21944637261

Committed 12 Feb 2026 11:24AM UTC coverage: 86.453% (+0.1%) from 86.341%

Build # 21944637261

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #77 from kit-data-manager/improv_code_cleanup

Various code fixes and cleanups
Cleaner type hints
Cleaner inheritance
More None checks

parse functions (parse_setup, parse_run, parse) do not return raw parse result anymore (was never used anywhere anyway)

Code now passes a static code check such as pyright.

Run Details

159 of 198 new or added lines in 30 files covered. (80.3%)

3 existing lines in 3 files now uncovered.

2425 of 2805 relevant lines covered (86.45%)

0.86 hits per line

Source File
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54.29

/src/parser/MetadataParser.py

from abc import ABC, abstractmethod
from typing import List, Optional
from io import StringIO

import xmltodict
import json
import logging

import configparser

from src.util import configparser_keep_keystring


#from configparser import ConfigParser, NoInterpolation

class MetadataParser(ABC):

    @staticmethod
    @abstractmethod
    def expected_input_format() -> str:
        pass

    @staticmethod
    @abstractmethod
    def supported_input_sources() -> List[str]:
        """
        Provides informative output about the input sources that are supported by implementation of this parser.
        The output is not specified and should only be used for informative reasons (such as logging and printing)
        :return:
        """
        pass
    
    def _read_input(self, payload) -> Optional[dict]:
        """
        creates metadata dictionary from payload
        :param payload: input String
        :return: metadata dict
        """
        if self.expected_input_format() == "text/xml":
            self.parsed_data = xmltodict.parse(payload)
            return self.parsed_data
        if self.expected_input_format() == "application/json":
            self.parsed_data = json.loads(payload)
            return self.parsed_data
        if self.expected_input_format() == "text/plain":
            
            self.parsed_data = {}
            config = configparser.ConfigParser(interpolation=configparser.Interpolation()) # disables interpolation explicitly
            config.optionxform = configparser_keep_keystring # do this if you do not want to read in data as lowercase
            config.read_string(payload)
            for section in config.sections():
                items = config.items(section)
                self.parsed_data[section] = dict(items)
            return self.parsed_data
        logging.error("Parsing of input format not implemented: {}",format(self.expected_input_format()))
        return None

1	from abc import ABC, abstractmethod	1✔
2	from typing import List, Optional	1✔
3	from io import StringIO	1✔
4
5	import xmltodict	1✔
6	import json	1✔
7	import logging	1✔
8
9	import configparser	1✔
10
11	from src.util import configparser_keep_keystring	1✔
12
13
14	#from configparser import ConfigParser, NoInterpolation
15
16	class MetadataParser(ABC):	1✔
17
18	@staticmethod	1✔
19	@abstractmethod	1✔
20	def expected_input_format() -> str:	1✔
21	pass	×
22
23	@staticmethod	1✔
24	@abstractmethod	1✔
25	def supported_input_sources() -> List[str]:	1✔
26	"""
27	Provides informative output about the input sources that are supported by implementation of this parser.
28	The output is not specified and should only be used for informative reasons (such as logging and printing)
29	:return:
30	"""
31	pass	×
32
33	def _read_input(self, payload) -> Optional[dict]:	1✔
34	"""
35	creates metadata dictionary from payload
36	:param payload: input String
37	:return: metadata dict
38	"""
39	if self.expected_input_format() == "text/xml":	1✔
40	self.parsed_data = xmltodict.parse(payload)	1✔
41	return self.parsed_data	1✔
42	if self.expected_input_format() == "application/json":	×
43	self.parsed_data = json.loads(payload)	×
44	return self.parsed_data	×
45	if self.expected_input_format() == "text/plain":	×
46
47	self.parsed_data = {}	×
48	config = configparser.ConfigParser(interpolation=configparser.Interpolation()) # disables interpolation explicitly	×
NEW 49	config.optionxform = configparser_keep_keystring # do this if you do not want to read in data as lowercase	×
50	config.read_string(payload)	×
51	for section in config.sections():	×
52	items = config.items(section)	×
53	self.parsed_data[section] = dict(items)	×
54	return self.parsed_data	×
55	logging.error("Parsing of input format not implemented: {}",format(self.expected_input_format()))	×
56	return None	×

kit-data-manager / tomo_mapper / 21944637261

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