
diff --git a/templates/idc/landing.html b/templates/idc/landing.html
@@ -45,19 +45,6 @@
                 </div>
             </div>
         </div>
-        <div class="row">
-            <div class="alert alert-warning alert-dismissible special-announcement">
-                <button type="button" class="close" data-dismiss="alert">
-                    <span aria-hidden="true">&times;</span><span class="sr-only">Close</span>
-                </button>
-                We have removed user accounts from our system. If you would like to provide feedback on this
-                decision or need help accessing your previously saved cohorts, please visit us at our
-                <a class="external-link" href="" url="https://discourse.canceridc.dev/t/idc-portal-sign-in-feature-deprecation/723"
-                     title="IDC Discourse Forum" data-toggle="modal" data-target="#external-web-warning">
-                    Discourse topic <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                </a>.
-            </div>
-        </div>
         <div class="buttons row">
             <div class="container-fluid">
             <div class="col-lg-12 col-md-12 col-sm-12 buttons-col">
