brainstem-python-api-tools 0.1.0__tar.gz

brainstem_python_api_tools-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Peter C. Petersen - BrainSTEM Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

brainstem_python_api_tools-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: brainstem_python_api_tools
+Version: 0.1.0
+Summary: A Python toolset for interacting with API of BrainSTEM.
+Home-page: https://github.com/brainstem-org/brainstem_python_api_tools
+Author: BrainSTEM Team
+Author-email: petersen.peter@gmail.com
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: jupyter
+
+# brainstem_python_api_tools
+Python toolset for interacting with the API of BrainSTEM
+
+Please see the tutorial script (brainstem_api_tutorial.py) for example calls

brainstem_python_api_tools-0.1.0/README.md

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+# brainstem_python_api_tools
+Python toolset for interacting with the API of BrainSTEM
+
+Please see the tutorial script (brainstem_api_tutorial.py) for example calls

brainstem_python_api_tools-0.1.0/brainstem_api_tools/__init__.py

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+from .brainstem_api_client import BrainstemClient, ModelType, PortalType

brainstem_python_api_tools-0.1.0/brainstem_api_tools/brainstem_api_client.py

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+import os
+from getpass import getpass
+import requests
+from requests.models import Response
+import json
+from enum import Enum
+
+
+class ModelType(Enum):
+    project = "project"
+    subject = "subject"
+    session = "session"
+    collection = "collection"
+    cohort = "cohort"
+    procedure = "procedure"
+    behavior = "behavior"
+    dataacquisition = "dataacquisition"
+    manipulation = "manipulation"
+    equipment = "equipment"
+    consumablestock = "consumablestock"
+    procedurelog = "procedurelog"
+    subjectlog = "subjectlog"
+    behavioralparadigm = "behavioralparadigm"
+    datastorage = "datastorage"
+    inventory = "inventory"
+    setup = "setup"
+    consumable = "consumable"
+    hardwaredevice = "hardwaredevice"
+    supplier = "supplier"
+    brainregion = "brainregion"
+    setuptype = "setuptype"
+    species = "species"
+    strain = "strain"
+    strainapproval = "strainapproval"
+    journal = "journal"
+    laboratory = "laboratory"
+    publication = "publication"
+    journalapproval = "journalapproval"
+    user = "user"
+    group = "group"
+
+
+class PortalType(Enum):
+    public = "public"
+    private = "private"
+    super = "super"
+
+
+class LoginError(Exception):
+    def __str__(self):
+        return f'User/password combination incorrect or user does not exist'
+
+
+class BrainstemClient:
+
+    def __init__(self,
+                 token: str = None) -> None:
+
+        # Server path
+        self._address = 'https://www.brainstem.org/api/'
+
+        if token:
+            self._token = token
+        else:
+            username = input("Please enter your username:")
+            password = getpass("Please enter your password:")
+
+            self._token = self.__set_token_authentication(
+                url=self._address + "token/",
+                username=username,
+                password=password,
+            )
+
+            print("Your authorization token is:\n", self._token)
+            print("\nPlease keep it in a safe place.")
+
+    def __set_token_authentication(self,
+                                   url: str,
+                                   username: str,
+                                   password: str) -> str:
+
+        headers = {
+            "accept": "application/json",
+            "Content-Type": "application/json"
+        }
+        params = {
+            "username": username,
+            "password": password
+        }
+        resp = requests.post(url, headers=headers, json=params)
+
+        if resp.status_code != 200:
+            raise LoginError()
+
+        token = json.loads(resp.text)['token']
+        return token
+
+    def __get_app_from_model(self, modelname: str) -> str:
+        app = None
+
+        if modelname in ['project', 'subject', 'session', 'collection', 'cohort',
+                         'projectmembershipinvitation',
+                         'projectgroupmembershipinvitation']:
+            app = 'stem'
+
+        elif modelname in ['procedure', 'behavior', 'dataacquisition', 'manipulation', 
+                           'equipment', 'consumablestock', 'procedurelog', 'subjectlog']:
+            app = 'modules'
+
+        elif modelname in ['behavioralparadigm', 'datastorage', 'inventory',
+                           'setup']:
+            app = 'personal_attributes'
+
+        elif any([x in modelname for x in
+                 ['consumable', 'hardwaredevice', 'supplier']]):
+            app = 'resources'
+
+        elif any([x in modelname for x in
+                 ['brainregion', 'setuptype',
+                  'species', 'strain']]):
+            app = 'taxonomies'
+
+        elif any([x in modelname for x in
+                 ['journal', 'laboratory', 'publication']]):
+            app = 'attributes'
+
+        elif modelname in ['user', 'group', 'groupmembershipinvitation',
+                           'groupmembershiprequest']:
+            app = 'users'
+
+        return app
+
+    def load_model(self,
+                   model: ModelType,
+                   portal: PortalType = "private",
+                   id: str = None,
+                   options: str = None,
+                   filters: dict = None,
+                   sort: list = None,
+                   include: list = None) -> Response:
+
+        app = self.__get_app_from_model(model)
+        if app is None:
+            resp = Response()
+            resp.status_code = 404
+            return resp
+
+        if options is None:
+            options = ""
+
+        if id:
+            query_parameters = id + "/" + options
+        else:
+            query_parameters = ""
+
+            if filters:
+                for key in filters.keys():
+                    if query_parameters == "":
+                        prefix = "?"
+                    else:
+                        prefix = "&"
+                    query_parameters += (prefix
+                                         + "filter{" + key + "}="
+                                         + filters[key])
+            if sort:
+                for elem in sort:
+                    if query_parameters == "":
+                        prefix = "?"
+                    else:
+                        prefix = "&"
+                    query_parameters += prefix + "sort[]=" + elem
+
+            if include:
+                for elem in include:
+                    if query_parameters == "":
+                        prefix = "?"
+                    else:
+                        prefix = "&"
+                    query_parameters += prefix + "include[]=" + elem + ".*"
+
+        request_url = (self._address + portal
+                       + "/" + app + "/" + model
+                       + "/" + query_parameters)
+
+        resp = requests.get(request_url,
+                            headers={"Authorization": "Bearer %s"
+                                     % self._token})
+        return resp
+
+    def save_model(self,
+                   model: ModelType,
+                   portal: PortalType = "private",
+                   id: str = None,
+                   data: dict = None,
+                   options: str = None) -> Response:
+
+        app = self.__get_app_from_model(model)
+        if app is None:
+            resp = Response()
+            resp.status_code = 404
+            return resp
+
+        if data is None:
+            data = {}
+
+        if options is None:
+            options = ""
+
+        # Check if entry already exists
+        if id is not None:
+            # This is an update request
+            request_url = (self._address + portal + "/" + app + "/" + model
+                           + "/" + id + "/" + options)
+            resp = requests.patch(request_url, json=data,
+                                  headers={"Authorization": "Bearer %s"
+                                           % self._token})
+
+        else:
+            # This is a create request
+            request_url = (self._address + portal + "/" + app + "/"
+                           + model + "/" + options)
+            resp = requests.post(request_url, json=data,
+                                 headers={"Authorization": "Bearer %s"
+                                          % self._token})
+
+        return resp
+
+    def delete_model(self,
+                     model: ModelType,
+                     portal: PortalType = "private",
+                     id: str = None):
+
+        app = self.__get_app_from_model(model)
+        if app is None:
+            resp = Response()
+            resp.status_code = 404
+            return resp
+
+        # Check if entry already exists
+        if id is not None:
+            request_url = (self._address + portal + "/" + app + "/" + model
+                           + "/" + id + "/")
+            resp = requests.delete(request_url,
+                                   headers={"Authorization": "Bearer %s"
+                                            % self._token})
+
+            return resp

brainstem_python_api_tools-0.1.0/brainstem_python_api_tools.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: brainstem_python_api_tools
+Version: 0.1.0
+Summary: A Python toolset for interacting with API of BrainSTEM.
+Home-page: https://github.com/brainstem-org/brainstem_python_api_tools
+Author: BrainSTEM Team
+Author-email: petersen.peter@gmail.com
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: jupyter
+
+# brainstem_python_api_tools
+Python toolset for interacting with the API of BrainSTEM
+
+Please see the tutorial script (brainstem_api_tutorial.py) for example calls

brainstem_python_api_tools-0.1.0/brainstem_python_api_tools.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+setup.py
+brainstem_api_tools/__init__.py
+brainstem_api_tools/brainstem_api_client.py
+brainstem_python_api_tools.egg-info/PKG-INFO
+brainstem_python_api_tools.egg-info/SOURCES.txt
+brainstem_python_api_tools.egg-info/dependency_links.txt
+brainstem_python_api_tools.egg-info/requires.txt
+brainstem_python_api_tools.egg-info/top_level.txt

brainstem_python_api_tools-0.1.0/brainstem_python_api_tools.egg-info/dependency_links.txt

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+

brainstem_python_api_tools-0.1.0/brainstem_python_api_tools.egg-info/requires.txt

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+requests
+jupyter

brainstem_python_api_tools-0.1.0/brainstem_python_api_tools.egg-info/top_level.txt

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+brainstem_api_tools

brainstem_python_api_tools-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"

brainstem_python_api_tools-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

brainstem_python_api_tools-0.1.0/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name="brainstem_python_api_tools",
+    version="0.1.0",
+    packages=find_packages(),
+    install_requires=[
+        "requests",
+        "jupyter",
+    ],
+    author="BrainSTEM Team",
+    author_email="petersen.peter@gmail.com",
+    description="A Python toolset for interacting with API of BrainSTEM.",
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown",
+    url="https://github.com/brainstem-org/brainstem_python_api_tools",
+    license="MIT",
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    python_requires='>=3.7',
+)