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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52.0

/src/parser/impl/ProjectDataParser.py

from typing import List

from src.model.RunMD import RunMD
from src.model.SchemaConcepts.TOMO_Image import TOMO_Image
from src.model.SchemaConcepts.codegen.SchemaClasses_TOMO import DatasetType
from src.parser.RunMD_Parser import RunMD_Parser
from src.util import normalize_path


class ProjectDataParser(RunMD_Parser):
    @staticmethod
    def supported_input_sources():
        return ['Thermofisher Helios']

    def parse_run(self, payload):
        parsed = self._read_input(payload)

        runMD = RunMD()

        if parsed and parsed.get("Project"):
            resultMD = parsed["Project"].get("Results")
            images = resultMD.get("Image")
            for imgmd in images:
                if imgmd.get("ImagePurpose") and imgmd["ImagePurpose"] in DatasetType:
                    fp = normalize_path(imgmd["@FilePath"])
                    img = TOMO_Image(localPath=fp)
                    runMD.add_image(img, DatasetType(imgmd["ImagePurpose"]))

        return runMD

    @staticmethod
    def expected_input_format():
        return "text/xml"

1	from typing import List	1✔
2
3	from src.model.RunMD import RunMD	1✔
4	from src.model.SchemaConcepts.TOMO_Image import TOMO_Image	1✔
5	from src.model.SchemaConcepts.codegen.SchemaClasses_TOMO import DatasetType	1✔
6	from src.parser.RunMD_Parser import RunMD_Parser	1✔
7	from src.util import normalize_path	1✔
8
9
10	class ProjectDataParser(RunMD_Parser):	1✔
11	@staticmethod	1✔
12	def supported_input_sources():	1✔
13	return ['Thermofisher Helios']	1✔
14
15	def parse_run(self, payload):	1✔
16	parsed = self._read_input(payload)	×
17
UNCOV 18	runMD = RunMD()	×
19
NEW 20	if parsed and parsed.get("Project"):	×
NEW 21	resultMD = parsed["Project"].get("Results")	×
NEW 22	images = resultMD.get("Image")	×
NEW 23	for imgmd in images:	×
NEW 24	if imgmd.get("ImagePurpose") and imgmd["ImagePurpose"] in DatasetType:	×
NEW 25	fp = normalize_path(imgmd["@FilePath"])	×
NEW 26	img = TOMO_Image(localPath=fp)	×
NEW 27	runMD.add_image(img, DatasetType(imgmd["ImagePurpose"]))	×
28
NEW 29	return runMD	×
30
31	@staticmethod	1✔
32	def expected_input_format():	1✔
33	return "text/xml"	×

kit-data-manager / tomo_mapper / 21944637261

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