Implemented feedback from external referee (Part 1)

cnr-ifn.mi/README.md

@@ -6,7 +6,7 @@ This repository contains the software developed during the internship at CNR-IFN
 
 -   **LabLogbook**: Integrated within the existing UdyniManagement Django project, LabLogbook is a web-based application designed for efficient experiment and sample management, coupled with a comprehensive digital logbook. Furthermore, it exposes RESTful APIs, laying the groundwork for the future development of a robust FAIR (Findable, Accessible, Interoperable, Reusable) data infrastructure within the UDynI laboratories.
 
-    **Important Note**: LabLogbook is not a standalone application. To run it, is necessary to set up the UdyniManagement project first by following the instructions provided below.
+    **Important Note**: LabLogbook is not a standalone application. To run it, it is necessary to set up the UdyniManagement project first by following the instructions provided below.
 
 
 ## UdyniManagement Setup
@@ -46,7 +46,7 @@ sudo apt install libsasl2-dev
 
 ### Django Project Configuration
 
-1.  **Apply Migrations:** These commands ensure your database schema is up-to-date with the project's models.
+1.  **Apply Migrations:** These commands ensure your database schema is up to date with the project's models.
 
     ```bash
     python3 manage.py makemigrations

cnr-ifn.mi/UdyniManagement/AccountManagement/forms.py

@@ -5,7 +5,7 @@
 from django.conf import settings
 
 from AccountManagement.models import RegistrationRequest # import the settings file
-from .ldap import UdyniLdap
+from AccountManagement.ldap import UdyniLdap
 
 UserModel = get_user_model()
 

cnr-ifn.mi/UdyniManagement/AccountManagement/urls.py

@@ -1,7 +1,7 @@
 from django.urls import path, reverse_lazy
 from django.views.generic.base import RedirectView
 
-from . import views
+from AccountManagement import views
 
 
 urlpatterns = [

cnr-ifn.mi/UdyniManagement/AccountManagement/views.py

@@ -22,9 +22,9 @@
 
 from UdyniManagement.menu import UdyniMenu
 from UdyniManagement.views import ListViewMenu, CreateViewMenu, TemplateViewMenu, UpdateViewMenu, DeleteViewMenu, FormViewMenu, udyni_error_view
-from .ldap import UdyniLdap
-from .forms import SetPasswordForm, PasswordChangeForm, PasswordResetForm, RegistrationForm, AccountCreationForm, AccountRejectionForm, UserDeleteForm, EditProfileForm
-from .models import RegistrationRequest
+from AccountManagement.ldap import UdyniLdap
+from AccountManagement.forms import SetPasswordForm, PasswordChangeForm, PasswordResetForm, RegistrationForm, AccountCreationForm, AccountRejectionForm, UserDeleteForm, EditProfileForm
+from AccountManagement.models import RegistrationRequest
 
 
 # =======================

cnr-ifn.mi/UdyniManagement/Accounting/forms.py

@@ -1,5 +1,5 @@
 from django import forms
-from .models import GAE
+from Accounting.models import GAE
 
 
 class GaeForm(forms.ModelForm):

cnr-ifn.mi/UdyniManagement/Accounting/urls.py

@@ -1,7 +1,7 @@
 from django.urls import path, reverse_lazy
 from django.views.generic.base import RedirectView
 
-from . import views
+from Accounting import views
 
 urlpatterns = [
     # Gestione GAE

cnr-ifn.mi/UdyniManagement/Accounting/utils.py

@@ -1,7 +1,7 @@
 import datetime
 from collections import OrderedDict
 from django.db.models import Q, F, Sum
-from .models import SplitBudget, SplitVariazione, SplitImpegno
+from Accounting.models import SplitBudget, SplitVariazione, SplitImpegno
 
 def create_split_accounting_detail(contab):
     # First we get the budget

cnr-ifn.mi/UdyniManagement/Accounting/views.py

@@ -13,10 +13,10 @@
 from UdyniManagement.menu import UdyniMenu
 from UdyniManagement.views import ListViewMenu, CreateViewMenu, TemplateViewMenu, UpdateViewMenu, DeleteViewMenu
 
-from .models import VoceSpesa, GAE, Stanziamento, Variazione, Impegno, Mandato
-from .models import SplitContab, SplitBudget, SplitImpegno, SplitVariazione
-from .forms import GaeForm
-from .utils import create_split_accounting_detail
+from Accounting.models import VoceSpesa, GAE, Stanziamento, Variazione, Impegno, Mandato
+from Accounting.models import SplitContab, SplitBudget, SplitImpegno, SplitVariazione
+from Accounting.forms import GaeForm
+from Accounting.utils import create_split_accounting_detail
 
 
 # =============================

cnr-ifn.mi/UdyniManagement/LabLogbook/forms.py

@@ -1,5 +1,5 @@
 from django import forms
-from .models import Comment, CommentContent
+from LabLogbook.models import Comment, CommentContent
 
 class CommentForm(forms.ModelForm):
     class Meta:

cnr-ifn.mi/UdyniManagement/LabLogbook/models.py

@@ -3,7 +3,6 @@
 from django.db import models
 from mptt.models import MPTTModel, TreeForeignKey  # used for Comments
 from django.contrib.auth import get_user_model
-from django.core.exceptions import ValidationError
 
 
 UserModel = get_user_model()

cnr-ifn.mi/UdyniManagement/LabLogbook/tests.py

@@ -2,7 +2,7 @@
 from django.urls import reverse
 from django.utils.timezone import now, timedelta
 from django.contrib.auth import get_user_model
-from .models import Laboratory, ExperimentalStation, Sample, Experiment, SampleForExperiment
+from LabLogbook.models import Laboratory, ExperimentalStation, Sample, Experiment, SampleForExperiment
 import json
 
 UserModel = get_user_model()

cnr-ifn.mi/UdyniManagement/LabLogbook/urls.py

@@ -1,5 +1,5 @@
-from . import views
-from . import views_api
+from LabLogbook import views
+from LabLogbook import views_api
 from UdyniManagement.views import EmptyView
 
 from django.urls import path, reverse_lazy

cnr-ifn.mi/UdyniManagement/LabLogbook/views.py

@@ -1,11 +1,10 @@
-from .models import Laboratory, Sample, ExperimentalStation, Experiment, SampleForExperiment, Measurement, File, Comment, CommentContent
-from .forms import CommentForm, CommentContentForm
+from LabLogbook.models import Laboratory, Sample, ExperimentalStation, Experiment, SampleForExperiment, Measurement, File, Comment, CommentContent
+from LabLogbook.forms import CommentForm, CommentContentForm
 from UdyniManagement.views import ListViewMenu, CreateViewMenu, UpdateViewMenu, DeleteViewMenu
 from UdyniManagement.menu import UdyniMenu
 
 from django.contrib.auth.mixins import PermissionRequiredMixin
 from django.views import View
-from django.db.models import Prefetch
 from django.shortcuts import get_object_or_404, render, redirect
 from django.urls import reverse_lazy
 

cnr-ifn.mi/UdyniManagement/LabLogbook/views_api.py

@@ -1,7 +1,7 @@
-from .models import ExperimentalStation
-from .models import Experiment
-from .models import SampleForExperiment
-from .models import Measurement, Sample, File, Comment, CommentContent
+from LabLogbook.models import ExperimentalStation
+from LabLogbook.models import Experiment
+from LabLogbook.models import SampleForExperiment
+from LabLogbook.models import Measurement, Sample, File, Comment, CommentContent
 
 import json
 from django.views import View

cnr-ifn.mi/UdyniManagement/Projects/forms.py

@@ -1,5 +1,5 @@
 from django import forms
-from .models import ResearcherRole, Project
+from Projects.models import ResearcherRole, Project
 
 
 class ResearcherRoleForm(forms.ModelForm):

cnr-ifn.mi/UdyniManagement/Projects/urls.py

@@ -1,7 +1,7 @@
 from django.urls import path, reverse_lazy
 from django.views.generic.base import RedirectView
 
-from . import views
+from Projects import views
 
 urlpatterns = [
     path('', RedirectView.as_view(url=reverse_lazy('project_view'), permanent=False), name='projects_index'),

cnr-ifn.mi/UdyniManagement/Projects/views.py

@@ -2,11 +2,11 @@
 from django.urls import reverse_lazy
 from django.db.models import F, Subquery
 
-from .models import Researcher, ResearcherRole, Project, WorkPackage, ConflictOfInterest
+from Projects.models import Researcher, ResearcherRole, Project, WorkPackage, ConflictOfInterest
 
 from django.contrib.auth.mixins import PermissionRequiredMixin
 
-from .forms import ResearcherRoleForm, ProjectForm
+from Projects.forms import ResearcherRoleForm, ProjectForm
 
 from django.views import View
 from UdyniManagement.views import ListViewMenu, CreateViewMenu, UpdateViewMenu, DeleteViewMenu

cnr-ifn.mi/UdyniManagement/Reporting/admin.py

@@ -1,5 +1,5 @@
 from django.contrib import admin
-from .models import BankHoliday, EpasCode, PersonnelCost, PresenceData, ReportingPeriod, ReportedWork, ReportedMission, ReportedWorkWorkpackage, TimesheetHours
+from Reporting.models import BankHoliday, EpasCode, PersonnelCost, PresenceData, ReportingPeriod, ReportedWork, ReportedMission, ReportedWorkWorkpackage, TimesheetHours
 
 # Register your models here.
 admin.site.register(BankHoliday)

cnr-ifn.mi/UdyniManagement/Reporting/timesheets.py

@@ -3,9 +3,9 @@
 
 from django.db.models import Q, F, Sum, Value, Subquery, OuterRef
 from django.db.models.functions import ExtractYear, ExtractMonth, Coalesce
-from .models import EpasCode, PresenceData, ReportedWork, ReportedMission, TimesheetHours
-from .utils import check_bank_holiday, get_workpackages_fractions
-from .utils import ReportingError
+from Reporting.models import EpasCode, PresenceData, ReportedWork, ReportedMission, TimesheetHours
+from Reporting.utils import check_bank_holiday, get_workpackages_fractions
+from Reporting.utils import ReportingError
 from Tags.templatetags import tr_month
 
 

cnr-ifn.mi/UdyniManagement/Reporting/utils.py

@@ -4,7 +4,7 @@
 from django.db.models import Q
 from Tags.templatetags.tr_month import month_num2it
 
-from .models import BankHoliday
+from Reporting.models import BankHoliday
 
 
 def process_presences(xls, researcher):

cnr-ifn.mi/UdyniManagement/Reporting/views.py

@@ -10,16 +10,16 @@
 from django.db.models.functions import ExtractYear, ExtractMonth, Concat, Coalesce, Floor, Least
 
 from Projects.models import Project, Researcher, ResearcherRole, WorkPackage, ConflictOfInterest
-from .models import EpasCode, BankHoliday, PersonnelCost, PresenceData, ReportingPeriod, ReportedWork, ReportedWorkWorkpackage, ReportedMission, TimesheetHours
+from Reporting.models import EpasCode, BankHoliday, PersonnelCost, PresenceData, ReportingPeriod, ReportedWork, ReportedWorkWorkpackage, ReportedMission, TimesheetHours
 
-from .forms import AddReportedMissionForm, EpasCodeUpdateForm, PresenceInputForm, ReportedWorkForm  #, ReportingAddForm
+from Reporting.forms import AddReportedMissionForm, EpasCodeUpdateForm, PresenceInputForm, ReportedWorkForm  #, ReportingAddForm
 
-from .utils import process_presences, summarize_presences, serialize_presences
-from .utils import unserialize_presences, check_presences_unique, check_bank_holiday
-from .utils import get_workpackages_fractions
-from .utils import ReportingError
-from .timesheets import CheckTimesheetData, GetTimesheetData
-from .print import PrintPFDTimesheet
+from Reporting.utils import process_presences, summarize_presences, serialize_presences
+from Reporting.utils import unserialize_presences, check_presences_unique, check_bank_holiday
+from Reporting.utils import get_workpackages_fractions
+from Reporting.utils import ReportingError
+from Reporting.timesheets import CheckTimesheetData, GetTimesheetData
+from Reporting.print import PrintPFDTimesheet
 
 from Tags.templatetags import tr_month
 

cnr-ifn.mi/UdyniManagement/UdyniManagement/settings/development.example.py

@@ -1,8 +1,8 @@
 # Development settings
 # NOTE: when running Django rename to development.py and set the environment variable DJANGO_SETTINGS_MODULE=UdyniManagement.settings.development
 
-from . import *  # Import base settings from settings/__init__.py
-from .development_logging import LOGGING  # Import logging configuration for production
+from UdyniManagement.settings import *  # Import base settings from settings/__init__.py
+from UdyniManagement.settings.development_logging import LOGGING  # Import logging configuration for production
 
 # Secret key
 SECRET_KEY = 'django-insecure-#m^ta)8wnr+v=@o*t5#n&coip**2brq!!j@b8i8-=_+j$3zo9='

cnr-ifn.mi/UdyniManagement/UdyniManagement/settings/production.example.py

@@ -1,8 +1,8 @@
 # Production settings
 # NOTE: when running Django rename to production.py and set the environment variable DJANGO_SETTINGS_MODULE=UdyniManagement.settings.production
 
-from . import *  # Import base settings from settings/__init__.py
-from production_logging import LOGGING  # Import logging configuration for production
+from UdyniManagement.settings import *  # Import base settings from settings/__init__.py
+from UdyniManagement.settings.production_logging import LOGGING  # Import logging configuration for production
 
 # Secret key
 SECRET_KEY = '*****************'  # Set this to a secure random value

cnr-ifn.mi/UdyniManagement/UdyniManagement/urls.py

@@ -15,8 +15,8 @@
 """
 from django.contrib import admin
 from django.urls import include, path
-from . import views
-from .menu import menu_include
+from UdyniManagement import views
+from UdyniManagement.menu import menu_include
 
 
 urlpatterns = [

cnr-ifn.mi/UdyniManagement/UdyniManagement/views.py

@@ -9,7 +9,7 @@
 from django.views.generic.edit import CreateView, UpdateView, DeleteView, FormView
 from django.contrib.auth.mixins import LoginRequiredMixin, PermissionRequiredMixin
 
-from .menu import UdyniMenu
+from UdyniManagement.menu import UdyniMenu
 
 
 # =============================================

cnr-ifn.mi/UdyniManagement/sigla/urls.py

@@ -1,6 +1,6 @@
 from django.urls import path, reverse_lazy
 
-from . import views
+from sigla import views
 
 
 urlpatterns = [

cnr-ifn.mi/UdyniManagement/sigla/views.py

@@ -12,7 +12,7 @@
 
 from UdyniManagement.menu import UdyniMenu
 
-from .sigla import SIGLA
+from sigla.sigla import SIGLA
 
 from Accounting.models import GAE
 

cnr-ifn.mi/udyninexus/udyninexus/__init__.py

@@ -1,9 +1,9 @@
-from .classes.NexusContainer import NexusContainer
-from .classes.Beam import Beam
-from .classes.Detector import Detector
-from .classes.Source import Source
-from .classes.Sample import Sample
-from .classes.Data import Axis, Data
-from .write_nexus import write_nexus
-from .exceptions import NexusSaveError, NexusValidationError
-from .logging_settings import set_log_level, set_log_file
+from udyninexus.classes.NexusContainer import NexusContainer
+from udyninexus.classes.Beam import Beam
+from udyninexus.classes.Detector import Detector
+from udyninexus.classes.Source import Source
+from udyninexus.classes.Sample import Sample
+from udyninexus.classes.Data import Axis, Data
+from udyninexus.write_nexus import write_nexus
+from udyninexus.exceptions import NexusSaveError, NexusValidationError
+from udyninexus.logging_settings import set_log_level, set_log_file

cnr-ifn.mi/udyninexus/udyninexus/classes/Beam.py

@@ -1,11 +1,24 @@
-from .Instrument import Instrument
-from ..utils import create_property_check_type, create_property_check_in_valid_values
-from .Source import Source
+from udyninexus.classes.Instrument import Instrument
+from udyninexus.classes.Source import Source
+from udyninexus.utils import create_property_check_type, create_property_check_in_valid_values
 
 from typing import Literal
 
 
 class Beam(Instrument):
+    """
+    Represents the characteristics of a beam used in spectroscopy experiments.
+
+    Attributes:
+        name_in_nexus (str): Identifier used in the NeXus file. The beam will be saved inside the 'instrument' group under the name 'beam\_\<name_in_nexus\>'.
+        beam_type (str): Specify the role of the beam ('pump' or 'probe').
+        parameter_reliability (str): Indicates how the beam characteristics were obtained ('measured', 'nominal').
+        incident_wavelength (int): Wavelength of the incident beam.
+        incident_wavelength_units (str): Units of the incident wavelength ('nm', 'um').
+        incident_polarization (int): Polarization value of the incident beam.
+        beam_polarization_type (str): Type of beam polarization ('linear', 'circular', 'elliptically', 'unpolarized').
+        associated_source (Source): Device that emitted the beam. In the NeXus file the path to the source will be specified in the 'associated_source' NXfield.
+    """
     def __init__(self,
             name_in_nexus: str = None,
             beam_type: Literal['pump', 'probe'] = None,

cnr-ifn.mi/udyninexus/udyninexus/classes/Data.py

@@ -1,9 +1,21 @@
-from ..utils import create_property_check_one_dimensional_axis_data, create_property_check_isinstance, create_property_check_type, create_property_check_type_for_lists
-from .Instrument import Instrument
+from udyninexus.classes.Instrument import Instrument
+from udyninexus.utils import create_property_check_one_dimensional_axis_data, create_property_check_isinstance, create_property_check_type, create_property_check_type_for_lists
+
 from typing import Optional, List, Any
 
 
 class Axis:
+    """
+    Represents a one-dimensional axis in data.
+
+    Attributes:
+        name (str): Name used to identify this axis in the NeXus file. This will be the key under which the signal data is stored.
+        data (List): A one-dimensional sequence of values representing the axis (e.g., range(10)).
+        units (str): The unit of measurement for the axis values (e.g., 'nm', 'ms'). Defaults to 'index' if not specified.
+        related_instrument (Instrument): Reference to the instrument that controls or is associated with this axis.\
+        If specified the signal data will be stored inside this instrument's group in the NeXus file and linked via an NXlink in the 'data' group.\
+        Otherwise the data of the axis will be directly saved inside the 'data' group.
+    """
     def __init__(self,
             name: str = None,
             data: Optional[List] = None,
@@ -23,6 +35,17 @@ def __init__(self,
 
 
 class Data:
+    """
+    Represents measured signal data.
+
+    Attributes:
+        signal_name (str): Name used to identify the signal in the NeXus file. This will be the key under which the signal data is stored.
+        signal_data: A multi-dimensional array of values representing the signal measurements.
+        signal_units (str): Unit of measurement for the signal values (e.g., 'nm', 'ms').
+        signal_related_instrument (Instrument): Reference to the instrument that measured the signal. The signal data will be stored inside this instrument's group in the NeXus file and linked via an NXlink in the 'data' group.
+        axes (List[Axis]): List of axes associated with the signal data.
+    """
+
     def __init__(self,
             signal_name: str = None,
             signal_data: Any = None, # it must be a data with a shape (multi dimensional array)