variantgrid-api 0.3.0__tar.gz

variantgrid_api-0.3.0/LICENSE

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+MIT License
+
+Copyright (c) 2024
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

variantgrid_api-0.3.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: variantgrid_api
+Version: 0.3.0
+Summary: A Python API client for VariantGrid
+Author-email: Dave Lawrence <davmlaw@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2024
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/SACGF/variantgrid_api
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: dataclasses-json
+
+# variantgrid_api

variantgrid_api-0.3.0/README.md

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+# variantgrid_api

variantgrid_api-0.3.0/pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "variantgrid_api"
+version = "0.3.0"
+description = "A Python API client for VariantGrid"
+authors = [
+    { name = "Dave Lawrence", email = "davmlaw@gmail.com" }
+]
+readme = "README.md"
+license = {file = "LICENSE"}
+requires-python = ">=3.8"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+]
+dependencies = [
+    "requests",
+    "dataclasses-json"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/SACGF/variantgrid_api"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+exclude = ["examples"]

variantgrid_api-0.3.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

variantgrid_api-0.3.0/src/variantgrid_api/api_client.py

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+import json
+import logging
+import os
+from typing import List
+
+import requests
+
+from variantgrid_api.data_models import EnrichmentKit, SequencingRun, SampleSheet, SampleSheetCombinedVCFFile, \
+    SampleSheetLookup, SequencingFile, QCGeneList, QCExecStats, QCGeneCoverage
+
+
+class VariantGridAPI:
+    def __init__(self, server, api_token):
+        self.server = server
+        self.headers = {"Authorization": f"Token {api_token}"}
+
+    def _get_url(self, url):
+        return os.path.join(self.server, url)
+
+    def _post(self, path, json_data):
+        url = self._get_url(path)
+        response = requests.post(url, headers=self.headers, json=json_data)
+        try:
+            json_response = response.json()
+        except Exception as e:
+            json_response = f"Couldn't convert JSON: {e}"
+        if not response.ok:
+            logging.info("url='%s', JSON data:", url)
+            logging.info(json.dumps(json_data))
+            logging.info("Response: %s", json_response)
+            response.raise_for_status()
+        return json_response
+
+    def create_experiment(self, experiment: str):
+        json_data = {
+            "name": experiment
+        }
+        return self._post("seqauto/api/v1/experiment/", json_data)
+
+    def create_enrichment_kit(self, enrichment_kit: EnrichmentKit):
+        return self._post("seqauto/api/v1/enrichment_kit/",
+                          enrichment_kit.to_dict())
+
+    def create_sequencing_run(self, sequencing_run: SequencingRun):
+        return self._post("seqauto/api/v1/sequencing_run/",
+                          sequencing_run.to_dict())
+
+    def create_sample_sheet(self, sample_sheet: SampleSheet):
+        json_data = sample_sheet.to_dict()
+        # We don't want all sequencing_run just the name
+        sequencing_run = json_data.pop("sequencing_run")
+        json_data["sequencing_run"] = sequencing_run["name"]
+        return self._post("seqauto/api/v1/sample_sheet/",
+                          json_data)
+
+    def create_sample_sheet_combined_vcf_file(self, sample_sheet_combined_vcf_file: SampleSheetCombinedVCFFile):
+        json_data = sample_sheet_combined_vcf_file.to_dict()
+        return self._post("seqauto/api/v1/sample_sheet_combined_vcf_file/",
+                          json_data)
+
+    def create_sequencing_data(self, sample_sheet_lookup: SampleSheetLookup, sequencing_files: List[SequencingFile]):
+        records = []
+        for sf in sequencing_files:
+            data = sf.to_dict()
+            # put into hierarchial JSON DRF expects
+            fastq_r1 = data.pop("fastq_r1")
+            fastq_r2 = data.pop("fastq_r2")
+            data["unaligned_reads"] = {
+                "fastq_r1": {"path": fastq_r1},
+                "fastq_r2": {"path": fastq_r2}
+            }
+            records.append(data)
+
+        json_data = {
+            "sample_sheet": sample_sheet_lookup.to_dict(),
+            "records": records
+        }
+        return self._post("seqauto/api/v1/sequencing_files/bulk_create",
+                          json_data)
+
+    def create_qc_gene_list(self, qc_gene_list: QCGeneList):
+        json_data = qc_gene_list.to_dict()
+        return self._post("seqauto/api/v1/qc_gene_list/",
+                          json_data)
+
+
+    def create_multiple_qc_gene_lists(self, qc_gene_lists: List[QCGeneList]):
+        json_data = {
+            "records": [
+                qcgl.to_dict() for qcgl in qc_gene_lists
+            ]
+        }
+        return self._post("seqauto/api/v1/qc_gene_list/bulk_create",
+                          json_data)
+
+    def create_qc_exec_stats(self, qc_exec_stats: QCExecStats):
+        json_data = qc_exec_stats.to_dict()
+        return self._post("seqauto/api/v1/qc_exec_summary/",
+                          json_data)
+
+    def create_multiple_qc_exec_stats(self, qc_exec_stats: List[QCExecStats]):
+        json_data = {
+            "records": [
+                qces.to_dict() for qces in qc_exec_stats
+            ]
+        }
+        return self._post("seqauto/api/v1/qc_exec_summary/bulk_create",
+                          json_data)
+
+    def create_multiple_qc_gene_coverage(self, qc_gene_coverage_list: List[QCGeneCoverage]):
+        json_data = {
+            "records": [
+                qcgc.to_dict() for qcgc in qc_gene_coverage_list
+            ]
+        }
+        return self._post("seqauto/api/v1/qc_gene_coverage/bulk_create",
+                          json_data)
+
+    def upload_file(self, filename: str):
+        url = self._get_url("upload/api/v1/file_upload")
+        with open(filename, "rb") as f:
+            kwargs = {
+                "files": {"file": f},
+                "params": {"path": filename}
+            }
+            return requests.post(url, headers=self.headers, **kwargs)

variantgrid_api-0.3.0/src/variantgrid_api/data_models.py

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+from datetime import date, datetime
+from dataclasses import dataclass, field
+from typing import Optional, List
+
+from dataclasses_json import dataclass_json, config
+
+
+@dataclass_json
+@dataclass
+class EnrichmentKit:
+    name: str
+    version: int
+
+
+@dataclass_json
+@dataclass
+class SequencingRun:
+    path: str
+    name: str
+    date: date
+    sequencer: str
+    experiment: str
+    enrichment_kit: EnrichmentKit
+
+
+@dataclass_json
+@dataclass
+class SequencingSample:
+    sample_id: str
+    sample_number: int
+    lane: int
+    barcode: str
+    enrichment_kit: EnrichmentKit
+    sample_project: Optional[str] = None
+    is_control: bool = False
+    failed: bool = False
+    data: List[dict] = field(default_factory=lambda: [], metadata=config(field_name="sequencingsampledata_set"))
+
+
+@dataclass_json
+@dataclass
+class SampleSheet:
+    path: str
+    sequencing_run: SequencingRun
+    file_last_modified: datetime
+    hash: str
+    sequencing_samples: List[SequencingSample] = field(metadata=config(field_name="sequencingsample_set"))
+
+
+@dataclass_json
+@dataclass
+class SampleSheetLookup:
+    """ 'Lookups' are used as arguments to find existing data on server - not enough details to create one,
+        but just enough to find one
+    """
+    sequencing_run: str
+    hash: str
+
+    @staticmethod
+    def from_sample_sheet(sample_sheet: SampleSheet) -> 'SampleSheetLookup':
+        return SampleSheetLookup(sequencing_run=sample_sheet.sequencing_run.name, hash=sample_sheet.hash)
+
+
+@dataclass_json
+@dataclass
+class Aligner:
+    name: str
+    version: str
+
+
+@dataclass_json
+@dataclass
+class VariantCaller:
+    name: str
+    version: str
+    run_params: Optional[str] = None
+
+
+@dataclass_json
+@dataclass
+class SampleSheetCombinedVCFFile:
+    path: str
+    sample_sheet_lookup: SampleSheetLookup = field(metadata=config(field_name="sample_sheet"))
+    variant_caller: VariantCaller
+
+
+@dataclass_json
+@dataclass
+class BamFile:
+    path: str
+    aligner: Optional[Aligner] = field(default=None, metadata=config(exclude=lambda x: x is None))
+
+
+@dataclass_json
+@dataclass
+class VCFFile:
+    path: str
+    variant_caller: Optional[VariantCaller] = field(default=None, metadata=config(exclude=lambda x: x is None))
+
+
+@dataclass_json
+@dataclass
+class SequencingFile:
+    sample_name: str
+    fastq_r1: str
+    fastq_r2: str
+    bam_file: BamFile
+    vcf_file: VCFFile
+
+
+@dataclass_json
+@dataclass
+class SequencingSampleLookup:
+    """ Only used as arguments to find existing sequencing sample on server - not enough details to create one """
+    sample_sheet_lookup: SampleSheetLookup = field(metadata=config(field_name="sample_sheet"))
+    sample_name: str
+
+
+@dataclass_json
+@dataclass
+class QC:
+    """ QC information needs to be matched against a particular BAM/VCF file (as there could be multiple)
+        We use this to match gene lists, exec stats and coverage below
+     """
+    sequencing_sample_lookup: SequencingSampleLookup = field(metadata=config(field_name="sequencing_sample"))
+    bam_file: BamFile
+    vcf_file: VCFFile
+
+
+@dataclass_json
+@dataclass
+class QCGeneList:
+    path: str
+    qc: QC
+    gene_list: List[str]
+
+
+@dataclass_json
+@dataclass
+class QCExecStats:
+    path: str
+    qc: QC
+    created: datetime
+    modified: datetime
+    hash: str
+    is_valid: bool
+    deduplicated_reads: int
+    indels_dbsnp_percent: float
+    mean_coverage_across_genes: float
+    mean_coverage_across_kit: float
+    median_insert: float
+    number_indels: int
+    number_snps: int
+    percent_10x_goi: float
+    percent_20x_goi: float
+    percent_20x_kit: float
+    percent_error_rate: float
+    percent_map_to_diff_chr: float
+    percent_read_enrichment: float
+    percent_reads: float
+    percent_softclip: float
+    percent_duplication: float
+    reads: int
+    sample_id_lod: float
+    sex_match: str
+    snp_dbsnp_percent: float
+    ts_to_tv_ratio: float
+    uniformity_of_coverage: float
+    percent_100x_goi: Optional[float] = None
+    percent_100x_kit: Optional[float] = None
+    percent_250x_goi: Optional[float] = None
+    percent_250x_kit: Optional[float] = None
+    percent_500x_goi: Optional[float] = None
+    percent_500x_kit: Optional[float] = None
+
+
+@dataclass_json
+@dataclass
+class QCGeneCoverage:
+    """ We send this up to associate coverage file path with sequencing sample
+        Then, later we upload the coverage file - and match via path """
+    qc: QC
+    path: str

variantgrid_api-0.3.0/src/variantgrid_api.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: variantgrid_api
+Version: 0.3.0
+Summary: A Python API client for VariantGrid
+Author-email: Dave Lawrence <davmlaw@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2024
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/SACGF/variantgrid_api
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: dataclasses-json
+
+# variantgrid_api

variantgrid_api-0.3.0/src/variantgrid_api.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+src/variantgrid_api/api_client.py
+src/variantgrid_api/data_models.py
+src/variantgrid_api.egg-info/PKG-INFO
+src/variantgrid_api.egg-info/SOURCES.txt
+src/variantgrid_api.egg-info/dependency_links.txt
+src/variantgrid_api.egg-info/requires.txt
+src/variantgrid_api.egg-info/top_level.txt

variantgrid_api-0.3.0/src/variantgrid_api.egg-info/dependency_links.txt

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+

variantgrid_api-0.3.0/src/variantgrid_api.egg-info/requires.txt

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+requests
+dataclasses-json

variantgrid_api-0.3.0/src/variantgrid_api.egg-info/top_level.txt

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+variantgrid_api