variantgrid-api 0.3.0__tar.gz → 1.0.0__tar.gz

{variantgrid_api-0.3.0 → variantgrid_api-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: variantgrid_api
-Version: 0.3.0
+Version: 1.0.0
 Summary: A Python API client for VariantGrid
 Author-email: Dave Lawrence <davmlaw@gmail.com>
 License: MIT License
@@ -35,5 +35,11 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: requests
 Requires-Dist: dataclasses-json
+Requires-Dist: samshee
+Dynamic: license-file
 
 # variantgrid_api
+
+Python API client for [VariantGrid](https://github.com/SACGF/variantgrid) Open source Variant database and analysis platform
+
+See [changelog](https://github.com/SACGF/variantgrid_api/blob/main/CHANGELOG.md)

variantgrid_api-1.0.0/README.md

@@ -0,0 +1,5 @@
+# variantgrid_api
+
+Python API client for [VariantGrid](https://github.com/SACGF/variantgrid) Open source Variant database and analysis platform
+
+See [changelog](https://github.com/SACGF/variantgrid_api/blob/main/CHANGELOG.md)

{variantgrid_api-0.3.0 → variantgrid_api-1.0.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "variantgrid_api"
-version = "0.3.0"
+version = "1.0.0"
 description = "A Python API client for VariantGrid"
 authors = [
     { name = "Dave Lawrence", email = "davmlaw@gmail.com" }
@@ -20,7 +20,8 @@ classifiers = [
 ]
 dependencies = [
     "requests",
-    "dataclasses-json"
+    "dataclasses-json",
+    "samshee"
 ]
 
 [project.urls]

{variantgrid_api-0.3.0 → variantgrid_api-1.0.0}/src/variantgrid_api/api_client.py

@@ -1,13 +1,21 @@
+import datetime
 import json
 import logging
 import os
-from typing import List
+from typing import List, Optional
 
 import requests
 
 from variantgrid_api.data_models import EnrichmentKit, SequencingRun, SampleSheet, SampleSheetCombinedVCFFile, \
     SampleSheetLookup, SequencingFile, QCGeneList, QCExecStats, QCGeneCoverage
 
+class DateTimeEncoder(json.JSONEncoder):
+    def default(self,o):
+        if isinstance(o,(datetime.date, datetime.datetime)):
+            return o.isoformat()
+        return super().default(o)
+
+
 
 class VariantGridAPI:
     def __init__(self, server, api_token):
@@ -19,15 +27,23 @@ class VariantGridAPI:
 
     def _post(self, path, json_data):
         url = self._get_url(path)
-        response = requests.post(url, headers=self.headers, json=json_data)
+        json_string = json.dumps(json_data, cls=DateTimeEncoder)
+        response = requests.post(url,
+                                 headers={**self.headers, "Content-Type": "application/json"},
+                                 data=json_string)
+
+        extra_error_message = f"{url=}, {json_string=}"
+        return self._handle_json_response(response, extra_error_message)
+
+    def _handle_json_response(self, response, extra_error_message: Optional[str] = None):
         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)
+            if extra_error_message:
+                logging.error(extra_error_message)
+            logging.error("Response: %s", json_response)
             response.raise_for_status()
         return json_response
 
@@ -123,4 +139,38 @@ class VariantGridAPI:
                 "files": {"file": f},
                 "params": {"path": filename}
             }
-            return requests.post(url, headers=self.headers, **kwargs)
+            response = requests.post(url, headers=self.headers, **kwargs)
+            extra_error_message = f"{filename=}"
+            return self._handle_json_response(response, extra_error_message)
+
+    ###############
+    ## Get methods
+
+    def _get(self, path, params=None):
+        url = self._get_url(path)
+        response = requests.get(url,
+                                params,
+                                headers=self.headers)
+
+        extra_error_message = f"{url=}, {params=}"
+        return self._handle_json_response(response, extra_error_message)
+
+    def sequencing_run_has_vcf(self, sequencing_run: SequencingRun, path: Optional[str] = None):
+        """ Returns whether the SequencingRun has a VCF associated with it. If path is set, VCF must match that path
+            otherwise - any VCF present will retur True """
+        return self.sequencing_run_name_has_vcf(sequencing_run.name, path)
+
+    def sequencing_run_name_has_vcf(self, sequencing_run_name: str, path: Optional[str] = None):
+        """ Returns whether the SequencingRun has a VCF associated with it. If path is set, VCF must match that path
+            otherwise - any VCF present will retur True """
+        data = self._get(f"seqauto/api/v1/sequencing_run/{sequencing_run_name}/")
+        found_vcf = False
+        for vcf in data["vcf_set"]:
+            if path is None or path in vcf["path"]:
+                found_vcf = True
+                break
+        return found_vcf
+
+
+
+

{variantgrid_api-0.3.0 → variantgrid_api-1.0.0}/src/variantgrid_api/data_models.py

@@ -1,3 +1,4 @@
+import re
 from datetime import date, datetime
 from dataclasses import dataclass, field
 from typing import Optional, List
@@ -22,15 +23,25 @@ class SequencingRun:
     experiment: str
     enrichment_kit: EnrichmentKit
 
+    @staticmethod
+    def get_date_from_name(name) -> Optional[datetime.date]:
+        date = None
+        if m := re.match(r".*_?([12]\d{5})_", name):
+            date_str = m.group(1)
+            dt = datetime.strptime(date_str, "%y%m%d")
+            date = dt.date()
+        return date
+
+
 
 @dataclass_json
 @dataclass
 class SequencingSample:
     sample_id: str
-    sample_number: int
-    lane: int
+    sample_number: int  # Sample sheet row (to keep in order)
     barcode: str
     enrichment_kit: EnrichmentKit
+    lane: Optional[int] = None
     sample_project: Optional[str] = None
     is_control: bool = False
     failed: bool = False
@@ -42,7 +53,7 @@ class SequencingSample:
 class SampleSheet:
     path: str
     sequencing_run: SequencingRun
-    file_last_modified: datetime
+    file_last_modified: float
     hash: str
     sequencing_samples: List[SequencingSample] = field(metadata=config(field_name="sequencingsample_set"))
 
@@ -144,34 +155,34 @@ class QCExecStats:
     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
+    deduplicated_reads: Optional[int] = None
+    indels_dbsnp_percent: Optional[float] = None
+    number_indels: Optional[int] = None
+    number_snps: Optional[int] = None
+    percent_10x_goi: Optional[float] = None
+    percent_20x_goi: Optional[float] = None
+    percent_20x_kit: Optional[float] = None
     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
+    percent_error_rate: Optional[float] = None
+    percent_map_to_diff_chr: Optional[float] = None
+    percent_reads: Optional[float] = None
+    percent_softclip: Optional[float] = None
+    reads: Optional[int] = None
+    sample_id_lod: Optional[float] = None
+    sex_match: Optional[str] = None
+    snp_dbsnp_percent: Optional[float] = None
+    ts_to_tv_ratio: Optional[float] = None
 
 
 @dataclass_json
@@ -180,4 +191,4 @@ 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
+    path: str

{variantgrid_api-0.3.0 → variantgrid_api-1.0.0}/src/variantgrid_api.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: variantgrid_api
-Version: 0.3.0
+Version: 1.0.0
 Summary: A Python API client for VariantGrid
 Author-email: Dave Lawrence <davmlaw@gmail.com>
 License: MIT License
@@ -35,5 +35,11 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: requests
 Requires-Dist: dataclasses-json
+Requires-Dist: samshee
+Dynamic: license-file
 
 # variantgrid_api
+
+Python API client for [VariantGrid](https://github.com/SACGF/variantgrid) Open source Variant database and analysis platform
+
+See [changelog](https://github.com/SACGF/variantgrid_api/blob/main/CHANGELOG.md)

{variantgrid_api-0.3.0 → variantgrid_api-1.0.0}/src/variantgrid_api.egg-info/requires.txt

@@ -1,2 +1,3 @@
 requests
 dataclasses-json
+samshee

variantgrid_api-0.3.0/README.md

@@ -1 +0,0 @@
-# variantgrid_api