Merge branch 'release/2.3.0'

conf/apache2.conf

@@ -32,5 +32,6 @@
         WSGIDaemonProcess iSkyLIMS python-home=/opt/iSkyLIMS/virtualenv python-path=/opt/iSkyLIMS
         WSGIProcessGroup iSkyLIMS
         WSGIScriptAlias / /opt/iSkyLIMS/iSkyLIMS/wsgi.py
+        WSGIPassAuthorization On
 
 </VirtualHost>

conf/pythonPackagesRequired.txt

@@ -19,6 +19,7 @@ paramiko
 pysmb
 django_extensions
 djangorestframework
+drf-yasg
 xlrd
 pandas
 openpyxl

conf/settings.py

@@ -47,6 +47,7 @@
     'django.contrib.staticfiles',
     'django_extensions',
     'rest_framework',
+    'drf_yasg',
     'django_cleanup', # should go after your apps
 ]
 
@@ -121,7 +122,23 @@
         'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',
     },
 ]
+SWAGGER_SETTINGS = {
+    'SECURITY_DEFINITIONS': {
+        'basic': {
+            'type': 'basic'
+        }
+    }
+}
 
+""" For using token in the authorization request
+    'api_key': {
+            'type': 'apiKey',
+            'in': 'header',
+            'name': 'Authorization'
+        }
+     
+"""
+# 'PERSIST_AUTH': True
 
 # Internationalization
 # https://docs.djangoproject.com/en/1.11/topics/i18n/

conf/urls.py

@@ -1,6 +1,17 @@
 from django.urls import include, path
 from django.contrib import admin
 from django.contrib.auth.views import LoginView
+from drf_yasg.views import get_schema_view
+from drf_yasg import openapi
+
+schema_view = get_schema_view(openapi.Info(
+    title="iSkyLIMS API",
+    default_version='v0.0.1',
+    description="iSkyLIMS API",
+    ),
+    public=True,
+)
+
 
 urlpatterns = [
     path('',include('iSkyLIMS_core.urls')),
@@ -16,4 +27,6 @@
 
     # REST FRAMEWORK URLS
     path('drylab/api/', include('iSkyLIMS_drylab.api.urls')),
+    path('wetlab/api/', include('iSkyLIMS_wetlab.api.urls')),
+    path('swagger/', schema_view.with_ui('swagger', cache_timeout=0))
 ]

iSkyLIMS_core/core_config.py

@@ -4,17 +4,23 @@
 
 ################# SAMPLE SETTINGS ##############################
 ### Headings used when recording information
-HEADING_FOR_RECORD_SAMPLES = [ 'Patient Code ID', 'Sample Name', 'Lab requested', 'Type of Sample', 'Species', 'Project/Service', 'Date sample reception', 'Sample Storage Location','Only recorded']
+HEADING_FOR_RECORD_SAMPLES = ['Patient Code ID', 'Sample Name', 'Lab requested', 'Type of Sample', 'Species', 'Project/Service', 'Date sample reception', 'Collection Sample Date', 'Sample Storage Location', 'Only recorded']
 
-HEADING_FOR_OPTIONAL_FIELD_SAMPLES = [ 'Patient Code ID', 'Lab requested', 'Species', 'Date sample reception', 'Sample Storage Location']
+HEADING_FOR_OPTIONAL_FIELD_SAMPLES = [ 'Patient Code ID', 'Lab requested', 'Species', 'Date sample reception', 'Collection Sample Date', 'Sample Storage Location']
 
 HEADING_FOR_DISPLAY_RECORDED_SAMPLES = ['Unique Sample ID', 'Sample CodeID', 'Sample Name', 'Date for entry in Lab', 'Type of Sample']
 
 HEADING_FOR_COMPLETION_SAMPLES_PRE_DEFINED = ['Date sample extraction' , 'Sample CodeID', 'Sample name']
 
-MAPPING_SAMPLE_FORM_TO_DDBB = [('Patient Code ID','p_code_id'), ('Sample Name', 'sampleName'), ('Lab requested', 'labRequest'),
-                ('Type of Sample','sampleType'), ('Species', 'species'),('Project/Service', 'project_service'),('Date sample extraction', 'sampleEntryDate'),
-                ('Sample Storage Location', 'sampleLocation'), ('Only recorded','onlyRecorded')]
+MAPPING_SAMPLE_FORM_TO_DDBB = [
+    ('Patient Code ID', 'p_code_id'), ('Sample Name', 'sampleName'),
+    ('Lab requested', 'labRequest'), ('Type of Sample', 'sampleType'),
+    ('Species', 'species'), ('Project/Service', 'project_service'),
+    ('Date sample extraction', 'sampleEntryDate'),
+    ('Collection Sample Date', 'collectionSampleDate'),
+    ('Sample Storage Location', 'sampleLocation'),
+    ('Only recorded', 'onlyRecorded')
+]
 
 HEADING_FOR_MOLECULE_PROTOCOL_DEFINITION = ['Sample ID','Sample Type', 'Molecule type', 'Type of Extraction', 'Extraction date', 'Protocol to be used']
 HEADING_FOR_MOLECULE_ADDING_PARAMETERS = ['Molecule Code ID', 'Lot Commercial Kit']
@@ -37,7 +43,11 @@
                                     'Used Protocol', 'UserID']
 
 ### Heading for display information on sample definition
-HEADING_FOR_SAMPLE_DEFINITION = ['Sample Name', 'Sample CodeID','Sample State', 'Recorded Date', 'Sample Type', 'Species', 'Number of reused', 'User']
+HEADING_FOR_SAMPLE_DEFINITION = [
+    'Sample Name', 'Sample CodeID', 'Sample State', 'Recorded Date',
+    'Collection Sample Date', 'Date sample reception', 'Sample Type', 'Species',
+    'Number of reused', 'User'
+]
 ### Heading for display information on molecule definition
 HEADING_FOR_MOLECULE_DEFINITION = ['Molecule CodeID', 'Molecule State','Extraction Date', 'Extraction Type', 'Molecule Type', 'Used for', 'Used Protocol', 'Number of reused']
 

iSkyLIMS_core/models.py

@@ -216,6 +216,9 @@ def __str__ (self):
     def get_sample_state (self):
         return '%s' %(self.sampleStateName)
 
+    def get_id(self):
+        return "%s" %(self.pk)
+
 
 class StatesForMolecule (models.Model):
     moleculeStateName = models.CharField(max_length=50)
@@ -667,7 +670,7 @@ class SampleProjectsFields (models.Model):
                 on_delete= models.CASCADE, null = True, blank = True)
     #sampleProjectsOptionValues = models.ManyToManyField(SamplesProjectsOptionValues, blank = True)
 
-    sampleProjectFieldName = models.CharField(max_length=50)
+    sampleProjectFieldName = models.CharField(max_length=80)
     sampleProjectFieldDescription = models.CharField(max_length= 400, null=True, blank=True)
     sampleProjectFieldOrder = models.IntegerField()
     sampleProjectFieldUsed = models.BooleanField()
@@ -768,30 +771,38 @@ def get_option_value(self):
     objects = SamplesProjectsOptionValuesManager()
 '''
 
-class SamplesManager (models.Manager):
 
-    def create_sample (self, sample_data):
-        ## Set to null in case that there is not samples_origin defined
+class SamplesManager (models.Manager):
 
+    def create_sample(self, sample_data):
         if sample_data['labRequest'] != '':
-            sample_data['labRequest'] = LabRequest.objects.get(labNameCoding__exact = sample_data['labRequest'])
+            sample_data['labRequest'] = LabRequest.objects.get(labNameCoding__exact=sample_data['labRequest'])
         else:
             sample_data['labRequest'] = None
         if sample_data['species'] != '':
-            sample_data['species'] = Species.objects.get(speciesName__exact = sample_data['species'])
+            sample_data['species'] = Species.objects.get(speciesName__exact=sample_data['species'])
         else:
             sample_data['species'] = None
-        new_sample = self.create(sampleState = StatesForSample.objects.get(sampleStateName__exact = sample_data['sampleState']),
-                            patientCore = sample_data['patient'],
-                            labRequest = sample_data['labRequest'], sampleProject = sample_data['sampleProject'],
-                            sampleType = SampleType.objects.get(sampleType__exact = sample_data['sampleType'], apps_name__exact = sample_data['app_name']) ,
-                            sampleUser = User.objects.get(username__exact = sample_data['user']),
-                            sampleCodeID = sample_data['sample_id'] , sampleName =  sample_data['sampleName'],
-                            uniqueSampleID = sample_data['new_unique_value'],
-                            species = sample_data['species'],
-                            sampleLocation = sample_data['sampleLocation'], onlyRecorded = sample_data['onlyRecorded'],
-                            #sampleEntryDate = datetime.datetime.strptime(sample_data['Date for entry in Lab'],'%Y-%m-%d %H:%M:%S'))
-                            sampleEntryDate = datetime.datetime.strptime(sample_data['sampleEntryDate'],'%Y-%m-%d %H:%M:%S'))
+        if 'completedDate' in sample_data:
+            completedDate = datetime.datetime.strptime(sample_data['completedDate'], '%Y-%m-%d %H:%M:%S')
+        else:
+            completedDate = None
+        import pdb; pdb.set_trace()
+        new_sample = self.create(
+            sampleState=StatesForSample.objects.get(sampleStateName__exact=sample_data['sampleState']),
+            patientCore=sample_data['patient'],
+            labRequest=sample_data['labRequest'],
+            sampleProject=sample_data['sampleProject'],
+            sampleType=SampleType.objects.get(sampleType__exact=sample_data['sampleType'], apps_name__exact=sample_data['app_name']),
+            sampleUser=User.objects.get(username__exact=sample_data['user']),
+            sampleCodeID=sample_data['sample_id'], sampleName=sample_data['sampleName'],
+            uniqueSampleID=sample_data['new_unique_value'],
+            species=sample_data['species'],
+            sampleLocation=sample_data['sampleLocation'], onlyRecorded=sample_data['onlyRecorded'],
+            sampleEntryDate=datetime.datetime.strptime(sample_data['sampleEntryDate'], '%Y-%m-%d %H:%M:%S'),
+            collectionSampleDate=datetime.datetime.strptime(sample_data['sampleEntryDate'], '%Y-%m-%d %H:%M:%S'),
+            completedDate=completedDate
+        )
 
         return new_sample
 
@@ -826,6 +837,7 @@ class Samples (models.Model):
     sampleName = models.CharField(max_length=255, null = True)
     sampleLocation = models.CharField(max_length=255, null = True, blank = True)
     sampleEntryDate = models.DateTimeField(auto_now_add = False, null =True)
+    collectionSampleDate = models.DateTimeField(auto_now_add = False, null =True)
     uniqueSampleID = models.CharField(max_length=8, null = True)
     sampleCodeID = models.CharField(max_length=60, null = True)
     numberOfReused = models.IntegerField(default=0)
@@ -869,12 +881,22 @@ def get_info_for_searching (self):
             sample_info.append('Not defined')
         return sample_info
 
-    def get_info_for_display (self):
+    def get_info_for_display(self):
+        if self.collectionSampleDate:
+            collectionSampleDate = self.collectionSampleDate.strftime("%d , %B , %Y")
+        else:
+            collectionSampleDate = ""
+        if self.sampleEntryDate:
+            sampleEntryDate = self.sampleEntryDate.strftime("%d , %B , %Y")
+        else:
+            sampleEntryDate = ""
         sample_info = []
         sample_info.append(self.sampleName)
         sample_info.append(self.sampleCodeID)
         sample_info.append(self.sampleState.get_sample_state())
         sample_info.append(self.generated_at.strftime("%d , %B , %Y"))
+        sample_info.append(collectionSampleDate)
+        sample_info.append(sampleEntryDate)
         sample_info.append(self.sampleType.get_name())
         sample_info.append(self.species.get_name())
         sample_info.append(self.numberOfReused)
@@ -1008,7 +1030,7 @@ class MoleculeUsedFor (models.Model):
     apps_name = models.CharField(max_length = 50)
     massiveUse = models.BooleanField(default= False)
 
-    def __str__ (self):
+    def __str__(self):
         return '%s' %(self.usedFor)
 
     def get_molecule_use_name (self):

iSkyLIMS_core/templates/iSkyLIMS_core/footer.html

@@ -41,7 +41,7 @@ <h4>Powered by :</h4>
 		</div>
 		<div class="row">
 			<div class="col-md-2 col-md-offset-5">
-				<p>Version 2.2.2</p>
+				<p>Version 2.3.0</p>
 			</div>
 		</div>
 		<!--// end row -->