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| name: MyPy | ||
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| on: [push] | ||
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| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.10", "3.11", "3.12"] | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install mypy | ||
| pip install -r requirements.txt | ||
| - name: Install stubs | ||
| run: | | ||
| mypy --install-types --non-interactive $(git ls-files '*.py') | ||
| - name: Analysing the code with pylint | ||
| run: | | ||
| mypy $(git ls-files '*.py') |
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| """Module for constants used in data collection.""" | ||
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| # files | ||
| LOVD_URL = "https://databases.lovd.nl/shared/genes" | ||
| LOVD_URL_EYS = "https://databases.lovd.nl/shared/genes/EYS" | ||
| LOVD_FILE_URL = "https://databases.lovd.nl/shared/download/all/gene" | ||
| LOVD_FILE_URL_EYS = "https://databases.lovd.nl/shared/download/all/gene/EYS" | ||
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| GNOMAD_URL = "https://gnomad.broadinstitute.org/gene" | ||
| GNOMAD_URL_EYS = "https://gnomad.broadinstitute.org/gene/ENSG00000188107?dataset=gnomad_r4" | ||
| GNOMAD_FILE_URL_EYS = ("https://drive.usercontent.google.com/u/0/uc?id=1crkDCVcC0PSnv0JPGj3FpemBs28" | ||
| "-T_3y&export=download") | ||
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| CLINVAR_URL = "https://www.ncbi.nlm.nih.gov/clinvar" | ||
| CLINVAR_URL_EYS = "https://www.ncbi.nlm.nih.gov/clinvar/?term=eys%5Bgene%5D&redir=gene" | ||
| CLINVAR_FILE_URL_EYS = ("https://drive.usercontent.google.com/u/0/uc?id=1RK5XBK3k5h0K6f-qfwJSQj7tlF" | ||
| "-H2U6u&export=download") | ||
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| # paths | ||
| DATA_PATH = "../data" | ||
| LOVD_PATH = DATA_PATH + "/lovd" | ||
| GNOMAD_PATH = DATA_PATH + "/gnomad" | ||
| CLINVAR_PATH = DATA_PATH + "/clinvar" | ||
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| # variable data types | ||
| LOVD_VARIABLES_DATA_TYPES = { | ||
| 'id': 'String', | ||
| 'name': 'String', | ||
| 'chromosome': 'Integer', | ||
| 'chrom_band': 'String', | ||
| 'imprinting': 'String', | ||
| 'refseq_genomic': 'String', | ||
| 'refseq_UD': 'String', | ||
| 'reference': 'String', | ||
| 'url_homepage': 'String', | ||
| 'url_external': 'String', | ||
| 'allow_download': 'Boolean', | ||
| 'id_hgnc': 'Integer', | ||
| 'id_entrez': 'Integer', | ||
| 'id_omim': 'Integer', | ||
| 'show_hgmd': 'Boolean', | ||
| 'show_genecards': 'Boolean', | ||
| 'show_genetests': 'Boolean', | ||
| 'show_orphanet': 'Boolean', | ||
| 'note_index': 'String', | ||
| 'note_listing': 'String', | ||
| 'refseq': 'String', | ||
| 'refseq_url': 'String', | ||
| 'disclaimer': 'Boolean', | ||
| 'disclaimer_text': 'String', | ||
| 'header': 'String', | ||
| 'header_align': 'Integer', | ||
| 'footer': 'String', | ||
| 'footer_align': 'Integer', | ||
| 'created_by': 'Integer', | ||
| 'created_date': 'Date', | ||
| 'edited_by': 'Integer', | ||
| 'edited_date': 'Date', | ||
| 'updated_by': 'Integer', | ||
| 'updated_date': 'Date', | ||
| 'transcriptid': 'Integer', | ||
| 'effectid': 'Integer', | ||
| 'position_c_start': 'Integer', | ||
| 'position_c_start_intron': 'Integer', | ||
| 'position_c_end': 'Integer', | ||
| 'position_c_end_intron': 'Integer', | ||
| 'VariantOnTranscript/DNA': 'String', | ||
| 'VariantOnTranscript/RNA': 'String', | ||
| 'VariantOnTranscript/Protein': 'String', | ||
| 'VariantOnTranscript/Exon': 'String', | ||
| 'symbol': 'String', | ||
| 'inheritance': 'String', | ||
| 'id_omin': 'Integer', | ||
| 'tissues': 'String', | ||
| 'features': 'String', | ||
| 'remarks': 'String', | ||
| 'geneid': 'String', | ||
| 'id_mutalyzer': 'Integer', | ||
| 'id_ncbi': 'String', | ||
| 'id_ensembl': 'String', | ||
| 'id_protein_ncbi': 'String', | ||
| 'id_protein_ensembl': 'String', | ||
| 'id_protein_uniprot': 'String', | ||
| 'position_c_mrna_start': 'Integer', | ||
| 'position_c_mrna_end': 'Integer', | ||
| 'position_c_cds_end': 'Integer', | ||
| 'position_g_mrna_start': 'Integer', | ||
| 'position_g_mrna_end': 'Integer', | ||
| 'diseaseid': 'Integer', | ||
| 'individualid': 'Integer', | ||
| 'Phenotype/Inheritance': 'String', | ||
| 'Phenotype/Age': 'String', | ||
| 'Phenotype/Additional': 'String', | ||
| 'Phenotype/Biochem_param': 'String', | ||
| 'Phenotype/Age/Onset': 'String', | ||
| 'Phenotype/Age/Diagnosis': 'String', | ||
| 'Phenotype/Severity_score': 'String', | ||
| 'Phenotype/Onset': 'String', | ||
| 'Phenotype/Protein': 'String', | ||
| 'Phenotype/Tumor/MSI': 'String', | ||
| 'Phenotype/Enzyme/CPK': 'String', | ||
| 'Phenotype/Heart/Myocardium': 'String', | ||
| 'Phenotype/Lung': 'String', | ||
| 'Phenotype/Diagnosis/Definite': 'String', | ||
| 'Phenotype/Diagnosis/Initial': 'String', | ||
| 'Phenotype/Diagnosis/Criteria': 'String', | ||
| 'variants_found': 'Integer', | ||
| 'Screening/Technique': 'String', | ||
| 'Screening/Template': 'String', | ||
| 'Screening/Tissue': 'String', | ||
| 'Screening/Remarks': 'String', | ||
| 'fatherid': 'String', | ||
| 'motherid': 'String', | ||
| 'panelid': 'Integer', | ||
| 'panel_size': 'Integer', | ||
| 'license': 'String', | ||
| 'Individual/Reference': 'String', | ||
| 'Individual/Remarks': 'String', | ||
| 'Individual/Gender': 'String', | ||
| 'Individual/Consanguinity': 'String', | ||
| 'Individual/Age_of_death': 'String', | ||
| 'Individual/VIP': 'String', | ||
| 'Individual/Data_av': 'String', | ||
| 'Individual/Treatment': 'String', | ||
| 'Individual/Origin/Population': 'String', | ||
| 'Individual/Individual_ID': 'String', | ||
| 'allele': 'Integer', | ||
| 'position_g_start': 'Integer', | ||
| 'position_g_end': 'Integer', | ||
| 'type': 'String', | ||
| 'average_frequency': 'Double', | ||
| 'VariantOnGenome/DBID': 'String', | ||
| 'VariantOnGenome/DNA': 'String', | ||
| 'VariantOnGenome/Frequency': 'String', | ||
| 'VariantOnGenome/Reference': 'String', | ||
| 'VariantOnGenome/Restriction_site': 'String', | ||
| 'VariantOnGenome/Published_as': 'String', | ||
| 'VariantOnGenome/Remarks': 'String', | ||
| 'VariantOnGenome/Genetic_origin': 'String', | ||
| 'VariantOnGenome/Segregation': 'String', | ||
| 'VariantOnGenome/dbSNP': 'String', | ||
| 'VariantOnGenome/VIP': 'String', | ||
| 'VariantOnGenome/Methylation': 'String', | ||
| 'VariantOnGenome/ISCN': 'String', | ||
| 'VariantOnGenome/DNA/hg38': 'String', | ||
| 'VariantOnGenome/ClinVar': 'String', | ||
| 'VariantOnGenome/ClinicalClassification': 'String', | ||
| 'VariantOnGenome/ClinicalClassification/Method': 'String', | ||
| 'screeningid': 'Integer', | ||
| 'variantid': 'Integer', | ||
| 'owned_by': 'Integer', | ||
| 'Individual/Origin/Geographic': 'String' | ||
| } |
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