Python.orthanc.query

Complexity

Total Complexity

20

Size/Duplication

Total Lines	140
Duplicated Lines	46.43 %

Importance

Changes

0

5 Methods

Rating	Name	Duplication	Size	Complexity
A	orthanc_query.getOrthanc()	21	21	3
A	orthanc_query.postOrthanc()	23	23	3
A	orthanc_query.flatUnZip()	0	26	5
A	orthanc_query.deleteOrthanc()	21	21	3
B	orthanc_query.getPatientZipOrthanc()	0	30	6

import requests

This module should have a docstring.

import logging

standard import "import logging" should be placed before "import requests"

import os

standard import "import os" should be placed before "import requests"

import shutil

standard import "import shutil" should be placed before "import requests"

import zipfile

standard import "import zipfile" should be placed before "import requests"

import sys

standard import "import sys" should be placed before "import requests"

from dotenv import load_dotenv
from PythonUtils.file import is_name_unique

Unable to import 'PythonUtils.file'

logging.basicConfig(stream=sys.stdout, level=logging.INFO)

class orthanc_query:

The name orthanc_query does not conform to the class naming conventions ([A-Z_][a-zA-Z0-9]+$).

This class should have a docstring.

The variable __class__ seems to be unused.

    @staticmethod

This code seems to be duplicated in your project.

    def getOrthanc(endpoint):

The name getOrthanc does not conform to the method naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

        """
        Get from a Orthanc endpoint
        :param endpoint:
        :return: bool on if such PSCID (INSTITUTIONID + PROJECTID + SUBJECTID) exist already.
        """
        logger = logging.getLogger('Orthanc_get')
        logger.info("Getting Orthanc endpoint: "+ endpoint + "at")
        success = load_dotenv()
        if not success:
            raise ImportError("Credential .env NOT FOUND! Please ensure .env is set with all the necessary credentials!")

This line is too long as per the coding-style (121/100).

        url = os.getenv("OrthancURL")
        updatedurl = url + endpoint
        logger.info(updatedurl)

        with requests.Session() as s:

The name s does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

            r = s.get(updatedurl)

The name r does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

            logger.info("Get Result:" + str(r.status_code) + r.reason)

            return r.status_code, r.json()

    @staticmethod

This code seems to be duplicated in your project.

    def postOrthanc(endpoint, data):

The name postOrthanc does not conform to the method naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

        """
        Get from a Orthanc endpoint
        :param endpoint:
        :param data
        :return: bool on if such PSCID (INSTITUTIONID + PROJECTID + SUBJECTID) exist already.
        """
        logger = logging.getLogger('Orthanc_post')
        logger.info("Post Orthanc endpoint: "+ endpoint + "at")
        success = load_dotenv()
        if not success:
            raise ImportError("Credential .env NOT FOUND! Please ensure .env is set with all the necessary credentials!")

This line is too long as per the coding-style (121/100).

        url = os.getenv("OrthancURL")
        updatedurl = url + endpoint
        logger.info(updatedurl)

        with requests.Session() as s:

The name s does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

            r = s.post(updatedurl, files=data)

The name r does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

            logger.info("Post Result:" + str(r.status_code) + r.reason)

            return r.status_code, r

    @staticmethod

This code seems to be duplicated in your project.

    def deleteOrthanc(endpoint):

The name deleteOrthanc does not conform to the method naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

        """
        Delete from a Orthanc endpoint
        :param endpoint:
        :return: bool on if such PSCID (INSTITUTIONID + PROJECTID + SUBJECTID) exist already.
        """
        logger = logging.getLogger('Orthanc_delete')
        logger.info("Deleting Orthanc endpoint: "+ endpoint + "at")
        success = load_dotenv()
        if not success:
            raise ImportError("Credential .env NOT FOUND! Please ensure .env is set with all the necessary credentials!")

This line is too long as per the coding-style (121/100).

        url = os.getenv("OrthancURL")
        updatedurl = url + endpoint
        logger.info(updatedurl)

        with requests.Session() as s:

The name s does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

            r = s.delete(updatedurl)

The name r does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

            logger.info("Deletion Result:" + str(r.status_code) + r.reason)

        return r.status_code, r.json()

    @staticmethod
    def getPatientZipOrthanc(endpoint):

The name getPatientZipOrthanc does not conform to the method naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

        """
        Get Orthanc endpoint archive ZIP files.
        :param endpoint:
        :return: status of the get requests, and the actual local file name saved in the process.
        """
        logger = logging.getLogger('Orthanc_getzip')
        logger.info("Downloading Orthanc endpoint: " + endpoint + " at")
        success = load_dotenv()
        if not success:
            raise ImportError("Credential .env NOT FOUND! Please ensure .env is set with all the necessary credentials!")

This line is too long as per the coding-style (121/100).

        url = os.getenv("OrthancURL")

        # endpiont should be something like /studies/SUTDY_UUID/
        query = url + "patients/" + endpoint + '/archive'
        logger.info(query)

        with requests.Session() as s:

The name s does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

            r = s.get(query, stream=True, verify=False)  # auth=(orthanc_user, orthanc_password)

The name r does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

            local_filename = endpoint + ".zip"
            # NOTE the stream=True parameter
            with open(local_filename, 'wb') as f:

The name f does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

                for chunk in r.iter_content(chunk_size=1024):
                    if chunk:  # filter out keep-alive new chunks
                        f.write(chunk)
                        # f.flush() commented by recommendation from J.F.Sebastian
        logger.info(str(r.status_code) + r.reason)
        return r.status_code, local_filename

    @staticmethod
    def flatUnZip(input_zip, out_dir):

The name flatUnZip does not conform to the method naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

        """
        Inpsired by https://stackoverflow.com/questions/4917284/extract-files-from-zip-without-keeping-the-structure-using-python-zipfile

This line is too long as per the coding-style (137/100).

        Added function to hanlde non-unique file names which are probably standarderized by Orthanc.
        :param input_zip:
        :param out_dir:
        :return:
        """

        with zipfile.ZipFile(input_zip) as zip_file:
            for member in zip_file.namelist():
                filename = os.path.basename(member)
                # skip directories
                if not filename:
                    continue

                # copy file (taken from zipfile's extract)
                source = zip_file.open(member)

                proposed_filename = os.path.join(out_dir, filename)
                # handle duplicate names!
                _, unique_output_filename = is_name_unique(proposed_filename)
                target = open(unique_output_filename, "wb")
                with source, target:
                    shutil.copyfileobj(source, target)