Merge pull request #14 from BBMRI-cz/import_issues

feat: move packages from src to root of the project

README.md

@@ -14,8 +14,8 @@ The MIABIS on FHIR profile full specification along with the guide is available
 
 ## Modules
 
-### 1. `MIABIS_on_FHIR`
-The `MIABIS_on_FHIR` module includes a set of classes to help developers:
+### 1. `miabis_model`
+The `miabis_model` 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.
@@ -37,14 +37,14 @@ This package is ideal for developers looking to work with MIABIS on FHIR resourc
 
 ## Installation
 ```bash 
-pip install MIABIS_on_FHIR
+pip install miabis_model
 ```
 ## How to use
 Here is how you can create a MIABIS on FHIR sample resource:
 
 ```python
-from MIABIS_on_FHIR import Sample
-from MIABIS_on_FHIR import StorageTemperature
+from miabis_model import Sample
+from miabis_model import StorageTemperature
 
 sample = Sample("sampleId", "donorId", "Urine", storage_temperature=StorageTemperature.TEMPERATURE_ROOM,
                 use_restrictions="No restrictions")
@@ -58,12 +58,12 @@ Here is an example on how to communicate with blaze server via the BlazeClient:
 
 ```python
 import datetime
-from MIABIS_on_FHIR import Gender
+from miabis_model import Gender
 from blaze_client import BlazeClient
-from MIABIS_on_FHIR import SampleDonor
+from miabis_model import SampleDonor
 
-client = BlazeClient("example_url","username","password")
+client = BlazeClient("example_url", "username", "password")
 
-donor = SampleDonor("donorId", Gender.MALE, birth_date=datetime.datetime(year=2000,month=12,day=12))
+donor = SampleDonor("donorId", Gender.MALE, birth_date=datetime.datetime(year=2000, month=12, day=12))
 donor_fhir_id = client.upload_donor(donor)
 ```

src/blaze_client/blaze_client.py → blaze_client/blaze_client.py

@@ -3,19 +3,19 @@
 from requests import Response
 from requests.adapters import HTTPAdapter, Retry
 
-from src.MIABIS_on_FHIR.biobank import Biobank
-from src.MIABIS_on_FHIR.collection import Collection
-from src.MIABIS_on_FHIR.collection_organization import CollectionOrganization
-from src.MIABIS_on_FHIR.condition import Condition
-from src.MIABIS_on_FHIR.diagnosis_report import DiagnosisReport
-from src.MIABIS_on_FHIR.network import Network
-from src.MIABIS_on_FHIR.network_organization import NetworkOrganization
-from src.MIABIS_on_FHIR.observation import Observation
-from src.MIABIS_on_FHIR.sample import Sample
-from src.MIABIS_on_FHIR.sample_donor import SampleDonor
-from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id, \
+from miabis_model.biobank import Biobank
+from miabis_model.collection import Collection
+from miabis_model.collection_organization import CollectionOrganization
+from miabis_model.condition import Condition
+from miabis_model.diagnosis_report import DiagnosisReport
+from miabis_model.network import Network
+from miabis_model.network_organization import NetworkOrganization
+from miabis_model.observation import Observation
+from miabis_model.sample import Sample
+from miabis_model.sample_donor import SampleDonor
+from miabis_model.util.parsing_util import get_nested_value, parse_reference_id, \
     get_material_type_from_detailed_material_type
-from src.blaze_client.NonExistentResourceException import NonExistentResourceException
+from blaze_client.NonExistentResourceException import NonExistentResourceException
 
 
 class BlazeClient:

src/MIABIS_on_FHIR/biobank.py → miabis_model/biobank.py

@@ -3,13 +3,13 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.organization import Organization
 
-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, \
+from miabis_model.incorrect_json_format import IncorrectJsonFormatException
+from miabis_model.util.config import FHIRConfig
+from miabis_model.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 miabis_model.util.parsing_util import get_nested_value, parse_contact
+from miabis_model.util.util import create_fhir_identifier, create_contact, create_country_of_residence, \
     create_codeable_concept_extension, create_string_extension
 
 

src/MIABIS_on_FHIR/collection.py → miabis_model/collection.py

@@ -9,13 +9,13 @@
 from fhirclient.models.quantity import Quantity
 from fhirclient.models.range import Range
 
-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.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, \
+from miabis_model.gender import Gender
+from miabis_model.incorrect_json_format import IncorrectJsonFormatException
+from miabis_model.storage_temperature import StorageTemperature
+from miabis_model.util.config import FHIRConfig
+from miabis_model.util.constants import COLLECTION_INCLUSION_CRITERIA, COLLECTION_MATERIAL_TYPE_CODES
+from miabis_model.util.parsing_util import get_nested_value, parse_reference_id
+from miabis_model.util.util import create_fhir_identifier, create_integer_extension, \
     create_codeable_concept_extension, \
     create_codeable_concept
 

src/MIABIS_on_FHIR/collection_organization.py → miabis_model/collection_organization.py

@@ -6,12 +6,12 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.organization import Organization
 
-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, \
+from miabis_model.incorrect_json_format import IncorrectJsonFormatException
+from miabis_model.util.config import FHIRConfig
+from miabis_model.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 miabis_model.util.parsing_util import get_nested_value, parse_contact, parse_reference_id
+from miabis_model.util.util import create_country_of_residence, create_contact, create_codeable_concept_extension, \
     create_string_extension, create_fhir_identifier
 
 

src/MIABIS_on_FHIR/condition.py → miabis_model/condition.py

@@ -7,10 +7,10 @@
 from fhirclient.models.fhirreference import FHIRReference
 from fhirclient.models.meta import Meta
 
-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.parsing_util import get_nested_value, parse_reference_id
-from src.MIABIS_on_FHIR.util.util import create_fhir_identifier
+from miabis_model.incorrect_json_format import IncorrectJsonFormatException
+from miabis_model.util.config import FHIRConfig
+from miabis_model.util.parsing_util import get_nested_value, parse_reference_id
+from miabis_model.util.util import create_fhir_identifier
 
 
 class Condition:

src/MIABIS_on_FHIR/diagnosis_report.py → miabis_model/diagnosis_report.py

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

src/MIABIS_on_FHIR/network.py → miabis_model/network.py

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

src/MIABIS_on_FHIR/network_organization.py → miabis_model/network_organization.py

@@ -4,11 +4,11 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.organization import Organization
 
-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 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, \
+from miabis_model.incorrect_json_format import IncorrectJsonFormatException
+from miabis_model.util.config import FHIRConfig
+from miabis_model.util.constants import NETWORK_COMMON_COLLAB_TOPICS
+from miabis_model.util.parsing_util import get_nested_value, parse_contact, parse_reference_id
+from miabis_model.util.util import create_fhir_identifier, create_contact, create_country_of_residence, \
     create_codeable_concept_extension, create_string_extension
 
 

src/MIABIS_on_FHIR/observation.py → miabis_model/observation.py

@@ -11,10 +11,10 @@
 from fhirclient.models.fhirreference import FHIRReference
 from fhirclient.models.meta import Meta
 
-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.parsing_util import get_nested_value, parse_reference_id
-from src.MIABIS_on_FHIR.util.util import create_fhir_identifier
+from miabis_model.incorrect_json_format import IncorrectJsonFormatException
+from miabis_model.util.config import FHIRConfig
+from miabis_model.util.parsing_util import get_nested_value, parse_reference_id
+from miabis_model.util.util import create_fhir_identifier
 
 
 class Observation:

src/MIABIS_on_FHIR/sample.py → miabis_model/sample.py

@@ -9,12 +9,12 @@
 from fhirclient.models.meta import Meta
 from fhirclient.models.specimen import Specimen, SpecimenCollection, SpecimenProcessing
 
-from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException
-from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature
-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, \
+from miabis_model.incorrect_json_format import IncorrectJsonFormatException
+from miabis_model.storage_temperature import StorageTemperature
+from miabis_model.util.config import FHIRConfig
+from miabis_model.util.constants import DETAILED_MATERIAL_TYPE_CODES
+from miabis_model.util.parsing_util import get_nested_value, parse_reference_id
+from miabis_model.util.util import create_fhir_identifier, create_codeable_concept, \
     create_codeable_concept_extension
 
 

src/MIABIS_on_FHIR/sample_donor.py → miabis_model/sample_donor.py

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

src/MIABIS_on_FHIR/util/parsing_util.py → miabis_model/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 miabis_model.util.constants import DETAILED_MATERIAL_TYPE_TO_COLLECTION_MATERIAL_TYPE_MAP
 
 
 def get_nested_value(data: dict, keys: list):

pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "MIABIS_on_FHIR"
-version = "1.0.0"
-description = "Library containing classes for easier handling of data according to the MIABIS on FHIR profile"
+version = "1.1.0"
+description = "Library containing classes for easier handling of data according to the MIABIS on FHIR profile, as well as client for communication with sample blaze server"
 readme = "README.md"
 authors = [{"name" = "Simon Konar", "email" = "[email protected]"}]
 license = { file = "LICENSE" }
@@ -26,11 +26,8 @@ requires-python = ">=3.11"
 [project.optional-dependencies]
  test=["pytest >= 8.3.0"]
 
-[tool.setuptools]
-package-dir = { "" = "src" }
 
 
 [tool.setuptools.packages.find]
-where = ["src"]
-include = ["MIABIS_on_FHIR*", "blaze_client*"]
+include = ["miabis_model*", "blaze_client*"]
 exclude =["test*"]

test/service/test_blaze_client.py

@@ -3,24 +3,22 @@
 
 import pytest as pytest
 import requests.exceptions
-from fhirclient.models.bundle import Bundle, BundleEntry, BundleEntryRequest
-from fhirclient.models.patient import Patient
 from requests.exceptions import HTTPError
 
-from src.MIABIS_on_FHIR.biobank import Biobank
-from src.MIABIS_on_FHIR.collection import Collection
-from src.MIABIS_on_FHIR.collection_organization import CollectionOrganization
-from src.MIABIS_on_FHIR.condition import Condition
-from src.MIABIS_on_FHIR.diagnosis_report import DiagnosisReport
-from src.MIABIS_on_FHIR.gender import Gender
-from src.MIABIS_on_FHIR.network import Network
-from src.MIABIS_on_FHIR.network_organization import NetworkOrganization
-from src.MIABIS_on_FHIR.observation import Observation
-from src.MIABIS_on_FHIR.sample import Sample
-from src.MIABIS_on_FHIR.sample_donor import SampleDonor
-from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature
-from src.blaze_client.NonExistentResourceException import NonExistentResourceException
-from src.blaze_client.blaze_client import BlazeClient
+from miabis_model import Biobank
+from miabis_model import Collection
+from miabis_model.collection_organization import CollectionOrganization
+from miabis_model import Condition
+from miabis_model import DiagnosisReport
+from miabis_model import Gender
+from miabis_model import Network
+from miabis_model import NetworkOrganization
+from miabis_model.observation import Observation
+from miabis_model import Sample
+from miabis_model import SampleDonor
+from miabis_model import StorageTemperature
+from blaze_client import NonExistentResourceException
+from blaze_client.blaze_client import BlazeClient
 
 
 class TestBlazeService(unittest.TestCase):

test/unit/model/test_biobank.py

@@ -1,6 +1,6 @@
 import unittest
 
-from src.MIABIS_on_FHIR.biobank import Biobank
+from miabis_model import Biobank
 
 
 class TestBiobank(unittest.TestCase):

test/unit/model/test_collection.py

@@ -2,9 +2,9 @@
 
 from fhirclient.models.group import Group
 
-from src.MIABIS_on_FHIR.collection import Collection
-from src.MIABIS_on_FHIR.gender import Gender
-from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature
+from miabis_model import Collection
+from miabis_model import Gender
+from miabis_model import StorageTemperature
 
 
 class TestCollection(unittest.TestCase):

test/unit/model/test_collection_org.py

@@ -1,6 +1,6 @@
 import unittest
 
-from src.MIABIS_on_FHIR.collection_organization import CollectionOrganization
+from miabis_model.collection_organization import CollectionOrganization
 
 
 class TestCollectionOrganization(unittest.TestCase):

test/unit/model/test_condition.py

@@ -1,6 +1,6 @@
 import unittest
 
-from src.MIABIS_on_FHIR.condition import Condition
+from miabis_model import Condition
 
 
 class TestCondition(unittest.TestCase):

test/unit/model/test_diagnosis_report.py

@@ -1,6 +1,6 @@
 import unittest
 
-from src.MIABIS_on_FHIR.diagnosis_report import DiagnosisReport
+from miabis_model import DiagnosisReport
 
 
 class TestDiagnosisReport(unittest.TestCase):

test/unit/model/test_network.py

@@ -1,6 +1,6 @@
 import unittest
 
-from src.MIABIS_on_FHIR.network import Network
+from miabis_model import Network
 
 
 class TestNetwork(unittest.TestCase):

test/unit/model/test_network_org.py

@@ -1,6 +1,6 @@
 import unittest
 
-from src.MIABIS_on_FHIR.network_organization import NetworkOrganization
+from miabis_model import NetworkOrganization
 
 
 class TestNetworkOrganization(unittest.TestCase):

test/unit/model/test_observation.py

@@ -1,7 +1,7 @@
 import datetime
 import unittest
 
-from src.MIABIS_on_FHIR.observation import Observation
+from miabis_model.observation import Observation
 
 
 class TestObservation(unittest.TestCase):