Merge pull request #13 from BBMRI-cz/package_refactoring

Package refactoring

README.md

@@ -1,3 +1,5 @@
+## Introduction
+
 MIABIS is focused on standardizing the data elements used to describe biobanks, research on samples, and related data.
 The goal of MIABIS is to enhance interoperability among biobanks that share valuable data and samples. MIABIS Core 2.0,
 introduced in 2016, established general attributes at an aggregated/metadata level for describing biobanks, sample
@@ -10,8 +12,28 @@ The foundation for this FHIR profile (all the attributes defined by MIABIS) is a
 
 The MIABIS on FHIR profile full specification along with the guide is available on the [simplifier platform](https://simplifier.net/miabis). 
 
-This Python package provides a set of classes that can be used to create, read, and validate MIABIS on FHIR resources, as well as to convert them to and from JSON format.
-This package aims to allow developers to easily work with MIABIS on FHIR resources in Python, while ensuring that the resources are compliant with the MIABIS on FHIR profile.
+## Modules
+
+### 1. `MIABIS_on_FHIR`
+The `MIABIS_on_FHIR` module includes a set of classes to help developers:
+- **Create** MIABIS on FHIR resources.
+- **Read** and **validate** these resources.
+- **Convert** resources to and from JSON format.
+
+This module ensures compliance with the MIABIS on FHIR profile, allowing developers to handle MIABIS resources confidently and efficiently in Python.
+
+### 2. `blaze_client`
+The `blaze_client` module simplifies communication with the [Samply.blaze](https://github.com/samply/blaze) FHIR storage server. Samply.blaze is a FHIR-compliant database designed for managing and storing FHIR resources. This module provides:
+- **Streamlined communication** with Samply.blaze, abstracting away the need for direct JSON response handling.
+- **BlazeClient** methods that simplify operations with the server, focusing on ease of use and minimizing boilerplate code.
+
+## Key Features
+- **Compliance**: Ensures MIABIS on FHIR resources meet the profile standards.
+- **Ease of Use**: Abstracts complex JSON interactions for a streamlined experience.
+- **Blaze Integration**: Seamless integration with Samply.blaze for FHIR resource management.
+
+This package is ideal for developers looking to work with MIABIS on FHIR resources and interact with FHIR storage servers using Python.
+
 
 ## Installation
 ```bash 
@@ -24,10 +46,24 @@ Here is how you can create a MIABIS on FHIR sample resource:
 from src.MIABIS_on_FHIR import Sample
 from src.MIABIS_on_FHIR import StorageTemperature
 
-sample = Sample("sampleId", "donorId", "Blood", storage_temperature=StorageTemperature.TEMPERATURE_GN,
+sample = Sample("sampleId", "donorId", "Urine", storage_temperature=StorageTemperature.TEMPERATURE_ROOM,
                 use_restrictions="No restrictions")
-# Convert the MoFSample object to a FHIR resource
+# Convert the Sample object to a FHIR resource
 sample_resource = sample.to_fhir("donorId")
 # Convert the FHIR resource to a JSON string
-sample_json = sample_resource.to_json()
-```
+sample_json = sample_resource.as_json()
+```
+
+Here is an example on how to communicate with blaze server via the BlazeClient:
+
+```python
+import datetime
+from src.MIABIS_on_FHIR import Gender
+from src.blaze_client import BlazeClient
+from src.MIABIS_on_FHIR import SampleDonor
+
+client = BlazeClient("example_url","username","password")
+
+donor = SampleDonor("donorId", Gender.MALE, birth_date=datetime.datetime(year=2000,month=12,day=12))
+donor_fhir_id = client.upload_donor(donor)
+```

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "MIABIS_on_FHIR"
-version = "1.0.0"
+version = "1.1.1dev01"
 description = "Library containing classes for easier handling of data according to the MIABIS on FHIR profile"
 readme = "README.md"
 authors = [{"name" = "Simon Konar", "email" = "[email protected]"}]
@@ -16,13 +16,21 @@ classifiers = [
 keywords = ["MIABIS", "FHIR", "model" , "profile", "data", "handling"]
 dependencies = [
     "simple-icd-10 >= 2.0.0",
-    "fhirclient >= 4.2.1"
+    "fhirclient >= 4.2.1",
+    "requests >= 2.32",
+    "python-dateutil >= 2.9.0"
+
 ]
 requires-python = ">=3.11"
 
 [project.optional-dependencies]
- test=["requests >= 2.32.0"]
+ test=["pytest >= 8.3.0"]
+
+[tool.setuptools]
+package-dir = { "" = "src" }
 
 
 [tool.setuptools.packages.find]
+where = ["src"]
+include = ["MIABIS_on_FHIR*", "blaze_client*"]
 exclude =["test*"]

src/MIABIS_on_FHIR/__init__.py

@@ -0,0 +1,13 @@
+from .biobank import Biobank
+from .collection import Collection
+from .collection_organization import CollectionOrganization
+from .condition import Condition
+from .diagnosis_report import DiagnosisReport
+from .gender import Gender
+from .incorrect_json_format import IncorrectJsonFormatException
+from .network import Network
+from .network_organization import NetworkOrganization
+from .observation import Observation
+from .sample import Sample
+from .sample_donor import SampleDonor
+from .storage_temperature import StorageTemperature

src/MIABIS_on_FHIR/biobank.py

@@ -3,14 +3,14 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.organization import Organization
 
-from src.MIABIS_on_FHIR.util._constants import BIOBANK_BIOPROCESSING_AND_ANALYTICAL_CAPABILITIES, \
+from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.constants import BIOBANK_BIOPROCESSING_AND_ANALYTICAL_CAPABILITIES, \
     BIOBANK_INFRASTRUCTURAL_CAPABILITIES, \
     BIOBANK_ORGANISATIONAL_CAPABILITIES, DEFINITION_BASE_URL
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_contact
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier, create_contact, create_country_of_residence, \
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_contact
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_contact, create_country_of_residence, \
     create_codeable_concept_extension, create_string_extension
-from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.config import FHIRConfig
 
 
 class Biobank:
@@ -30,14 +30,14 @@ def __init__(self, identifier: str, name: str, alias: str, country: str, contact
         :param contact_surname: surname of the contact person
         :param contact_email: email of the contact person
         :param infrastructural_capabilities: The technical infrastructural capabilities that
-        the biobank can offer to the clients. Available values in the _constants.py file
+        the biobank can offer to the clients. Available values in the constants.py file
         :param organisational_capabilities: The organisational capabilities and services that
-        the biobank can provide to support clients. Available values in the _constants.py file
+        the biobank can provide to support clients. Available values in the constants.py file
         :param bioprocessing_and_analysis_capabilities: The bioprocessing and analytical services
-        that the biobank can offer to the clients. Available values in the _constants.py file
+        that the biobank can offer to the clients. Available values in the constants.py file
         :param quality__management_standards: The standards that the biobank is certified or accredited for.
         :param juristic_person: The legal entity that is responsible for the biobank.
-        Available values in the _constants.py file
+        Available values in the constants.py file
         """
         self.identifier = identifier
         self.name = name
@@ -316,7 +316,7 @@ def to_fhir(self) -> Organization:
                                         self.juristic_person))
         if self.description is not None:
             extensions.append(create_string_extension(
-                FHIRConfig.get_extension_url("biobank","description"),
+                FHIRConfig.get_extension_url("biobank", "description"),
                 self.description))
         if extensions:
             fhir_organization.extension = extensions

src/MIABIS_on_FHIR/collection.py

@@ -9,16 +9,15 @@
 from fhirclient.models.quantity import Quantity
 from fhirclient.models.range import Range
 
-from src.MIABIS_on_FHIR.util._constants import COLLECTION_INCLUSION_CRITERIA, COLLECTION_MATERIAL_TYPE_CODES, \
-    DEFINITION_BASE_URL
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_reference_id
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier, create_integer_extension, \
-    create_codeable_concept_extension, \
-    create_codeable_concept
 from src.MIABIS_on_FHIR.gender import Gender
 from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
 from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature
-from src.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.constants import COLLECTION_INCLUSION_CRITERIA, COLLECTION_MATERIAL_TYPE_CODES
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_integer_extension, \
+    create_codeable_concept_extension, \
+    create_codeable_concept
 
 
 class Collection:
@@ -40,7 +39,7 @@ def __init__(self, identifier: str, name: str, managing_collection_org_id: str,
         :param storage_temperatures: List of storage temperatures of the samples in the collection.
         :param material_types: List of material types of the samples in the collection.
         :param diagnoses: List of diagnoses of the subjects in the collection.
-         Available values in the _constants.py file
+         Available values in the constants.py file
         :param number_of_subjects: Number of subjects in the collection.
         :param inclusion_criteria: Inclusion criteria for the subjects in the collection.
         :param sample_ids: List of sample identifiers belonging to the collection.

src/MIABIS_on_FHIR/collection_organization.py

@@ -6,14 +6,13 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.organization import Organization
 
-from src.MIABIS_on_FHIR.util._constants import COLLECTION_DESIGN, COLLECTION_SAMPLE_COLLECTION_SETTING, \
+from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.constants import COLLECTION_DESIGN, COLLECTION_SAMPLE_COLLECTION_SETTING, \
     COLLECTION_SAMPLE_SOURCE, COLLECTION_DATASET_TYPE, COLLECTION_USE_AND_ACCESS_CONDITIONS
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_contact, parse_reference_id
-from src.MIABIS_on_FHIR.util._util import create_country_of_residence, create_contact, \
-    create_codeable_concept_extension, \
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_contact, parse_reference_id
+from src.MIABIS_on_FHIR.util.util import create_country_of_residence, create_contact, create_codeable_concept_extension, \
     create_string_extension, create_fhir_identifier
-from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.config import FHIRConfig
 
 
 class CollectionOrganization:
@@ -43,12 +42,12 @@ def __init__(self, identifier: str, name: str, managing_biobank_id: str,
         :param alias: Alias of the collection.
         :param url: URL of the collection.
         :param description: Description of the collection.
-        :param dataset_type: Type of the dataset. Available values in the _constants.py file
-        :param sample_source: Source of the samples. Available values in the _constants.py file
-        :param sample_collection_setting: Setting of the sample collection. Available values in the _constants.py file
-        :param collection_design: Design of the collection. Available values in the _constants.py file
+        :param dataset_type: Type of the dataset. Available values in the constants.py file
+        :param sample_source: Source of the samples. Available values in the constants.py file
+        :param sample_collection_setting: Setting of the sample collection. Available values in the constants.py file
+        :param collection_design: Design of the collection. Available values in the constants.py file
         :param use_and_access_conditions: Conditions for use and access of the collection.
-         Available values in the _constants.py file
+         Available values in the constants.py file
         :param publications: Publications related to the collection.
         """
 

src/MIABIS_on_FHIR/condition.py

@@ -1,16 +1,16 @@
 from typing import Self
+
 import fhirclient.models.condition as fhir_condition
 import simple_icd_10 as icd10
 from fhirclient.models.codeableconcept import CodeableConcept
 from fhirclient.models.coding import Coding
 from fhirclient.models.fhirreference import FHIRReference
 from fhirclient.models.meta import Meta
 
-from src.MIABIS_on_FHIR.util._constants import DEFINITION_BASE_URL
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_reference_id
 from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier
-from src.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier
 
 
 class Condition:

src/MIABIS_on_FHIR/diagnosis_report.py

@@ -6,11 +6,10 @@
 from fhirclient.models.fhirreference import FHIRReference
 from fhirclient.models.meta import Meta
 
-from src.MIABIS_on_FHIR.util._constants import DEFINITION_BASE_URL
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_reference_id
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier
 from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier
 
 
 class DiagnosisReport:

src/MIABIS_on_FHIR/network.py

@@ -5,10 +5,10 @@
 from fhirclient.models.group import Group
 from fhirclient.models.meta import Meta
 
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_reference_id
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier
 from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier
 
 
 class Network:

src/MIABIS_on_FHIR/network_organization.py

@@ -4,12 +4,12 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.organization import Organization
 
-from src.MIABIS_on_FHIR.util._constants import NETWORK_COMMON_COLLAB_TOPICS, DEFINITION_BASE_URL
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_contact, parse_reference_id
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier, create_contact, create_country_of_residence, \
-    create_codeable_concept_extension, create_string_extension
 from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.constants import NETWORK_COMMON_COLLAB_TOPICS
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_contact, parse_reference_id
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_contact, create_country_of_residence, \
+    create_codeable_concept_extension, create_string_extension
 
 
 class NetworkOrganization:

src/MIABIS_on_FHIR/observation.py

@@ -1,22 +1,20 @@
 from datetime import datetime
-from dateutil import parser as date_parser
 from typing import Self
 
 import fhirclient.models.observation as fhir_observation
 import simple_icd_10 as icd10
+from dateutil import parser as date_parser
 from dateutil.parser import ParserError
 from fhirclient.models.codeableconcept import CodeableConcept
 from fhirclient.models.coding import Coding
-from fhirclient.models.fhirdate import FHIRDate
 from fhirclient.models.fhirdatetime import FHIRDateTime
 from fhirclient.models.fhirreference import FHIRReference
 from fhirclient.models.meta import Meta
 
-from src.MIABIS_on_FHIR.util._constants import DEFINITION_BASE_URL
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_reference_id
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier
 from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier
 
 
 class Observation:

src/MIABIS_on_FHIR/sample.py

@@ -9,13 +9,13 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.specimen import Specimen, SpecimenCollection, SpecimenProcessing
 
-from src.MIABIS_on_FHIR.util._constants import DETAILED_MATERIAL_TYPE_CODES, DEFINITION_BASE_URL
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value, parse_reference_id
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier, create_codeable_concept, \
-    create_codeable_concept_extension
 from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
 from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature
-from src.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.constants import DETAILED_MATERIAL_TYPE_CODES
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_codeable_concept, \
+    create_codeable_concept_extension
 
 
 class Sample:

src/MIABIS_on_FHIR/sample_donor.py

@@ -6,12 +6,12 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.patient import Patient
 
-from src.MIABIS_on_FHIR.util._constants import DONOR_DATASET_TYPE, DEFINITION_BASE_URL
-from src.MIABIS_on_FHIR.util._parsing_util import get_nested_value
-from src.MIABIS_on_FHIR.util._util import create_fhir_identifier, create_codeable_concept_extension
 from src.MIABIS_on_FHIR.gender import Gender
 from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.config import FHIRConfig
+from src.MIABIS_on_FHIR.util.constants import DONOR_DATASET_TYPE
+from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value
+from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_codeable_concept_extension
 
 
 class SampleDonor:

src/MIABIS_on_FHIR/util/_parsing_util.py → src/MIABIS_on_FHIR/util/parsing_util.py

@@ -1,7 +1,7 @@
 from dateutil import parser as date_parser
 from datetime import date
 
-from src.MIABIS_on_FHIR.util._constants import DETAILED_MATERIAL_TYPE_TO_COLLECTION_MATERIAL_TYPE_MAP
+from src.MIABIS_on_FHIR.util.constants import DETAILED_MATERIAL_TYPE_TO_COLLECTION_MATERIAL_TYPE_MAP
 
 
 def get_nested_value(data: dict, keys: list):

src/blaze_client/__init__.py

@@ -0,0 +1,2 @@
+from .blaze_client import BlazeClient
+from .NonExistentResourceException import NonExistentResourceException