Updated to v1.0 #12
Updated to v1.0 #12
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mwalzer
commented
Mar 24, 2021
mwalzer
commented
- still needs more love for the semantic validation part
- automated documentation build and integration to rtfd.io would be nice
init w/o mzqc obj, mzQC dict as validation argument, cv load errors now don't break
![sonatype-lift[bot]](https://avatars.githubusercontent.com/in/9843?s=60&v=4){kind=small}
| # self.schema = json.loads(schema_in.read().decode()) | ||
| # with open('tests/schema.json', 'r') as s: | ||
| # self.schema = json.loads(s.read()) | ||
| with urllib.request.urlopen(self.schema_url, timeout=2) as schema_in: |
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blacklist: Audit url open for permitted schemes. Allowing use of file:/ or custom schemes is often unexpected.
(at-me in a reply with help or ignore)
| else: | ||
| raise ValidationError(f'Duplicate quality metric: ' | ||
| f'accession = {quality_metric.accession}') | ||
| cv_err = self._cvmatch(cv_parameter, voc_par[0]) |
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Incompatible parameter type: Expected pronto.term.Term for 2nd positional only parameter to call SemanticCheck._cvmatch but got SemanticError.
(at-me in a reply with help or ignore)
| @@ -361,11 +372,13 @@ class MetaDataParameters(jsonobject): | |||
| def __init__(self, | |||
| # fileProvenance: str="", | |||
| # cv_params: List[CvParameter] = None , | |||
| label: str = "", | |||
| inputFiles: List[InputFile] = None, | |||
| analysisSoftware: List[AnalysisSoftware]=None | |||
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Incompatible variable type: analysisSoftware is declared to have type List[AnalysisSoftware] but is used as type None.
(at-me in a reply with help or ignore)
| @@ -424,18 +437,33 @@ class MzQcFile(jsonobject): | |||
| MzQcFile Object representation for mzQC schema type MzQcFile | |||
|
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| """ | |||
| def __init__(self, creationDate: Union[datetime,str] = datetime.now().replace(microsecond=0), version: str = "0.0.11", | |||
| def __init__(self, creationDate: Union[datetime,str] = datetime.now().replace(microsecond=0), version: str = "1.0.0", | |||
| contactName: str = "", contactAddress: str = "", description: str = "", | |||
| runQualities: List[RunQuality]=None, | |||
| setQualities: List[SetQuality]=None, | |||
| controlledVocabularies: List[ControlledVocabulary]=None | |||
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Incompatible variable type: controlledVocabularies is declared to have type List[ControlledVocabulary] but is used as type None.
(at-me in a reply with help or ignore)
| @@ -361,11 +372,13 @@ class MetaDataParameters(jsonobject): | |||
| def __init__(self, | |||
| # fileProvenance: str="", | |||
| # cv_params: List[CvParameter] = None , | |||
| label: str = "", | |||
| inputFiles: List[InputFile] = None, | |||
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Incompatible variable type: inputFiles is declared to have type List[InputFile] but is used as type None.
(at-me in a reply with help or ignore)
| @@ -424,18 +437,33 @@ class MzQcFile(jsonobject): | |||
| MzQcFile Object representation for mzQC schema type MzQcFile | |||
|
|
|||
| """ | |||
| def __init__(self, creationDate: Union[datetime,str] = datetime.now().replace(microsecond=0), version: str = "0.0.11", | |||
| def __init__(self, creationDate: Union[datetime,str] = datetime.now().replace(microsecond=0), version: str = "1.0.0", | |||
| contactName: str = "", contactAddress: str = "", description: str = "", | |||
| runQualities: List[RunQuality]=None, | |||
There was a problem hiding this comment.
Incompatible variable type: runQualities is declared to have type List[RunQuality] but is used as type None.
(at-me in a reply with help or ignore)
| @@ -424,18 +437,33 @@ class MzQcFile(jsonobject): | |||
| MzQcFile Object representation for mzQC schema type MzQcFile | |||
|
|
|||
| """ | |||
| def __init__(self, creationDate: Union[datetime,str] = datetime.now().replace(microsecond=0), version: str = "0.0.11", | |||
| def __init__(self, creationDate: Union[datetime,str] = datetime.now().replace(microsecond=0), version: str = "1.0.0", | |||
| contactName: str = "", contactAddress: str = "", description: str = "", | |||
| runQualities: List[RunQuality]=None, | |||
| setQualities: List[SetQuality]=None, | |||
There was a problem hiding this comment.
Incompatible variable type: setQualities is declared to have type List[SetQuality] but is used as type None.
(at-me in a reply with help or ignore)
| f'name = {cv_parameter.name}')) | ||
| #? Check that cv in file and obo must match in id,name,ty | ||
| else: | ||
| voc_par: List[SemanticError] = list(filter(None, [cvoc.get(cv_parameter.accession) for cvoc in file_vocabularies.values()])) |
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Incompatible variable type: voc_par is declared to have type List[SemanticError] but is used as type List[Union[pronto.relationship.Relationship, pronto.term.Term]].
(at-me in a reply with help or ignore)
| parso==0.8.2 | ||
| pexpect==4.8.0 | ||
| pickleshare==0.7.5 | ||
| Pillow==8.3.1 |
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Critical OSS Vulnerability:
pkg:pypi/pillow@8.3.1
1 Critical, 0 Severe, 0 Moderate, 0 Unknown vulnerabilities have been found across 1 dependencies
Components
pkg:pypi/pillow@8.3.1
CRITICAL Vulnerabilities (1)
[CVE-2021-23437] The package pillow 5.2.0 and before 8.3.2 are vulnerable to Regular Expression D...
The package pillow 5.2.0 and before 8.3.2 are vulnerable to Regular Expression Denial of Service (ReDoS) via the getrgb function.
CVSS Score: 7.5
CVSS Vector: CVSS:3.0/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H
try with no-cache-dir
and rename straggler urls
hopefully.
which is container build and push with latest and release tag
