Merge pull request #207 from brain-image-library/feature/metadata-version

Feature/metadata version

Author: ltuite96

ingest/migrations/0014_metadataversion.py

@@ -0,0 +1,26 @@
+# Generated by Django 3.2.13 on 2022-07-20 18:30
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ingest', '0013_alter_dataset_abstract'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='MetadataVersion',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('metadata_version', models.CharField(blank=True, max_length=64, null=True)),
+                ('dataset_doi', models.CharField(blank=True, max_length=512, null=True)),
+                ('dataset_status', models.CharField(blank=True, max_length=256, null=True)),
+                ('dataset_id_dm', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='ingest.descriptivemetadata')),
+                ('dataset_id_ds', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='ingest.dataset')),
+                ('event', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='ingest.eventslog')),
+            ],
+        ),
+    ]

ingest/models.py

@@ -318,6 +318,7 @@ class EventsLog(models.Model):
     project_id = models.ForeignKey(Project, on_delete=models.SET_NULL, null = True, blank=True)
     notes = models.CharField(max_length=256)
     timestamp = models.DateTimeField()
+    #Add field for embargo information
     event_type = models.CharField(max_length=64, default="", choices=[('mail_tapes_to_bil', 'Mail Tapes To BIL'), ('tapes_received', 'Tapes Received'), ('tapes_ready_for_qc', 'Tapes Ready For QC'), ('move_to_collection', 'Move To Collection'), ('request_brainball', 'Request Brainball'), ('Mail_brainball_from_bil', 'Mail Brainball From BIL'), ('mail_brainball_to_bil', 'Mail Brainball To BIL'), ('received_brainball', 'Received Brainball'), ('collection_created', 'Collection Created'), ('metadata_uploaded', 'Metadata Uploaded'), ('request_validation', 'Request Validation'), ('request_submission', 'Request Submission'), ('request_embargo', 'Request Embargo'), ('collection_public', 'Collection Public'), ('request_withdrawal', 'Request Withdrawal'), ('data_curated', 'Data Curated'), ('collection_validated', 'Collected Validated'), ('user_action_required', 'User Action Required'),])
 
 class Contributor(models.Model):
@@ -423,3 +424,12 @@ class Instrument(models.Model):
     data_set = models.ForeignKey(Dataset, on_delete=models.SET_NULL, blank=True, null=True)
     specimen = models.ForeignKey(Specimen, on_delete=models.SET_NULL, blank=True, null=True)
 
+class MetadataVersion(models.Model):
+    dataset_id_dm = models.ForeignKey(DescriptiveMetadata, on_delete = models.SET_NULL, blank = True, null = True)
+    dataset_id_ds = models.ForeignKey(Dataset, on_delete=models.SET_NULL, blank=True, null=True)
+    metadata_version = models.CharField(max_length=64, blank=True, null=True)
+    dataset_doi = models.CharField(max_length=512, blank=True, null=True)
+    dataset_status= models.CharField(max_length=256, blank=True, null=True)
+    event = models.ForeignKey(EventsLog, on_delete=models.SET_NULL, blank=True, null=True)
+
+

ingest/static/ingest/style.css

@@ -1,6 +1,9 @@
 .header {
     background-color: #161b33; /* dark blue */
-    border-radius: 0px;
+    border-radius:0px;
+    z-index: 99;
+    position:fixed;
+    width: 100%;
 }
 
 .navbar-header { 
@@ -87,6 +90,7 @@
 
 h1, h2, h3, h4 {
     font-family: 'Lato';
+    margin-top: 70px;
 }
 
 p {

ingest/tables.py

@@ -118,8 +118,8 @@ def render_validation_status(self, value):
 
     class Meta:
         model = Collection
-        exclude = ['celery_task_id_submission', 'celery_task_id_validation', 'user']
-        template_name = 'ingest/bootstrap_ingest.html'
+        exclude = ['celery_task_id_submission', 'celery_task_id_validation', 'user', 'modality',]
+        template_name = 'django_tables2/bootstrap.html'
 
 class CollectionRequestTable(tables.Table):
     """ The table used in the collection list. """

ingest/templates/ingest/descriptive_metadata_upload.html

@@ -26,8 +26,7 @@ <h3>Step 3 of 3: Upload metadata for associated submission</h3>
 {% if collections %}
 <ul class="list-group">
   <li class="list-group-item">Download and fill out either the <a href="{% static 'ingest/BILMetadataV2Template.xlsx' %}">Excel</a> or <a href="{% static '/ingest/BILMetadataV2Template.ods' %}">LibreOffice Calc</a> template. </li>
-  <li class="list-group-item">Choose a collection, then upload your metadata.</li>.
-  <p> If the project you are looking for is not in this list, it must be added by the PI of your project. </p>
+  <li class="list-group-item">Choose a collection, then upload your metadata.</li>
 </ul>
   <hr>  
     {% csrf_token %}

ingest/views.py

@@ -413,14 +413,15 @@ def descriptive_metadata_list(request):
         table = DescriptiveMetadataTable(
             DescriptiveMetadata.objects.filter(user=request.user), exclude=['user'])
         RequestConfig(request).configure(table)
-        descriptive_metadata = DescriptiveMetadata.objects.filter(user=request.user)
+        descriptive_metadata = DescriptiveMetadata.objects.filter(user=request.user).last()
 
         datasets_list = []
         collections = Collection.objects.filter(user=request.user)
         for c in collections:
-            sheets = Sheet.objects.filter(collection_id=c.id).all()
-            for s in sheets:
-                datasets = Dataset.objects.filter(sheet_id=s.id)
+            sheets = Sheet.objects.filter(collection_id=c.id).last()
+            #for s in sheets:
+            if sheets != None:
+                datasets = Dataset.objects.filter(sheet_id=sheets.id)
                 for d in datasets:
                     datasets_list.append(d)
 
@@ -799,16 +800,17 @@ def collection_detail(request, pk):
     try:
         datasets_list = []
         collection = Collection.objects.get(id=pk)
-        sheets = Sheet.objects.filter(collection_id=collection.id).all()
-        for s in sheets:
-            datasets = Dataset.objects.filter(sheet_id=s.id)
+        sheets = Sheet.objects.filter(collection_id=collection.id).last()
+        #for s in sheets:
+        if sheets != None:
+            datasets = Dataset.objects.filter(sheet_id=sheets.id)
             for d in datasets:
                 datasets_list.append(d)
     except ObjectDoesNotExist:
         raise Http404
     # the metadata associated with this collection
     #image_metadata_queryset = collection.imagemetadata_set.all()
-    descriptive_metadata_queryset = collection.descriptivemetadata_set.all()
+    descriptive_metadata_queryset = collection.descriptivemetadata_set.last()
     # this is what is triggered if the user hits "Upload to this Collection"
     if request.method == 'POST' and 'spreadsheet_file' in request.FILES:
         spreadsheet_file = request.FILES['spreadsheet_file']
@@ -2216,7 +2218,7 @@ def descriptive_metadata_upload(request):
             # datapath = '/home/shared_bil_dev/testetc/' 
 
             # for development locally
-            #datapath = '/Users/ecp/Desktop/bil_metadata_uploads' 
+            #datapath = '/Users/ltuite96/Desktop/bil_metadata_uploads' 
 
             spreadsheet_file = request.FILES['spreadsheet_file']