From e1e591a6365190a0ac7cf705d0d7bc38385f8dbc Mon Sep 17 00:00:00 2001
From: suliciac <lluciacoll.llu@gmail.com>
Date: Mon, 31 Mar 2025 10:36:43 +0200
Subject: [PATCH 1/3] remove openneuro button/upload; work without ethernet
 connection

---
 ui/src/Finalize.vue | 45 ---------------------------------------------
 1 file changed, 45 deletions(-)

diff --git a/ui/src/Finalize.vue b/ui/src/Finalize.vue
index 9cf32e0b..33b94740 100755
--- a/ui/src/Finalize.vue
+++ b/ui/src/Finalize.vue
@@ -45,24 +45,6 @@
                 <el-button style="width: 250px" type="primary" @click="download(`ezBIDS_template.json`)"
                     >Download configuration/template</el-button
                 >
-                <p>Or send the dataset to other cloud resources.</p>
-                <p>
-                    <el-dropdown v-if="hasAuth">
-                        <el-button style="margin-right: 10px">
-                            Send to <b>Brainlife.io</b>&nbsp;
-                            <font-awesome-icon :icon="['fas', 'angle-down']" />
-                        </el-button>
-                        <template #dropdown>
-                            <el-dropdown-menu>
-                                <el-dropdown-item @click="sendBrainlife()">Send to brainlife</el-dropdown-item>
-                                <el-dropdown-item @click="sendBrainlife('DWI')"
-                                    >Send to brainlife and run DWI Pipeline</el-dropdown-item
-                                >
-                            </el-dropdown-menu>
-                        </template>
-                    </el-dropdown>
-                    <el-button @click="sendOpenneuro">Send to <b>OpenNeuro</b></el-button>
-                </p>
 
                 <p style="background-color: #0001; padding: 20px; padding-top: 10px">
                     If you have re-named the original DICOM patient names for your BIDS subject/session names, you can
@@ -256,33 +238,6 @@ export default defineComponent({
             URL.revokeObjectURL(link.href);
         },
 
-        sendBrainlife(pipeline?: 'DWI') {
-            const pipelineString = pipeline ? `&pipeline=${pipeline}` : '';
-            window.open(
-                `https://brainlife.io/projects#ezbids=${this.session._id}${pipelineString}`,
-                `_brainlife.${this.session._id}`
-            );
-        },
-
-        async sendOpenneuro() {
-            try {
-                const res = await axios.get(`${this.config.apihost}/download/${this.session._id}/token`);
-                const shortLivedJWT = res.data;
-
-                const url = `${this.config.apihost}/download/${this.session._id}/bids/${this.ezbids.datasetDescription.Name}?token=${shortLivedJWT}`;
-
-                const fullurl = new URL(url, document.baseURI).href;
-                window.open('https://openneuro.org/import?url=' + encodeURI(fullurl));
-
-            } catch (e) {
-                console.error(e);
-                ElNotification({
-                    message: 'there was an error downloading the data',
-                    type: 'error',
-                });
-            }
-        },
-
         isValid(cb: (err?: string) => void) {
             if (this.session.status != 'finished') return cb('Please finalize the page first');
             cb();

From 72485a10f0dc0eefbee0231126a68fe29c6a866c Mon Sep 17 00:00:00 2001
From: suliciac <lluciacoll.llu@gmail.com>
Date: Wed, 2 Apr 2025 12:26:57 +0200
Subject: [PATCH 2/3] add upload from terminal file; extra software
 requirement: jq

---
 ezbids-upload.sh | 50 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100755 ezbids-upload.sh

diff --git a/ezbids-upload.sh b/ezbids-upload.sh
new file mode 100755
index 00000000..c5c871a6
--- /dev/null
+++ b/ezbids-upload.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+FOLDER=$1
+SESSION=$2
+
+API_URL="http://localhost:8082"
+UI_URL="http://localhost:3000/ezbids/convert"
+
+
+if [ ! -z "$FOLDER" ]; then
+    cd $FOLDER
+fi
+
+if [ -z "$SESSION" ]; then
+    SESSION=$(
+        curl "$API_URL/session" \
+            -X "POST" \
+            -H "Content-Type: application/json" | jq -r '._id'
+    )
+    # DEBUG line 
+    echo "DEBUG: Session ID is '$SESSION'"
+fi
+
+
+echo ""
+echo "Session ID: $SESSION"
+echo ""
+
+
+FOLDER_NAME=$(basename `pwd`)
+
+echo "Uploading `pwd`"
+#for file in $(find * -type f); do
+find * -type f | while IFS= read -r file; do
+    echo "Uploading $file"
+    curl "$API_URL/upload-multi/$SESSION" \
+        -H "Authorization: Bearer ${bearerToken}" \
+        -F "paths=$FOLDER_NAME/$file" \
+        -F "mtimes=1706756151" \
+        -F "files=@$file"
+    echo
+done
+
+
+echo "Marking as done"
+curl "$API_URL/session/uploaded/$SESSION" \
+  -X 'PATCH'
+
+echo ""
+echo "$UI_URL/#$SESSION"

From 8dd7488774b4a8e095eed09372cfbf24bc53f0b1 Mon Sep 17 00:00:00 2001
From: suliciac <lluciacoll.llu@gmail.com>
Date: Tue, 8 Apr 2025 15:24:44 +0200
Subject: [PATCH 3/3] upload from terminal file

---
 ezbids-upload.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/ezbids-upload.sh b/ezbids-upload.sh
index c5c871a6..13c77830 100755
--- a/ezbids-upload.sh
+++ b/ezbids-upload.sh
@@ -17,8 +17,6 @@ if [ -z "$SESSION" ]; then
             -X "POST" \
             -H "Content-Type: application/json" | jq -r '._id'
     )
-    # DEBUG line 
-    echo "DEBUG: Session ID is '$SESSION'"
 fi