implemented issue part 2

conf/first_install_tables.json

@@ -1512,84 +1512,100 @@
     "model": "wetlab.runstates",
     "pk": 1,
     "fields": {
-        "run_state_name": "Pre-Recorded"
+        "run_state_name": "pre_recorded",
+        "state_display": "Pre Recorded",
+        "description": "Run name is defined but pending for input data.",
+        "show_in_stats": false
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 2,
     "fields": {
-        "run_state_name": "Recorded"
+        "run_state_name": "recorded",
+        "state_display": "Recorded",
+        "description": "Run name is defined.",
+        "show_in_stats": true
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 3,
     "fields": {
-        "run_state_name": "Sample Sent"
+        "run_state_name": "sample_sent",
+        "state_display": "Sample Sent",
+        "description": "Run has copied sample sheet on remote server.",
+        "show_in_stats": false
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 4,
     "fields": {
-        "run_state_name": "Processing Run"
+        "run_state_name": "processing_run",
+        "state_display": "Processing Run",
+        "description": "Run is handled on the sequencer.",
+        "show_in_stats": false
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 5,
     "fields": {
-        "run_state_name": "Processed Run"
+        "run_state_name": "processed_run",
+        "state_display": "Processed Run",
+        "description": "Run is already processed on sequencer.",
+        "show_in_stats": false
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 6,
     "fields": {
-        "run_state_name": "Processing Bcl2fastq"
+        "run_state_name": "processing_bcl2fastq",
+        "state_display": "Processing Bcl2fastq",
+        "description": "Bcl2fastq is running",
+        "show_in_stats": false
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 7,
     "fields": {
-        "run_state_name": "Processed Bcl2fastq"
+        "run_state_name": "processed_bcl2fastq",
+        "state_display": "Processed Bcl2fastq",
+        "description": "Bcl2fastq already completed",
+        "show_in_stats": true
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 8,
     "fields": {
-        "run_state_name": "Completed"
+        "run_state_name": "completed",
+        "state_display": "Completed",
+        "description": "Run is completed and all processes are finished.",
+        "show_in_stats": false
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 9,
     "fields": {
-        "run_state_name": "Cancelled"
+        "run_state_name": "cancelled",
+        "state_display": "Cancelled",
+        "description": "Run was manually cancelled while running on sequencer.",
+        "show_in_stats": true
     }
 },
 {
     "model": "wetlab.runstates",
     "pk": 10,
     "fields": {
-        "run_state_name": "Error"
-    }
-},
-{
-    "model": "wetlab.runstates",
-    "pk": 11,
-    "fields": {
-        "run_state_name": "Processing Metrics"
-    }
-},
-{
-    "model": "wetlab.runstates",
-    "pk": 12,
-    "fields": {
-        "run_state_name": "Processing Demultiplexing"
+        "run_state_name": "error",
+        "state_display": "Error",
+        "description": "There was an issue while processing the run",
+        "show_in_stats": true
     }
 },
 {
@@ -1996,6 +2012,33 @@
         "generated_at": "2021-01-28T22:59:03.042"
     }
 },
+{
+    "model": "wetlab.configsetting",
+    "pk": 15,
+    "fields": {
+        "configuration_name": "ALLOW_REPEAT_SAMPLE_NAMES",
+        "configuration_value": "FALSE",
+        "generated_at": "2024-05-28T22:59:03.142"
+    }
+},
+{
+    "model": "wetlab.configsetting",
+    "pk": 16,
+    "fields": {
+        "configuration_name": "ALLOW_REPEAT_SAMPLE_NAMES_PER_RESEARCHER",
+        "configuration_value": "FALSE",
+        "generated_at": "2024-05-28T22:59:04.042"
+    }
+},
+{
+    "model": "wetlab.configsetting",
+    "pk": 17,
+    "fields": {
+        "configuration_name": "ALLOW_SAMPLE_NAMES_WITH_UNDERSCORE",
+        "configuration_value": "FALSE",
+        "generated_at": "2024-05-28T22:59:05.042"
+    }
+},
 {
     "model": "wetlab.collectionindexvalues",
     "pk": 2073,

core/utils/graphics.py

@@ -1,25 +1,18 @@
-def preparation_3D_pie(heading, sub_title, theme, source_data):
-    """_summary_
+def preparation_3D_pie(
+    heading: str, sub_title: str, theme: str, source_data: dict
+) -> dict:
+    """Join the parameters to create a dictionary with two keys: chart and data.
+    The chart key contains the heading, sub_title, theme, numberPrefix, showlegend, placevaluesInside, showpercentvalues, rotatevalues, showCanvasBg, showCanvasBase, canvasBaseDepth, canvasBgDepth, canvasBaseColor, canvasBgColor, exportEnabled.
+    The data key contains a list of dictionaries with the keys label and value.
 
-    Parameters
-    ----------
-    heading : str
-        text to insert on top of graphic
-    sub_title : str
-        additional text to include in graphic
-    axis_x_description : str
-        description of x axis
-    axis_y_description : str
-        description
-    theme : str
-        name of the available themes to be used for the graphic
-    source_data : dict
-        Dictionary containing value for the graphic
+    Args:
+        heading (str): title of the chart
+        sub_title (str): additional information
+        theme (str): theme of the chart
+        source_data (dict): dictionary with the data to be displayed
 
-    Returns
-    -------
-    _type_
-        _description_
+    Returns:
+        dict: dictionary with the keys chart and data
     """
     data_source = {}
     data_source["chart"] = {
@@ -58,15 +51,30 @@ def preparation_3D_pie(heading, sub_title, theme, source_data):
 
 
 def preparation_graphic_data(
-    heading,
-    sub_caption,
-    x_axis_name,
-    y_axis_name,
-    theme,
-    input_data,
-    label_key=None,
-    label_value=None,
-):
+    heading: str,
+    sub_caption: str,
+    x_axis_name: str,
+    y_axis_name: str,
+    theme: str,
+    input_data: dict,
+    label_key: str = None,
+    label_value: str = None,
+) -> dict:
+    """Join the parameters to create a dictionary with two keys: chart and data.
+
+    Args:
+        heading (str): heading of the chart
+        sub_caption (str): sub_caption of the chart
+        x_axis_name (str): name of the x axis
+        y_axis_name (str): name of the y axis
+        theme (str): theme of the chart
+        input_data (dict): data to be displayed
+        label_key (str, optional): key name from the input dict. Defaults to None.
+        label_value (str, optional): value field in the innput dict. Defaults to None.
+
+    Returns:
+        dict: dictionary with the keys chart and data
+    """
     data_source = {}
     data_source["chart"] = {
         "caption": heading,

core/utils/samples.py

@@ -6,6 +6,7 @@
 
 from django.contrib.auth.models import User
 from django.db.models import CharField, Count, F, Func, Prefetch, Value
+from django.db.models.functions import Lower
 
 # Local imports
 import core.core_config
@@ -193,20 +194,24 @@ def save_recorded_samples(samples_data, req_user, app_name):
     return samples_data
 
 
-def validate_sample_data(sample_data, req_user, app_name):
-    """Sample data validation
+def validate_sample_data(
+    sample_data: json,
+    req_user: str,
+    app_name: str,
+    repeat_allowed: bool = False,
+    allow_user_repeat: bool = False,
+) -> tuple:
+    """sample data validation
 
-    Parameters
-    ----------
-    sample_data
-        sample data formatted in json obtained from jspreadsheet
-    req_user
-        requesting user
-    app_name
-        application name (wetlab, drylab, core, etc.)
+    Args:
+        sample_data (json): sample data formatted in json obtained from jspreadsheet
+        req_user (str): requested user name
+        app_name (str): application name (wetlab, drylab, core, etc.)
+        repeat_allowed (bool, optional): allow or not that sample can be repeated. Defaults to False.
+        allow_user_repeat (bool, optional): if allowed to be repeated check if same request user is allowed have repeated sample names. Defaults to False.
 
-    Returns
-    -------
+    Returns:
+        tuple: returns result as boolean and a dictionary with the following keys
         validation
             list with validation info for each sample with format:
             [{"Sample Name": "test 01",
@@ -222,6 +227,27 @@ def validate_sample_data(sample_data, req_user, app_name):
     sample_name_list = []
     line = 0
     result = True
+    not_allowed_sample_names = {}
+    # collect the sample names already in the database in case that the user
+    #  is not allowed to repeat
+    if not repeat_allowed:
+        if not allow_user_repeat:
+            if core.models.Samples.objects.filter(
+                sample_user__username__exact=req_user
+            ).exists():
+                existing_sample_name_list = list(
+                    core.models.Samples.objects.filter(
+                        sample_user__username__iexact=req_user
+                    ).values_list("sample_name", flat=True)
+                )
+        else:
+            existing_sample_name_list = list(
+                core.models.Samples.objects.all().values_list(
+                    Lower("sample_name", flat=True)
+                )
+            )
+        # convert to dict to speed up the search
+        not_allowed_sample_names = dict.fromkeys(existing_sample_name_list, 0)
     for sample in sample_data:
         line += 1
         sample_dict = {}
@@ -237,7 +263,10 @@ def validate_sample_data(sample_data, req_user, app_name):
             validation.append(sample_dict)
             continue
 
-        if sample["sample_name"] not in sample_name_list:
+        if repeat_allowed or (
+            sample["sample_name"].lower() not in sample_name_list
+            and sample["sample_name"].lower() not in not_allowed_sample_names
+        ):
             sample_name_list.append(sample["sample_name"])
         else:
             error_cause = core.core_config.ERROR_REPEATED_SAMPLE_NAME.copy()