Update repository

manage.py

-#!/usr/bin/env python
-"""Django's command-line utility for administrative tasks."""
-import os
-import sys
-
-
-def main():
-    """Run administrative tasks."""
-    os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'newapi.settings')
-    try:
-        from django.core.management import execute_from_command_line
-    except ImportError as exc:
-        raise ImportError(
-            "Couldn't import Django. Are you sure it's installed and "
-            "available on your PYTHONPATH environment variable? Did you "
-            "forget to activate a virtual environment?"
-        ) from exc
-    execute_from_command_line(sys.argv)
-
-
-if __name__ == '__main__':
-    main()

mynewapi/admin.py

-from django.contrib import admin
-
-# Register your models here.

mynewapi/apps.py

-from django.apps import AppConfig
-
-
-class MynewapiConfig(AppConfig):
-    name = 'mynewapi'

mynewapi/migrations/models/report.py

-from django.db import models, StatisticalReport
-from neomodel import StructuredNode, StringProperty, IntegerProperty,UniqueIdProperty, RelationshipTo, DateTimeProperty, BooleanProperty
-
-class Report(StructuredNode):
- 	report_path=StringProperty()
- 	report_source=StringProperty()
- 	report_size=StringProperty()
- 	
- 	# Relationships
- 	is_statisticalreport=RelationshipTo(StatisticalReport, 'IS')
\ No newline at end of file

mynewapi/migrations/models/rsf.py

-from django.db import models, report, DPStep, MTZfile, ScalepackFile, Reference, Construct
-from neomodel import StructuredNode, StringProperty, IntegerProperty,UniqueIdProperty, RelationshipTo, DateTimeProperty, BooleanProperty
-
-class RefelctionStructureFactors(StructuredNode):
- 	rsf_source=StringProperty()
- 	rsf_filesize=StringProperty()
- 	rsf_filepath=StringProperty()
-
- 	# Relationships
- 	input_as_ref=RelationshipTo(DPStep, 'INPUT_AS_REFERENCE')
- 	input_of=RelationshipTo(DPStep, 'INPUT')
- 	generates_mtz=RelationshipTo(MTZfile, 'GENERATES')
- 	generates_scalepack=RelationshipTo(ScalepackFile, 'GENERATES')
- 	labelled=RelationshipTo(Reference, 'LABELLED')
- 	belongs=RelationshipTo(Construct, 'BELONGS')
\ No newline at end of file

mynewapi/models.py

-from django.db import models
-from neomodel import StructuredNode, StringProperty, IntegerProperty,UniqueIdProperty, RelationshipTo, DateTimeProperty, BooleanProperty
-
-# class City(StructuredNode):
-#     code = StringProperty(unique_index=True, required=True)
-#     name = StringProperty(index=True, default="city")
-
-#####################################
-# Nodes and properties of the model #
-#####################################
-
-class LigandsFitting(StructuredNode):
-	uid=UniqueIdProperty()
-	dp_step_name = StringProperty()
-	created_at=DateTimeProperty()
-	updated_at=DateTimeProperty()
-	pipedream_id=IntegerProperty()
-	score=IntegerProperty()
-	fitting_success=BooleanProperty()
-
-class Refinement(StructuredNode):
-	uid=UniqueIdProperty()
-	dp_step_name=StringProperty()
-	created_at=DateTimeProperty()
-	updated_at=DateTimeProperty()
-
-class PostRefinement(StructuredNode):
-	uid=UniqueIdProperty()
-	dp_step_name=StringProperty()
-	pipedream_id=IntegerProperty()
-	created_at=DateTimeProperty()
-	updated_at=DateTimeProperty()
-
-class ReductionScaling(StructuredNode):
-	uid=UniqueIdProperty()
-	dp_step_name=StringProperty()
-	created_at=DateTimeProperty()
-	updated_at=DateTimeProperty()
-
-class autoPROC(StructuredNode):
-	uid=UniqueIdProperty()
-	tool_name=StringProperty()
-
-class Buster(StructuredNode):
-	uid=UniqueIdProperty()
-	tool_name=StringProperty()
-
-class Rhofit(StructuredNode):
-	uid=UniqueIdProperty()
-	tool_name=StringProperty()
-
-class StatisticalReport(StructuredNode):
-	uid=UniqueIdProperty()
-	report_name=StringProperty()
-
-class ComputingHost(StructuredNode):
-	ch_softwares=StringProperty()
-	ch_softwares_number=IntegerProperty()
-
-class StorageHost(StructuredNode):
-	sh_files=StringProperty()
-	sh_files_number=IntegerProperty()
-
-##########################################################################
-
-class Report(StructuredNode):
- 	report_path=StringProperty()
- 	report_source=StringProperty()
- 	report_size=StringProperty()
-
- 	# Relationships
- 	is_statisticalreport=RelationshipTo(StatisticalReport, 'IS')
-
-class RefelctionStructureFactors(StructuredNode):
- 	rsf_source=StringProperty()
- 	rsf_filesize=StringProperty()
- 	rsf_filepath=StringProperty()
-
- 	# Relationships
- 	input_as_ref=RelationshipTo(DPStep, 'INPUT_AS_REFERENCE')
- 	input_of=RelationshipTo(DPStep, 'INPUT')
- 	generates_mtz=RelationshipTo(MTZfile, 'GENERATES')
- 	generates_scalepack=RelationshipTo(ScalepackFile, 'GENERATES')
- 	labelled=RelationshipTo(Reference, 'LABELLED')
- 	belongs=RelationshipTo(Construct, 'BELONGS')
-
-class DPStep(StructuredNode):
- 	
- 	# Relationships
- 	is_fitting=RelationshipTo(LigandsFitting, 'IS')
- 	is_refinement=RelationshipTo(Refinement, 'IS')
- 	is_postrefinement=RelationshipTo(PostRefinement, 'IS')
- 	is_reductionscaling=RelationshipTo(ReductionScaling, 'IS')
- 	with_tool_1=RelationshipTo(autoPROC, 'WITH')
- 	with_tool_2=RelationshipTo(Rhofit, 'WITH')
- 	with_tool_3=RelationshipTo(Buster, 'WITH')
- 	genereates_report=RelationshipTo(Report, 'GENERATES')
- 	# generates_coordinates=RelationshipTo(Coordinates, 'GENERATES')
- 	generates_rsf=RelationshipTo(RefelctionStructureFactors, 'GENERATES')
-
-class Coordinates(StructuredNode):
- 	coordinates_source=StringProperty(unique_index=True, required=True)
- 	coordinates_filesize=StringProperty(unique_index=True, required=True)
- 	coordinates_filepath=StringProperty(unique_index=True, required=True)
-
- 	# Relationships
- 	input_as_ref=RelationshipTo(DPStep, 'INPUT_AS_REFERENCE')
- 	input_of=RelationshipTo(DPStep, 'INPUT')
- 	has_pdb=RelationshipTo(PDBFile, 'HAS')
- 	has_mmcif=RelationshipTo(mmCIFFile, 'HAS')
- 	belongs=RelationshipTo(Construct, 'BELONGS')
- 	labelled=RelationshipTo(Reference, 'LABELLED')
-
-
-class DataCollection (StructuredNode):
- 	collection_type=StringProperty()
- 	collection_size=StringProperty()
-
- 	# Relationships
- 	genereates_dataset=RelationshipTo(Datatset, 'GENERATES')
-
-class Datatset(StructuredNode):
- 	dataset_file_no=IntegerProperty()
- 	dataset_size=StringProperty()
-
- 	# Relationships
- 	input_of=RelationshipTo(DPStep, 'INPUT')
- 	stored=RelationshipTo(StorageHost, 'STORED')
- 	belongs=RelationshipTo(Construct, 'BELONGS')
-
-class mmCIFFile(StructuredNode):
-	uid=UniqueIdProperty()
-	coordinates_filetype=StringProperty(unique_index=True, required=True)
-
-class PDBFile(StructuredNode):
-	uid=UniqueIdProperty()
-	coordinates_filetype=StringProperty(unique_index=True, required=True)
-
-class MTZfile(StructuredNode):
-	uid=UniqueIdProperty()
-	rsf_filetype = StringProperty(unique_index=True, required=True)
-
-class ScalepackFile(StructuredNode):
-	uid=UniqueIdProperty()
-	rsf_filetype = StringProperty(unique_index=True, required=True)
-
-class Reference(StructuredNode):
-	uid=UniqueIdProperty()
-
-class OCF(StructuredNode):
-	
-	# Relationships
-	has_rsf=RelationshipTo(RefelctionStructureFactors, 'HAS')
-	has_coordinates=RelationshipTo(Coordinates, 'HAS')
-
-class Construct(StructuredNode):
-	
-	# Relationships
-	has_ocf=RelationshipTo(OCF, 'HAS')
-	has_storage_host=RelationshipTo(StorageHost, 'HAS')
-	has_computing_host=RelationshipTo(ComputingHost, 'HAS')
-
-
-class Ligand(StructuredNode):
-	 
-	# Relationships
- 	associated=RelationshipTo(Datatset, 'ASSOCIATED')
-

mynewapi/tests.py

-from django.test import TestCase
-
-# Create your tests here.

mynewapi/views.py

-from django.shortcuts import render
-
-# Create your views here.

newapi/asgi.py

-"""
-ASGI config for newapi project.
-
-It exposes the ASGI callable as a module-level variable named ``application``.
-
-For more information on this file, see
-https://docs.djangoproject.com/en/3.1/howto/deployment/asgi/
-"""
-
-import os
-
-from django.core.asgi import get_asgi_application
-
-os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'newapi.settings')
-
-application = get_asgi_application()

newapi/settings.py

-"""
-Django settings for newapi project.
-
-Generated by 'django-admin startproject' using Django 3.1.6.
-
-For more information on this file, see
-https://docs.djangoproject.com/en/3.1/topics/settings/
-
-For the full list of settings and their values, see
-https://docs.djangoproject.com/en/3.1/ref/settings/
-"""
-
-from pathlib import Path
-import os 
-
-# Build paths inside the project like this: BASE_DIR / 'subdir'.
-BASE_DIR = Path(__file__).resolve().parent.parent
-
-
-# Quick-start development settings - unsuitable for production
-# See https://docs.djangoproject.com/en/3.1/howto/deployment/checklist/
-
-# SECURITY WARNING: keep the secret key used in production secret!
-SECRET_KEY = '=013nqbp3o8hr9e*it$b1um^%ke*uxqvt5qnp=xe6@^20a)d!b'
-
-# SECURITY WARNING: don't run with debug turned on in production!
-DEBUG = True
-
-ALLOWED_HOSTS = []
-
-
-# Application definition
-
-INSTALLED_APPS = [
-    'django.contrib.admin',
-    'django.contrib.auth',
-    'django.contrib.contenttypes',
-    'django.contrib.sessions',
-    'django.contrib.messages',
-    'django.contrib.staticfiles',
-
-    'mynewapi.apps.MynewapiConfig',
-    'django_neomodel'
-]
-
-MIDDLEWARE = [
-    'django.middleware.security.SecurityMiddleware',
-    'django.contrib.sessions.middleware.SessionMiddleware',
-    'django.middleware.common.CommonMiddleware',
-    'django.middleware.csrf.CsrfViewMiddleware',
-    'django.contrib.auth.middleware.AuthenticationMiddleware',
-    'django.contrib.messages.middleware.MessageMiddleware',
-    'django.middleware.clickjacking.XFrameOptionsMiddleware',
-]
-
-ROOT_URLCONF = 'newapi.urls'
-
-TEMPLATES = [
-    {
-        'BACKEND': 'django.template.backends.django.DjangoTemplates',
-        'DIRS': [],
-        'APP_DIRS': True,
-        'OPTIONS': {
-            'context_processors': [
-                'django.template.context_processors.debug',
-                'django.template.context_processors.request',
-                'django.contrib.auth.context_processors.auth',
-                'django.contrib.messages.context_processors.messages',
-            ],
-        },
-    },
-]
-
-WSGI_APPLICATION = 'newapi.wsgi.application'
-
-
-# Database
-# https://docs.djangoproject.com/en/3.1/ref/settings/#databases
-
-DATABASES = {
-    'default': {
-        'ENGINE': 'django.db.backends.sqlite3',
-        'NAME': BASE_DIR / 'db.sqlite3',
-    }
-}
-
-NEOMODEL_NEO4J_BOLT_URL = os.environ.get('NEO4J_BOLT_URL','bolt://neo4j:neo4@localhost:7687')
-
-
-
-# Password validation
-# https://docs.djangoproject.com/en/3.1/ref/settings/#auth-password-validators
-
-AUTH_PASSWORD_VALIDATORS = [
-    {
-        'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator',
-    },
-    {
-        'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator',
-    },
-    {
-        'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator',
-    },
-    {
-        'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',
-    },
-]
-
-
-# Internationalization
-# https://docs.djangoproject.com/en/3.1/topics/i18n/
-
-LANGUAGE_CODE = 'en-us'
-
-TIME_ZONE = 'UTC'
-
-USE_I18N = True
-
-USE_L10N = True
-
-USE_TZ = True
-
-
-# Static files (CSS, JavaScript, Images)
-# https://docs.djangoproject.com/en/3.1/howto/static-files/
-
-STATIC_URL = '/static/'