Merge branch 'develop'

.github/workflows/run_tests.yml

@@ -8,20 +8,23 @@ on:
 
 jobs:
  build:
- runs-on: ubuntu-latest
+ runs-on: ${{ matrix.os }}
  strategy:
  matrix:
- python-version: [2.7, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9]
+ os: [ubuntu-latest]
+ python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v4
  - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v2
+ uses: actions/setup-python@v5
  with:
  python-version: ${{ matrix.python-version }}
  - name: Install dependencies
  run: |
  python -m pip install --upgrade pip
- pip install coveralls nose
- - name: Test with nosetests
+ pip install coveralls nose2 nose2[coverage_plugin]>=0.6.5
+
+ - name: Test with nose2
  run: |
- nosetests tests hl7apy --with-doctest --with-coverage --cover-package hl7apy
+ nose2 tests hl7apy  

README.md

@@ -24,7 +24,7 @@ Documentation can be found [here](http://crs4.github.io/hl7apy/).
 Installation
 ------------
 
-HL7apy is platform independent and supports Python 2.7 and Python 3.4, 3.5, 3.6, 3.7
+HL7apy is platform independent and supports Python 2.7 and Python 3.[4-12]
 
 To install it get the latest release from [GitHub](https://github.com/crs4/hl7apy/releases) and launch the following command:
 

VERSION

@@ -1 +1 @@
-1.3.4
+1.3.5

docs/index.rst

@@ -19,7 +19,7 @@ The main features includes:
 
 Currently supported HL7 versions are: 2.1, 2.2, 2.3, 2.3.1, 2.4, 2.5, 2.5.1, 2.6, 2.7, 2.8, 2.8.1, 2.8.2
 
-Current version is 1.3.4
+Current version is 1.3.5
 
 To get started visit the :ref:`Getting started <tutorial>` section
 
@@ -28,7 +28,7 @@ This project is not affiliated with the HL7 organization: the library is just co
 Installation
 ============
 
-HL7apy is platform independent and supports Python 2.7 and Python 3.4, 3.5, 3.6, 3.7
+HL7apy is platform independent and supports Python 2.7 and Python 3.[4-12]
 
 To install it get the latest release from `GitHub <https://github.com/crs4/hl7apy/releases>`_ and launch the following
 command:

docs/release_notes.rst

@@ -2,6 +2,12 @@
 
 Release Notes
 =============
+New in 1.3.5
+
+ * Fix multithreading issue (#95)
+ * Fix SIU structures (#104)
+ * Removes print statement (#106)
+
 New in 1.3.4
 
  * Bug fixes regarding dates

hl7apy/__init__.py

@@ -20,18 +20,22 @@
 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 from __future__ import absolute_import
+
 import os
-import sys
+
 try:
  from collections.abc import MutableMapping
 except ImportError:
  from collections import MutableMapping
+
 import importlib
+
 try:
  import cPickle as pickle
 except ImportError:
  import pickle
 
+
 from hl7apy.exceptions import UnsupportedVersion, InvalidEncodingChars, UnknownValidationLevel
 from hl7apy.consts import DEFAULT_ENCODING_CHARS, DEFAULT_ENCODING_CHARS_27, DEFAULT_VERSION, VALIDATION_LEVEL
 
@@ -233,9 +237,7 @@ def load_library(version):
  """
  check_version(version)
  module_name = SUPPORTED_LIBRARIES[version]
- lib = sys.modules.get(module_name)
- if lib is None:
- lib = importlib.import_module(module_name)
+ lib = importlib.import_module(module_name)
  return lib
 
 

hl7apy/base_datatypes.py

@@ -33,8 +33,9 @@
 """
 
 from __future__ import absolute_import
-import re
+
 import numbers
+import re
 from datetime import datetime
 from decimal import Decimal
 from functools import cmp_to_key
@@ -65,6 +66,7 @@ class BaseDataType(object):
  greater than the :attr:`max_length`. Only if :attr:`validation_level` is
  :attr:`STRICT <VALIDATION_LEVEL.STRICT>`
  """
+
  def __init__(self, value, max_length=None, validation_level=None):
  if validation_level is None:
  validation_level = get_default_validation_level()
@@ -113,6 +115,7 @@ class TextualDataType(BaseDataType):
  :raise: :exc:`MaxLengthReached <hl7apy.exceptions.MaxLengthReached>` When the :attr:`value`'s length is
  greater than :attr:`max_length`
  """
+
  def __init__(self, value, max_length=32, highlights=None,
  validation_level=None):
  self.highlights = highlights
@@ -132,7 +135,7 @@ def _get_translations(self, encoding_chars):
  (encoding_chars['REPETITION'], '{esc}R{esc}'.format(esc=escape_char)),)
 
  def _get_escape_char_regex(self, escape_char):
- return r'(?<!%s[HNFSTRE])%s(?![HNFSTRE]%s)' % tuple(3*[re.escape(escape_char)])
+ return r'(?<!%s[HNFSTRE])%s(?![HNFSTRE]%s)' % tuple(3 * [re.escape(escape_char)])
 
  def _escape_value(self, value, encoding_chars=None):
  escape_char = encoding_chars['ESCAPE']
@@ -196,6 +199,7 @@ class NumericDataType(BaseDataType):
  :raise: :exc:`hl7apy.exceptions.MaxLengthReached` When the `value`'s length is greater than `max_length`
 
  """
+
  def __init__(self, value=None, max_length=16,
  validation_level=None):
  super(NumericDataType, self).__init__(value, max_length,
@@ -238,6 +242,7 @@ class WD(TextualDataType):
 
  :attr:`max_length` is 0
  """
+
  def __init__(self, value, highlights=None,
  validation_level=None):
  super(WD, self).__init__(value, 199, highlights, validation_level)
@@ -332,6 +337,7 @@ class ST(TextualDataType):
 
  :attr:`max_length` is 199
  """
+
  def __init__(self, value, highlights=None,
  validation_level=None):
  super(ST, self).__init__(value, 199, highlights, validation_level)
@@ -344,6 +350,7 @@ class FT(TextualDataType):
 
  :attr:`max_length` is 65536
  """
+
  def __init__(self, value, highlights=None,
  validation_level=None):
  super(FT, self).__init__(value, 65536, highlights, validation_level)
@@ -356,6 +363,7 @@ class ID(TextualDataType):
 
  :attr:`max_length` None
  """
+
  def __init__(self, value, highlights=None,
  validation_level=None):
  # max_length is None bacause it depends from the HL7 table
@@ -370,6 +378,7 @@ class IS(TextualDataType):
 
  :attr:`max_length` is 20
  """
+
  def __init__(self, value, highlights=None,
  validation_level=None):
  super(IS, self).__init__(value, 20, highlights, validation_level)
@@ -383,6 +392,7 @@ class TX(TextualDataType):
 
  :attr:`max_length` is 65536
  """
+
  def __init__(self, value, highlights=None,
  validation_level=None):
  super(TX, self).__init__(value, 65536, highlights, validation_level)
@@ -395,6 +405,7 @@ class GTS(TextualDataType):
 
  :attr:`max_length` is 199
  """
+
  def __init__(self, value, highlights=None,
  validation_level=None):
  super(GTS, self).__init__(value, 199, highlights, validation_level)
@@ -423,14 +434,15 @@ def __init__(self, value=None,
 
 class SI(NumericDataType):
  """
- Class for NM datatype. It extends NumericDatatype and the parameters are the same of the superclass
+ Class for SI datatype. It extends NumericDatatype and the parameters are the same of the superclass
 
  :attr:`max_length` is 4.
 
  The type of ``value`` must be `int` or :class:`numbers.Integral`
 
  :raise: :exc:`ValueError` raised when the value is not of one of the correct type
  """
+
  def __init__(self, value=None,
  validation_level=None):
  if value is not None and not isinstance(value, numbers.Integral):
@@ -450,8 +462,8 @@ class TN(TextualDataType):
 
  :raise: :exc:`ValueError` raised when the value does not match the expected format
  """
- def __init__(self, value, validation_level=None):
 
+ def __init__(self, value, validation_level=None):
  regexp = r'(\d\d\s)?(\(\d+\))?(\d+-?\d+)(X\d+)?(B\d+)?(C.+)?'
  if not re.match(regexp, value):
  raise ValueError('Invalid value for TN data')

hl7apy/core.py

@@ -105,7 +105,7 @@ def _valid_child_name(child_name, expected_parent):
 def _valid_z_message_name(name):
  if name is None:
  return False
- regex = '^z[a-z0-9]{2}_z[a-z0-9]{2}$'
+ regex = r'^z[a-z0-9]{2}_z[a-z0-9]{2}$'
  return re.match(regex, name, re.IGNORECASE) is not None
 
 
@@ -114,7 +114,7 @@ def _valid_z_segment_name(name):
 
 
 def _valid_z_field_name(name):
- regex = '^z[a-z1-9]{2}_\d+$'
+ regex = r'^z[a-z1-9]{2}_\d+$'
  return re.match(regex, name, re.IGNORECASE) is not None
 
 

hl7apy/exceptions.py

@@ -47,7 +47,7 @@ class ValidationError(HL7apyException):
 
  >>> from hl7apy.parser import parse_message
  >>> from hl7apy.validation import VALIDATION_LEVEL
- >>> msh = 'MSH|^~\&|SENDING APP|SENDING FAC|REC APP|REC FAC|20080115153000||ADT^A01^ADT_A01|' \
+ >>> msh = 'MSH|^~\\&|SENDING APP|SENDING FAC|REC APP|REC FAC|20080115153000||ADT^A01^ADT_A01|' \
  '0123456789|P|2.5||||AL\\r'
  >>> evn = 'EVN||20080115153000||AAA|AAA|20080114003000\\r'
  >>> pid = 'PID|1||123-456-789^^^HOSPITAL^MR||SURNAME^NAME^A|||M|||1111 SOMEWHERE STREET^^SOMEWHERE^^^USA||' \

hl7apy/factories.py

@@ -99,7 +99,6 @@ def datatype_factory(datatype, value, version=None, validation_level=None):
  except KeyError:
  raise InvalidDataType(datatype)
  except ValueError as e:
- print(e)
  if Validator.is_strict(validation_level):
  raise e
  # TODO: Do we really want this? In that case the parent's datatype must be changed accordingly

hl7apy/parser.py

@@ -58,7 +58,7 @@ def parse_message(message, validation_level=None, find_groups=True, message_prof
 
  :return: an instance of :class:`Message <hl7apy.core.Message>`
 
- >>> message = "MSH|^~\&|GHH_ADT||||20080115153000||OML^O33^OML_O33|0123456789|P|2.5||||AL\\rPID|1||" \
+ >>> message = "MSH|^~\\&|GHH_ADT||||20080115153000||OML^O33^OML_O33|0123456789|P|2.5||||AL\\rPID|1||" \
  "566-554-3423^^^GHH^MR||EVERYMAN^ADAM^A|||M|||2222 HOME STREET^^ANN ARBOR^MI^^USA||555-555-2004|||M\\r"
  >>> m = parse_message(message)
  >>> print(m)
@@ -634,7 +634,7 @@ def parse_subcomponent(text, name=None, datatype='ST', version=None, validation_
 
 
 def _split_msh(content):
- m = re.match("^MSH(?P<field_sep>\S)", content)
+ m = re.match(r"^MSH(?P<field_sep>\S)", content)
  if m is not None: # if the regular expression matches, it is an HL7 message
  field_sep = m.group('field_sep') # get the field separator (first char after MSH)
  msh = content.split("\r", 1)[0] # get the first segment

hl7apy/utils.py

@@ -113,7 +113,7 @@ def get_datetime_info(value):
 
 
 def _split_offset(value):
- offset = re.search('\d*((\+(1[0-4]|0[0-9])|(-(1[0-2]|0[0-9])))([0-5][0-9]))$', value)
+ offset = re.search(r'\d*((\+(1[0-4]|0[0-9])|(-(1[0-2]|0[0-9])))([0-5][0-9]))$', value)
  if offset:
  offset = offset.groups()[0]
  return value.replace(offset, ''), offset