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Update tests #97

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merged 5 commits into from
Nov 20, 2024
Merged

Update tests #97

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5578e5b
Update tests
SteffenBrinckmann Nov 18, 2024
76b8798
include github action
SteffenBrinckmann Nov 18, 2024
8fc7087
Improved tests and included rocrate validator
SteffenBrinckmann Nov 19, 2024
68377f0
Add traceback to pytest
SteffenBrinckmann Nov 19, 2024
370ea9c
Correct the installed lib
SteffenBrinckmann Nov 19, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/pytest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,10 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install pytest rocrate
pip install pytest rocrate jsonschema roc-validator
- name: Test with pytest
run: |
pytest --tb=no -s
pytest --tb=short -s
continue-on-error: true
- name: Create action summary
run: |
Expand Down
132 changes: 132 additions & 0 deletions tests/schema.json
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@@ -0,0 +1,132 @@
{
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"@context": {
"type": "string",
"format": "uri"
},
"@graph": {
"type": "array",
"items": {
"type": "object",
"properties": {
"@id": {
"type": "string"
},
"@type": {
"type": "string"
},
"about": {
"type": "object",
"properties": {
"@id": {
"type": "string"
}
}
},
"conformsTo": {
"type": "object",
"properties": {
"@id": {
"type": "string",
"format": "uri"
}
}
},
"dateCreated": {
"type": "string",
"format": "date-time"
},
"sdPublisher": {
"type": "object",
"properties": {
"@id": {
"type": "string"
}
}
},
"version": {
"type": "string"
},
"author": {
"type": "object",
"properties": {
"@id": {
"type": "string"
}
}
},
"dateModified": {
"type": "string",
"format": "date-time"
},
"name": {
"type": "string"
},
"encodingFormat": {
"type": "string"
},
"url": {
"type": "string",
"format": "uri"
},
"genre": {
"type": "string"
},
"creativeWorkStatus": {
"type": "string"
},
"identifier": {
"type": "string"
},
"keywords": {
"type": "string"
},
"hasPart": {
"type": "array",
"items": {
"type": "object",
"properties": {
"@id": {
"type": "string"
}
}
}
},
"comment": {
"type": "array",
"items": {
"type": "object",
"properties": {
"@id": {
"type": "string"
},
"@type": {
"type": "string"
},
"dateCreated": {
"type": "string",
"format": "date-time"
},
"text": {
"type": "string"
},
"author": {
"type": "object",
"properties": {
"@id": {
"type": "string"
}
}
}
}
}
}
},
"required": ["@id", "@type"]
}
}
},
"required": ["@context", "@graph"]
}
26 changes: 15 additions & 11 deletions tests/test_00_pypi_rocrate.py
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Expand Up @@ -5,14 +5,16 @@
"""
import os
import json
import unittest
import unittest, traceback
import tempfile
from pathlib import Path
from zipfile import ZIP_DEFLATED
from zipfile import Path as ZPath
from zipfile import ZipFile
from rocrate.rocrate import ROCrate

LABEL = 'pypi_rocrate'
verbose = False

class Test_1(unittest.TestCase):
"""
derived class for this test
Expand All @@ -35,25 +37,27 @@ def test_main(self):
fileName = os.path.join(root, name)
print(f'\n\nTry to parse: {fileName}')
with ZipFile(fileName, 'r', compression=ZIP_DEFLATED) as elnFile:
p = ZPath(elnFile)
dirName = sorted(p.iterdir())[0]
dirName = os.path.splitext(os.path.basename(fileName))[0]
try:
dirpath = Path(tempfile.mkdtemp())
elnFile.extractall(dirpath)
temppath= dirpath.joinpath(dirName.name)
crate = ROCrate(temppath)
tempPath= [i for i in dirpath.iterdir() if i.is_dir()][0]
crate = ROCrate(tempPath)
for e in crate.get_entities():
print(f' {e.id}: {e.type}')
if verbose:
print(f' {e.id}: {e.type}')
if fileName not in logJson:
logJson[fileName] = {'pypi_rocrate':True}
logJson[fileName] = {LABEL:True}
else:
logJson[fileName] = logJson[fileName] | {'pypi_rocrate':True}
logJson[fileName] = logJson[fileName] | {LABEL:True}
except Exception:
print(" ***** ERROR: Could not parse content of this file!! *****")
print(f" Temporary folder: ",tempPath)
print(traceback.format_exc())
if fileName not in logJson:
logJson[fileName] = {'pypi_rocrate':False}
logJson[fileName] = {LABEL:False}
else:
logJson[fileName] = logJson[fileName] | {'pypi_rocrate':False}
logJson[fileName] = logJson[fileName] | {LABEL:False}
success = False
json.dump(logJson, open('tests/logging.json', 'w'))
assert success
29 changes: 15 additions & 14 deletions tests/test_01_params_metadata_json.py
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Expand Up @@ -8,6 +8,7 @@
from zipfile import Path as ZPath
from zipfile import ZipFile


class Test_2(unittest.TestCase):
"""
derived class for this test
Expand All @@ -26,8 +27,9 @@ def test_main(self):
# runtime global variables
METADATA_FILE = 'ro-crate-metadata.json'
OUTPUT_INFO = False
OUTPUT_COUNTS = True
OUTPUT_COUNTS = False
KNOWN_KEYS = DATASET_MANDATORY+DATASET_SUGGESTED+FILE_MANDATORY+FILE_SUGGESTED+['@id', '@type']
LABEL = 'params_metadata_json'

# log-file
if Path('tests/logging.json').exists():
Expand All @@ -52,24 +54,25 @@ def processNode(graph, nodeID):
# CHECK IF MANDATORY AND SUGGESTED KEYWORDS ARE PRESENT
if '@type' not in node:
print('**ERROR: all nodes must have @type. check:', nodeID)
return False
if node['@type'] == 'Dataset':
for key in DATASET_MANDATORY:
if not key in node:
if key not in node:
print(f'**ERROR in dataset: "{key}" not in @id={node["@id"]}')
globalSuccess = False
for key in DATASET_SUGGESTED:
if not key in node and OUTPUT_INFO:
if key not in node and OUTPUT_INFO:
print(f'**INFO for dataset: "{key}" not in @id={node["@id"]}')
elif node['@type'] == 'File':
for key in FILE_MANDATORY:
if not key in node:
if key not in node:
print(f'**ERROR in file: "{key}" not in @id={node["@id"]}')
globalSuccess = False
for key in FILE_SUGGESTED:
if not key in node and OUTPUT_INFO:
if key not in node and OUTPUT_INFO:
print(f'**INFO for file: "{key}" not in @id={node["@id"]}')
# CHECK PROPERTIES FOR ALL KEYS
if any([str(i).strip()=='' for i in node.values()]):
if any(not str(i).strip() for i in node.values()):
print(f'**WARNING: {nodeID} contains empty values in the key-value pairs')
# SPECIFIC CHECKS ON CERTAIN KEYS
if isinstance(node.get('keywords', ''), list):
Expand All @@ -89,16 +92,14 @@ def processNode(graph, nodeID):
print(f'\n\nParse: {fileName}')
with ZipFile(fileName, 'r', compression=ZIP_DEFLATED) as elnFile:
success = True
p = ZPath(elnFile)
dirName = sorted(p.iterdir())[0]
metadataJsonFile = dirName.joinpath(METADATA_FILE)
metadataContent = json.loads(metadataJsonFile.read_bytes())
metadataJsonFile = [i for i in elnFile.namelist() if i.endswith(METADATA_FILE)][0]
metadataContent = json.loads(elnFile.read(metadataJsonFile))
graph = metadataContent["@graph"]
# find information from master node
ro_crate_nodes = [i for i in graph if i["@id"] == METADATA_FILE]
if len(ro_crate_nodes) == 1:
for key in ROCRATE_NOTE_MANDATORY:
if not key in ro_crate_nodes[0]:
if key not in ro_crate_nodes[0]:
print(f'**ERROR: "{key}" not in @id={METADATA_FILE}')
else:
print(f'**ERROR: @id={METADATA_FILE} does not uniquely exist ')
Expand All @@ -109,9 +110,9 @@ def processNode(graph, nodeID):
for partI in main_node['hasPart']:
success = processNode(graph, partI['@id']) and success
if fileName not in logJson:
logJson[fileName] = {'params_metadata_json':success}
logJson[fileName] = {LABEL:success}
else:
logJson[fileName] = logJson[fileName] | {'params_metadata_json':success}
logJson[fileName] = logJson[fileName] | {LABEL:success}

# count occurances of all keys
counts = {}
Expand All @@ -133,4 +134,4 @@ def processNode(graph, nodeID):
print(f'{prefix}{k:15}: {v}')
print('\n\nSuccess:', success)
json.dump(logJson, open('tests/logging.json', 'w'))
assert success
assert success #if this fails on your local test, great. It is a summary such that github actions report correctly
49 changes: 49 additions & 0 deletions tests/test_02_schema.py
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@@ -0,0 +1,49 @@
#!/usr/bin/python3
"""
Validate if rocrate of pypi can open and parse it. This is a test if we follow general ro-crate guidelines.
https://pypi.org/project/rocrate/
"""
import os
import json
import unittest
from pathlib import Path
from zipfile import ZIP_DEFLATED
from zipfile import ZipFile
from jsonschema import Draft202012Validator

LABEL = 'schema'
METADATA_FILE = 'ro-crate-metadata.json'

class Test_1(unittest.TestCase):
"""
derived class for this test
"""
def test_main(self):
"""
main function
"""
# log-file
if Path('tests/logging.json').exists():
logJson = json.load(open('tests/logging.json'))
else:
logJson = {}

schema = json.load(open('tests/schema.json', 'r', encoding='utf-8'))
validator = Draft202012Validator(schema=schema)
validator.check_schema(schema=schema)
success = True
for root, _, files in os.walk(".", topdown=False):
for name in files:
if not name.endswith('.eln'):
continue
fileName = os.path.join(root, name)
print(f'\nInspect: {name}')
with ZipFile(fileName, 'r', compression=ZIP_DEFLATED) as elnFile:
metadataJsonFile = [i for i in elnFile.namelist() if i.endswith(METADATA_FILE)][0]
metadataContent = json.loads(elnFile.read(metadataJsonFile))
for error in sorted(validator.iter_errors(metadataContent), key=str):
print(f'- {error.message}')
success = False
logJson[fileName] = logJson.get(fileName,{}) | {LABEL: success}
json.dump(logJson, open('tests/logging.json', 'w'))
assert success
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