qmenta-client 2.1.dev1508__tar.gz

qmenta_client-2.1.dev1508/PKG-INFO

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+Metadata-Version: 2.3
+Name: qmenta-client
+Version: 2.1.dev1508
+Summary: Python client lib to interact with the QMENTA platform.
+Author: QMENTA
+Author-email: dev@qmenta.com
+Requires-Python: >=3.10,<4.0
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: future (>=0.18.2,<0.19.0)
+Requires-Dist: qmenta-core (>=4.0.1,<5.0.0)
+Project-URL: Homepage, https://www.qmenta.com/

qmenta_client-2.1.dev1508/pyproject.toml

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+[tool.poetry]
+name = "qmenta-client"
+version = "2.1.dev1508"
+description = "Python client lib to interact with the QMENTA platform."
+authors = ["QMENTA <dev@qmenta.com>"]
+homepage = "https://www.qmenta.com/"
+classifiers=[
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+]
+packages = [
+    { include = "qmenta", from = "src" }
+]
+
+[tool.poetry.dependencies]
+python = "^3.10"
+future = "^0.18.2"
+qmenta-core = "^4.0.1"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.1.2"
+sphinx = "^5.0"
+sphinx-rtd-theme = "^1.0.0"
+dom-toml = "^0.6.0"
+scriv = {version = "^0.15.2", extras = ["toml"]}
+coverage = "^7.2.5"
+flake8 = "^7.1.2"
+
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.scriv]
+format = "md"
+md_header_level = "2"
+insert_marker = "scriv-insert-here"

qmenta_client-2.1.dev1508/src/qmenta/__init__.py

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+__path__ = __import__("pkgutil").extend_path(__path__, __name__)

qmenta_client-2.1.dev1508/src/qmenta/client/Account.py

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+from __future__ import print_function
+
+import logging
+from urllib3.exceptions import HTTPError
+
+from qmenta.core import platform
+from qmenta.core import errors
+
+from .Project import Project
+from .utils import load_json
+
+logger_name = "qmenta.client"
+
+
+class Account:
+    """
+    It represents your QMENTA account and implements the HTTP connection
+    with the server. Once it is instantiated it will act as an identifier
+    used by the rest of objects.
+
+    Parameters
+    ----------
+    username : str
+        Username on the platform. To get one go to https://platform.qmenta.com
+    password : str
+        The password assigned to the username.
+    base_url : str
+        The base url of the platform.
+    verify_certificates : bool
+        verify SSL certificates?
+
+    Attributes
+    ----------
+    auth : qmenta.core.platform.Auth
+        The Auth object used for communication with the platform
+    """
+
+    def __init__(self, username, password, base_url="https://platform.qmenta.com", verify_certificates=True):
+
+        self._cookie = None
+        self.username = username
+        self.password = password
+        self.baseurl = base_url
+        self.verify_certificates = verify_certificates
+        self.auth = None
+        self.login()
+
+    def __repr__(self):
+        rep = "<Account session for {}>".format(self.username)
+        return rep
+
+    def login(self):
+        """
+        Login to the platform.
+
+        Raises
+        ------
+        qmenta.core.platform.ConnectionError
+            When the connection to the platform fails.
+        qmenta.core.platform.InvalidLoginError
+            When invalid credentials are provided.
+        """
+        logger = logging.getLogger(logger_name)
+        try:
+            auth = platform.Auth.login(self.username, self.password, base_url=self.baseurl, ask_for_2fa_input=True)
+        except errors.PlatformError as e:
+            logger.error("Failed to log in: {}".format(e))
+            self.auth = None
+            raise
+
+        self.auth = auth
+        logger.info("Logged in as {}".format(self.username))
+
+    def logout(self):
+        """
+        Logout from the platform.
+
+        Raises
+        ------
+        qmenta.core.errors.PlatformError
+            When the logout was not successful
+        """
+
+        logger = logging.getLogger(logger_name)
+        try:
+            platform.parse_response(platform.post(self.auth, "logout"))
+        except errors.PlatformError as e:
+            logger.error("Logout was unsuccessful: {}".format(e))
+            raise
+
+        logger.info("Logged out successfully")
+
+    def get_project(self, project_id):
+        """
+        Retrieve a project instance, given its id, which can be obtained
+        checking account.projects.
+
+        Parameters
+        ----------
+        project_id : int or str
+            ID of the project to retrieve, either the numeric ID or the name
+
+        Returns
+        -------
+        Project
+            A project object representing the desired project
+        """
+        if type(project_id) is int or type(project_id) is float:
+            return Project(self, int(project_id))
+        elif type(project_id) is str:
+            projects = self.projects
+            projects_match = [proj for proj in projects if proj["name"] == project_id]
+            if not projects_match:
+                raise Exception(f"Project {project_id} does not exist or is not available for this user.")
+            return Project(self, int(projects_match[0]["id"]))
+
+    @property
+    def projects(self):
+        """
+        List all the projects available to the current user.
+
+        Returns
+        -------
+        list[dict]
+            List of project information (name, and id)
+        """
+        logger = logging.getLogger(logger_name)
+
+        try:
+            data = platform.parse_response(platform.post(self.auth, "projectset_manager/get_projectset_list"))
+        except errors.PlatformError as e:
+            logger.error("Failed to get project list: {}".format(e))
+            raise
+
+        titles = []
+        for project in data:
+            titles.append({"name": project["name"], "id": project["_id"]})
+        return titles
+
+    def add_project(self, project_abbreviation, project_name, description="", users=None, from_date="", to_date=""):
+        """
+        Add a new project to the user account.
+
+        Parameters
+        ----------
+        project_abbreviation : str
+            Abbreviation of the project name.
+        project_name : str
+            Project name.
+        description : str
+            Description of the project.
+        users : list[str]
+            List of users to which this project is available.
+        from_date : str
+            Date of beginning of the project.
+        to_date : str
+            Date of ending of the project.
+
+        Returns
+        -------
+        bool
+            True if project was correctly added, False otherwise
+        """
+        if users is None:
+            users = []
+        logger = logging.getLogger(logger_name)
+        for project in self.projects:
+            if project["name"] == project_name:
+                logger.error("Project name or abbreviation already exists.")
+                return False
+
+        try:
+            platform.parse_response(
+                platform.post(
+                    self.auth,
+                    "projectset_manager/upsert_project",
+                    data={
+                        "name": project_name,
+                        "description": description,
+                        "from_date": from_date,
+                        "to_date": to_date,
+                        "abbr": project_abbreviation,
+                        "users": "|".join(users),
+                    },
+                )
+            )
+        except errors.PlatformError as e:
+            logger.error(e)
+            return False
+
+        for project in self.projects:
+            if project["name"] == project_name:
+                logger.info("Project was successfully created.")
+                return Project(self, int(project["id"]))
+        logger.error("Project could note be created.")
+        return False
+
+    def _send_request(
+        self,
+        path,
+        req_parameters=None,
+        req_headers=None,
+        stream=False,
+        return_raw_response=False,
+        response_timeout=900.0,
+    ):
+        """
+        TODO: not used and contains warnings, maybe we should delete it.
+
+        Send a request to the QMENTA Platform.
+
+        Interaction with the server is performed as POST requests.
+
+        Parameters
+        ----------
+        req_parameters : dict
+            Data to send in the POST request.
+        req_headers : dict
+            Extra headers to include in the request:
+        stream : bool
+            Defer downloading the response body until accessing the
+            response.content attribute.
+        return_raw_response : bool
+            When True, return the response from the
+            server as-is. When False (by default),
+            parse the answer as json to return a
+            dictionary.
+        response_timeout : float
+            The timeout time in seconds to wait for the response.
+        """
+
+        req_headers = req_headers or {}
+        req_url = "/".join((self.baseurl, path))
+        if self._cookie is not None:
+            req_headers["Cookie"] = self._cookie
+        req_headers["Mint-Api-Call"] = "1"
+
+        logger = logging.getLogger(logger_name)
+        try:
+            if path == "upload":
+                response = self.pool.request(
+                    "POST",
+                    req_url,
+                    body=req_parameters,
+                    headers=req_headers,
+                    timeout=response_timeout,
+                    preload_content=not stream,
+                )
+            else:
+                response = self.pool.request(
+                    "POST",
+                    req_url,
+                    req_parameters or {},
+                    headers=req_headers,
+                    timeout=response_timeout,
+                    preload_content=not stream,
+                )
+            if response.status >= 400:
+                raise HTTPError("STATUS {}: {}".format(response.status, response.reason))
+        except Exception as e:
+            error = "Could not send request. ERROR: {0}".format(e)
+            logger.error(error)
+            raise
+
+        # Set the login cookie in our object
+        if "set-cookie" in response.headers:
+            self._cookie = response.headers["set-cookie"]
+
+        if return_raw_response:
+            return response
+
+        # raise exception if there is no response from server
+        if not response:
+            error = "No response from server."
+            logger.error(error)
+            raise Exception(error)
+
+        try:
+            parsed_content = load_json(response.data)
+        except Exception:
+            error = "Could not parse the response as JSON data: {}".format(response.data)
+            logger.error(error)
+            raise
+
+        # throw exceptions if anything strange happened
+        if "error" in parsed_content:
+            error = parsed_content["error"] or "Unknown error"
+            logger.error(error)
+            raise Exception(error)
+        elif "success" in parsed_content and parsed_content["success"] == 3:
+            error = parsed_content["message"]
+            logger.error(error)
+            raise Exception(error)
+        return parsed_content

qmenta_client-2.1.dev1508/src/qmenta/client/File.py

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+import glob
+import json
+import os
+from collections import defaultdict
+from tempfile import TemporaryDirectory, mkstemp
+
+import pandas as pd
+from pydicom import dcmread
+
+import qmenta.client
+from qmenta.client.utils import unzip_dicoms
+
+
+class File:
+    """
+    It represents files stored in the QMENTA Platform.
+    Once it is instantiated it will act as an identifier used by the rest of
+    objects.
+
+    :param project: A QMENTA Project instance
+    :type project: qmenta.client.Project
+
+    :param subject_name: The name of the subject you want to work with
+    :type subject_name: str
+
+    :param ssid: The ssid of the subject you want to work with
+    :type ssid: str
+
+    :param file_name: The file_name of the file you want to work with
+    :type file_name: str
+
+    `ff_container = File(project, "MRB", "1", "gre_field_mapping_3.zip")`
+    """
+
+    def __init__(self, project: qmenta.client.Project, subject_name: str, ssid: str, file_name: str):
+        self.file_name = file_name
+        self.project = project
+        self._container_id = None
+        for cont in self.project.list_input_containers():
+            if cont["patient_secret_name"] == subject_name and cont["ssid"] == ssid:
+                self._container_id = cont["container_id"]
+                break
+        if self.file_name.endswith(".zip"):
+            self._file_type = "DICOM"
+        elif self.file_name.endswith(".nii"):
+            self._file_type = "NIfTI"
+        elif self.file_name.endswith(".nii.gz"):
+            self._file_type = "NIfTI-GZ"
+
+    def __str__(self):
+        return self.file_name
+
+    def pull_scan_sequence_info(self, specify_dicom_tags=None, output_format: str = "csv"):
+        """
+        Pulling scan sequence information (e.g. series number, series type,
+        series description, number of files, file formats available)
+        via the API in CSV/TSV or JSON format.
+
+        Additionally, pulling specified DICOM headers themselves via tha API.
+
+        It downloads the file defined in the File object and extracts the
+        DICOM information. Nifti is not supported at the moment
+
+        :param specify_dicom_tags:  tags to extract from DICOM header
+        :type output_format:  list
+
+        :param output_format:  A file output type. Supported formats: "csv",
+        "tsv", "json", dict
+        :type output_format:  str
+
+        :return:
+        :rtype dict:
+        """
+        if specify_dicom_tags is None:
+            specify_dicom_tags = list()
+        valid_output_formats = ["csv", "tsv", "json", "dict"]
+        assert output_format in valid_output_formats, f"Output format not valid. Choose one of {valid_output_formats}"
+
+        with TemporaryDirectory() as temp_dir:
+            local_file_name = mkstemp(dir=temp_dir) + ".zip"
+            self.project.download_file(self._container_id, self.file_name, local_file_name, overwrite=False)
+            if self._file_type == "DICOM":
+                unzip_dicoms(local_file_name, temp_dir, exclude_members=None)
+                dicoms = glob.glob(os.path.join(temp_dir, "*"))
+                output_data = defaultdict(list)
+                number_files = 0
+                for dcm_file in dicoms:
+                    try:
+                        open_file = dcmread(dcm_file)
+                        number_files += 1
+                        if number_files == 1:
+                            # only needed for one file, all have the same data.
+                            for attribute in specify_dicom_tags:
+                                # error handling of attributes send by the user
+                                assert len(attribute) == 2, "Invalid length of DICOM Attribute"
+                                assert isinstance(attribute[0], int), "Invalid type of DICOM Attribute"
+                                output_data["dicom tag"].append(open_file[attribute].tag)
+                                output_data["attribute"].append(open_file[attribute].name)
+                                output_data["value"].append(open_file[attribute].value)
+                    except Exception as e:
+                        print(str(e))
+                        pass
+
+        output_data["dicom tag"].append("N/A")
+        output_data["attribute"].append("Number of files")
+        output_data["value"].append(number_files)
+
+        if output_format == "csv":
+            pd.DataFrame(output_data).to_csv(f"scan_sequence_info.{output_format}", index=False)
+
+        elif output_format == "tsv":
+            pd.DataFrame(output_data).to_csv(f"scan_sequence_info.{output_format}", sep="\t", index=False)
+
+        elif output_format == "json":
+            with open(f"scan_sequence_info.{output_format}", "w") as fp:
+                json.dump(output_data, fp)
+
+        elif output_format == "dict":
+            return output_data