Merge pull request #52 from daisybio/refactorKonstantin

Shareable links and custom save time for analyses

.gitignore

@@ -223,4 +223,6 @@ cython_debug/
 # IntelliJ like IDEs (e.g. PyCharm)
 .idea
 
-tmp*
+tmp*
+container/nease_events
+

container/domain/Process/nease_output.py

@@ -1,3 +1,4 @@
+import json
 import pickle
 import traceback
 from io import StringIO
@@ -8,6 +9,7 @@
 
 from matplotlib import pyplot as plt
 
+from domain.models import NeaseSaveLocationMapping
 from domain.nease import nease
 from domain.nease.process import webify_table
 from django.conf import settings
@@ -16,12 +18,14 @@
 images_path = os.path.join(settings.MEDIA_ROOT, 'images/')
 data_path = os.path.join(settings.MEDIA_ROOT, 'nease_tables/')
 nease_path = 'nease_events/'
+# The subdirectories contain files saved for one week, one month, and six months. To be very lenient, we calculated every month with 31 days.
+days_to_folder = {"0": nease_path+"zero_days/", "7": nease_path+"seven_days/", "31": nease_path+"thirtyone_days/", "186": nease_path+"onehundredeightysix_days/"}
+default_path = days_to_folder["7"]
 
-for path in [images_path, data_path, nease_path]:
+for path in [images_path, data_path] + list(days_to_folder.values()):
     if not os.path.exists(path):
         os.makedirs(path)
 
-
 # web_tables_options is a dictionary that contains the options for webifying the tables
 web_tables_options = {
     'domains': {'link_col': ['Gene name', 'Gene stable ID', 'Exon stable ID', 'Pfam ID'],
@@ -50,7 +54,7 @@
 }
 
 
-def run_nease(data, organism, params):
+def run_nease(data, organism, params, file_name='', custom_name=''):
     run_id = str(uuid.uuid4())
     image_path = images_path + run_id
 
@@ -97,7 +101,8 @@ def run_nease(data, organism, params):
             value.drop(columns=['Unnamed: 0'], inplace=True)
 
     # save events to pickle
-    events.save(nease_path + run_id)
+    events.save(default_path + run_id)
+    NeaseSaveLocationMapping(run_id=run_id, saved_for_days=7, file_name=file_name, custom_name=custom_name).save()
     return events, info_tables, run_id
 
 
@@ -126,7 +131,13 @@ def read_extra_spaces(file_obj):
 
 
 def get_nease_events(run_id):
-    events = nease.load(nease_path + run_id + '.pkl')
+    days = NeaseSaveLocationMapping.get_saved_for_days(run_id)
+    if days not in days_to_folder:
+        file_path = default_path
+    else:
+        file_path = days_to_folder[str(days)]
+    print(f"Loading events from {file_path + run_id + '.pkl'}")
+    events = nease.load(file_path + run_id + '.pkl')
     info_tables = {}
     try:
         domains = webify_table(pd.read_csv(f"{data_path}{run_id}_domains.csv"), web_tables_options['domains'])
@@ -243,6 +254,27 @@ def create_plot(terms, pvalues, cut_off, filename):
     plt.clf()
     plt.close()
 
+def change_save_timing(run_id, days):
+    mapping = NeaseSaveLocationMapping.objects.get(run_id=run_id)
+    current_days_folder = mapping.get_number_of_saved_for_days()
+    if days not in days_to_folder:
+        new_file_path = default_path
+    else:
+        new_file_path = days_to_folder[str(days)]
+    if current_days_folder not in days_to_folder:
+        old_file_path = default_path
+    else:
+        old_file_path = days_to_folder[str(current_days_folder)]
+    # move the file
+    os.rename(old_file_path + run_id + '.pkl', new_file_path + run_id + '.pkl')
+    # update the database
+    mapping.saved_for_days = int(days)
+    mapping.save()
+
+    return json.dumps(
+        {"logmessage": "Changing the save timing from " + str(current_days_folder) + " to " + str(days) + " was successful.",
+         "days_left": mapping.days_left()}
+    )
 
 def match_name_with_format(filename):
     name_matches = {'deltapsi': 'MAIJQ',

container/domain/migrations/0001_initial.py

@@ -0,0 +1,38 @@
+# Generated by Django 2.2.28 on 2024-09-09 12:32
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Domain',
+            fields=[
+                ('pfam_id', models.CharField(db_index=True, max_length=10, primary_key=True, serialize=False)),
+                ('symbol', models.CharField(max_length=20)),
+                ('description', models.CharField(max_length=150)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Gene',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('ensembl_id', models.CharField(max_length=20)),
+                ('gene_symbol', models.CharField(db_index=True, max_length=20)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='NeaseSaveLocationMapping',
+            fields=[
+                ('run_id', models.CharField(db_index=True, max_length=36, primary_key=True, serialize=False)),
+                ('saved_for_days', models.IntegerField()),
+                ('date_of_creation', models.DateTimeField(auto_now_add=True)),
+            ],
+        ),
+    ]

container/domain/migrations/0002_neasesavelocationmapping_name.py

@@ -0,0 +1,18 @@
+# Generated by Django 2.2.28 on 2024-09-09 13:22
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('domain', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='neasesavelocationmapping',
+            name='name',
+            field=models.CharField(default='', max_length=255),
+        ),
+    ]

container/domain/migrations/0003_auto_20240910_1357.py

@@ -0,0 +1,27 @@
+# Generated by Django 2.2.28 on 2024-09-10 11:57
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('domain', '0002_neasesavelocationmapping_name'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='neasesavelocationmapping',
+            name='name',
+        ),
+        migrations.AddField(
+            model_name='neasesavelocationmapping',
+            name='custom_name',
+            field=models.CharField(default='', max_length=255),
+        ),
+        migrations.AddField(
+            model_name='neasesavelocationmapping',
+            name='file_name',
+            field=models.CharField(default='', max_length=255),
+        ),
+    ]

container/domain/models.py

@@ -1,4 +1,5 @@
 from django.db import models
+from django.utils import timezone
 
 
 class Gene(models.Model):
@@ -16,3 +17,28 @@ class Domain(models.Model):
 
     #def __str__(self):
     #   return f"Pfam: {self.pfam_id} - Symbol: {self.symbol}"
+
+class NeaseSaveLocationMapping(models.Model):
+    run_id = models.CharField(max_length=36, primary_key=True, db_index=True)
+    saved_for_days = models.IntegerField()
+    date_of_creation = models.DateTimeField(auto_now_add=True)
+    file_name = models.CharField(max_length=255, default='')
+    custom_name = models.CharField(max_length=255, default='')
+
+    # Method to query the database for the run_id and return the saved_for_days
+    @staticmethod
+    def get_saved_for_days(run_id):
+        return str(NeaseSaveLocationMapping.objects.get(run_id=run_id).saved_for_days)
+
+    def get_number_of_saved_for_days(self):
+        return str(self.saved_for_days)
+
+    # Calculate how many days are left until deletion, negative values are set to 0
+    def days_left(self):
+        return max(0, self.saved_for_days - (timezone.now() - self.date_of_creation).days)
+
+    # Get the custom name and return None if it is empty
+    def get_custom_name(self):
+        if self.custom_name == '':
+            return None
+        return self.custom_name

container/domain/static/domain/initStore.js

@@ -100,7 +100,7 @@
         const newValue =
           value == null
             ? null
-            : { value, expiresAt: getExpiration(expiresInDays), name }
+            : { value, expiresAt: getExpiration(expiresInDays), name , createdAt: Date.now()}
         setExpiration(newValue?.expiresAt)
         storage.set(prefixedKey, newValue)
       },

container/domain/static/domain/loadStore.js

@@ -16,16 +16,16 @@ function removeExpiredData(key) {
 }
 
 // Function to create an HTML template
-function createHtmlTemplate(data, expiresInDays = 7) {
+function createHtmlTemplate(data) {
     // subtract 7 days from the expiry date
-    const createdDate = new Date(data.expiresAt) - (expiresInDays * 24 * 60 * 60 * 1000);
+    const createdDate = new Date(data.createdAt);
     // format to readable date
     const formattedDate = new Date(createdDate).toLocaleString();
 
     return `
      <div class="row">
       <div class="col-md-12 my-1">
-        <div class="card previous-card" onclick="prevAnalysis('${data.value}', '${data.name}')">
+        <div class="card previous-card" onclick="prevAnalysis('${data.value}')">
           <div class="card-body">
             <h6 class="card-title" style="display: inline; font-weight: bold">${data.name}</h6>
             <p class="card-text mx-1" style="display: inline; color: gray">●</p>
@@ -49,8 +49,7 @@ function appendTemplateToDiv(template, divId) {
     }
 }
 
-function prevAnalysis(id, name) {
+function prevAnalysis(id) {
     document.getElementById('previous_analyses_input').value = id;
-    document.getElementById('previous_analyses_name').value = name;
     document.getElementById('submit').click();
 }