Merge branch 'v5.0.0'

Author: Genarito

DEPLOYING.md

@@ -45,6 +45,7 @@ The following are the steps to perform a deployment in production. In case you w
         - `CGDS_CHUNK_SIZE`: size **in bytes** of the chunk in which the files of a CGDS study are downloaded, the bigger it is, the faster the download is, but the more server memory it consumes. Default `2097152`, i.e. 2MB.
         - `THRESHOLD_ORDINAL`: number of different values for the GEM (CNA) information to be considered ordinal, if the number is <= to this value then it is considered categorical/ordinal and a boxplot is displayed, otherwise, it is considered continuous and the common correlation graph is displayed. Default `5`.
         - `THRESHOLD_GEM_SIZE_TO_COLLECT`: GEM file size threshold (in MB) for the GEM dataset to be available in memory. This has a HUGE impact on the performance of the analysis. If the size is less than or equal to this threshold, it is allocated in memory, otherwise, it will be read lazily from the disk. If None GGCA automatically allocates in memory when the GEM dataset size is small (<= 100MB). Therefore, if you want to force to always use RAM to improve performance you should set a very high threshold, on the contrary, if you want a minimum memory usage at the cost of poor performance, set it to `0`. Default `None`.
+        - `MIN_PASSWORD_LEN`:  Defines the minimum required length for user passwords when updating their profile. If the provided password is shorter than this length, the update will be rejected. Default `8`.
     - PostgreSQL:
         - `POSTGRES_USERNAME`: PostgreSQL connection username. **Must be equal to** `POSTGRES_USER`.
         - `POSTGRES_PASSWORD`: PostgreSQL connection password. **Must be equal to** `POSTGRES_PASSWORD`.
@@ -179,7 +180,7 @@ To integrate with [Modulector][modulector] and/or [BioAPI][bioapi] using `docker
                name: 'multiomix-network'
    ```
 3. The new versions of BioAPI and Modulector already come with service names suitable for integration with Multiomix. But **if you have any old version of those platforms**, change the Modulector and BioAPI configuration so that it does not conflict with the Multiomix configuration:
-   1. Rename all the services in the Modulector and BioAPI `docker-compose.yml` files with the suffix `_modulector` and `_bioapi`. And rename `web` service to `modulector` or `bioapi` respectively. **NOTE:** do not forget to rename the `depends_on` parameters, and the database connection parameters to point to the new services names.
+   1. Rename all the services in the Modulector and BioAPI `docker-compose.yml` files with the suffix `_modulector` and `_bioapi`. For example `mongo_bioapi`, `web_bioapi` and `nginx_bioapi` in the case of BioAPI. **NOTE:** do not forget to rename the `depends_on` parameters, and the database connection parameters to point to the new services names.
    2. Change the following block in the NGINX configuration files. In Modulector it's `config/nginx/conf.d/modulector.conf`, in BioAPI it's `/nginx/conf.d/default.conf`:
    ```
    # Old
@@ -191,7 +192,7 @@ To integrate with [Modulector][modulector] and/or [BioAPI][bioapi] using `docker
    # New
    upstream web {
      ip_hash;
-     server modulector:8000; # Or bioapi, dependening on which config file you're 
+     server web_modulector:8000; # Or web_bioapi, dependening on which config file you're editing
    }
    ```
 4. Set Multiomix parameters:

docker-compose_dist.yml

@@ -60,7 +60,7 @@ services:
 
     # Celery worker for correlation analysis
     correlation-analysis-worker:
-        image: omicsdatascience/multiomix:5.4.0-celery
+        image: omicsdatascience/multiomix:5.5.0-celery
         restart: 'always'
         depends_on:
             - db
@@ -77,7 +77,7 @@ services:
 
     # Celery worker for feature selection experiments
     fs-experiments-worker:
-        image: omicsdatascience/multiomix:5.4.0-celery
+        image: omicsdatascience/multiomix:5.5.0-celery
         restart: 'always'
         depends_on:
             - db
@@ -94,7 +94,7 @@ services:
 
     # Celery worker for statistical validations and trained models
     stats-worker:
-        image: omicsdatascience/multiomix:5.4.0-celery
+        image: omicsdatascience/multiomix:5.5.0-celery
         restart: 'always'
         depends_on:
             - db
@@ -111,7 +111,7 @@ services:
 
     # Celery worker for inference experiments
     inference-worker:
-        image: omicsdatascience/multiomix:5.4.0-celery
+        image: omicsdatascience/multiomix:5.5.0-celery
         restart: 'always'
         depends_on:
             - db
@@ -128,7 +128,7 @@ services:
 
     # Celery worker for sync CGDSStudies
     sync-datasets-worker:
-        image: omicsdatascience/multiomix:5.4.0-celery
+        image: omicsdatascience/multiomix:5.5.0-celery
         restart: 'always'
         depends_on:
             - db
@@ -145,7 +145,7 @@ services:
 
     # Django Backend Server
     multiomix:
-        image: omicsdatascience/multiomix:5.4.0
+        image: omicsdatascience/multiomix:5.5.0
         restart: 'always'
         # environment:
             # DJANGO_SETTINGS_MODULE: 'multiomics_intermediate.settings_prod'

src/api_service/migrations/0061_alter_experiment_shared_users.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.2.15 on 2024-10-23 13:51
+
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('api_service', '0060_experiment_shared_users'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='experiment',
+            name='shared_users',
+            field=models.ManyToManyField(blank=True, related_name='shared_users_correlation_analysis', to=settings.AUTH_USER_MODEL),
+        ),
+    ]

src/api_service/mrna_service.py

@@ -13,10 +13,28 @@ class MRNAService(object):
 
     def __init__(self):
         modulector_settings = settings.MODULECTOR_SETTINGS
-        self.url_modulector_prefix = f"http://{modulector_settings['host']}:{modulector_settings['port']}"
+        self.url_modulector_prefix = self.__build_url(modulector_settings)
 
         bioapi_settings = settings.BIOAPI_SETTINGS
-        self.url_bioapi_prefix = f"http://{bioapi_settings['host']}:{bioapi_settings['port']}"
+        self.url_bioapi_prefix = self.__build_url(bioapi_settings)
+
+    @staticmethod
+    def __build_url(settings: Dict[str, Any]) -> str:
+        """
+        Constructs the URL based on the settings provided.
+        If the port is the default for the protocol (80 for http, 443 for https), it is omitted.
+        Otherwise, the port is included in the URL.
+        @param settings: Dictionary containing protocol, host, and port information.
+        @return: Constructed URL as a string.
+        """
+        protocol = settings['protocol']
+        host = settings['host']
+        port = settings['port']
+
+        if (protocol == 'http' and port == 80) or (protocol == 'https' and port == 443):
+            return f"{protocol}://{host}"
+        else:
+            return f"{protocol}://{host}:{port}"
 
     @staticmethod
     def __generate_rest_query_params(get_request: QueryDict) -> str:

src/api_service/serializers.py

@@ -5,7 +5,7 @@
 from .models import Experiment, ExperimentSource, GeneGEMCombination, GeneMiRNACombination, GeneCNACombination, \
     GeneMethylationCombination, ExperimentClinicalSource
 from rest_framework import serializers
-
+from django.contrib.auth import get_user_model
 
 class GeneGEMCombinationSerializer(serializers.ModelSerializer):
     """GeneGEMCombination serializer"""
@@ -58,11 +58,17 @@ class Meta:
         model = ExperimentSource
         fields = '__all__'
 
+class LimitedUserSerializer(serializers.ModelSerializer):
+    """A lightweight serializer for User model"""
+    class Meta:
+        model = get_user_model()
+        fields = ['id', 'username']
 
 class ExperimentSerializer(serializers.ModelSerializer):
     """Experiment serializer"""
     mRNA_source = ExperimentSourceSerializer()
     gem_source = ExperimentSourceSerializer()
+    user = LimitedUserSerializer()
     tag = TagSerializer()
 
     class Meta:
@@ -83,7 +89,9 @@ class Meta:
             'p_values_adjustment_method',
             'type',
             'tag',
-            'clinical_source_id'
+            'clinical_source_id',
+            'is_public',
+            'user'
         ]
 
 

src/api_service/urls.py

@@ -71,5 +71,19 @@
          name='survival_data'),
     path('mirna-data', views.mirna_data_action, name='mirna_data'),
     path('methylation-data', views.methylation_data_action, name='methylation_data'),
-    path('stop-experiment', views.stop_experiment_action, name='stop_experiment')
+    path('stop-experiment', views.stop_experiment_action, name='stop_experiment'),
+    path('non-institutions', views.InstitutionNonExperimentsSharedListView.as_view(), name='institution-non-experiments-list'),
+    path('non-institutions/<int:experiment_id>/', views.InstitutionNonExperimentsSharedListView.as_view()),
+    path('non-users', views.UsersNonExperimentsSharedListView.as_view(), name='user-non-experiments-list'),
+    path('non-users/<int:experiment_id>/', views.UsersNonExperimentsSharedListView.as_view()),
+    path('share-experiment-to-institution', views.AddInstitutionToExperimentView.as_view(), name='share-experiment-to-institution'),
+    path('share-experiment-to-user', views.AddUserToExperimentView.as_view(), name='share-experiment-to-user'),
+    path('shared-institution', views.UsersExperimentsSharedListView.as_view(), name='shared-institution'),
+    path('shared-users/<int:experiment_id>/', views.UsersExperimentsSharedListView.as_view(), ),
+    path('shared-users', views.InstitutionExperimentsSharedListView.as_view(), name='shared-users'),
+    path('shared-institution/<int:experiment_id>/', views.InstitutionExperimentsSharedListView.as_view(), ),
+    path('switch-institution-public-view', views.ToggleExperimentPublicView.as_view(), name='switch-experiment-public-view'),
+    path('remove-institution', views.RemoveInstitutionFromExperimentView.as_view(), name='remove-institution'),
+    path('remove-user', views.RemoveUserFromExperimentView.as_view(), name='remove-user')
+
 ]