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core_api.py
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core_api.py
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from logging import NullHandler
import requests
from requests.auth import HTTPBasicAuth
import os
import json
from datetime import datetime
import jaxlims_api as db
import read_config as cfg
from datetime import timedelta
import re
import my_logger
import csv
impcCodeLookups = {
'IMPC_ABR_001_001': '',
'IMPC_ABR_004_001': '',
'IMPC_ABR_006_001': '',
'IMPC_ABR_008_001': '',
'IMPC_ABR_010_001': '',
'IMPC_ABR_012_001': '',
'IMPC_ABR_014_001': '',
'IMPC_ABR_028_001': '',
'IMPC_ABR_036_001': '',
'IMPC_ABR_037_001': '',
'IMPC_ABR_038_001': '',
'IMPC_ABR_039_001': '',
'IMPC_ABR_040_001': '',
'IMPC_ABR_041_001': '',
'IMPC_ABR_042_001': '',
'IMPC_ABR_043_001': '',
'IMPC_ABR_044_001': '',
'IMPC_ABR_045_001': '',
'IMPC_ABR_046_001': '',
'IMPC_ABR_047_001': '',
'IMPC_ABR_048_001': '',
'IMPC_ABR_049_001': '',
'IMPC_ABR_050_001': '',
'IMPC_ABR_051_001': '',
'IMPC_ABR_052_001': '',
'IMPC_ABR_053_001': '',
'IMPC_ABR_054_001': '',
'IMPC_ACS_001_001': '',
'IMPC_ACS_002_001': '',
'IMPC_ACS_003_001': '',
'IMPC_ACS_004_001': '',
'IMPC_ACS_005_001': '',
'IMPC_ACS_006_001': '',
'IMPC_ACS_007_001': '',
'IMPC_ACS_008_001': '',
'IMPC_ACS_009_001': '',
'IMPC_ACS_010_001': '',
'IMPC_ACS_011_001': '',
'IMPC_ACS_012_001': '',
'IMPC_ACS_013_001': '',
'IMPC_ACS_014_001': '',
'IMPC_ACS_015_001': '',
'IMPC_ACS_016_001': '',
'IMPC_ACS_017_001': '',
'IMPC_ACS_018_001': '',
'IMPC_ACS_019_001': '',
'IMPC_ACS_020_001': '',
'IMPC_ACS_021_001': '',
'IMPC_ACS_022_001': '',
'IMPC_ACS_023_001': '',
'IMPC_ACS_024_001': '',
'IMPC_ACS_025_001': '',
'IMPC_ACS_026_001': '',
'IMPC_ACS_027_001': '',
'IMPC_ACS_028_001': '',
'IMPC_ACS_029_001': '',
'IMPC_ACS_030_001': '',
'IMPC_ACS_031_001': '',
'IMPC_ACS_032_001': '',
'IMPC_ACS_033_001': '',
'IMPC_ACS_034_001': '',
'IMPC_ACS_035_001': '',
'IMPC_ACS_036_001': '',
'IMPC_ACS_037_001': '',
'IMPC_ACS_038_001': '',
'IMPC_ACS_039_001': '',
'IMPC_ACS_040_001': '',
'IMPC_BWT_001_001': '',
'IMPC_BWT_002_001': '',
'IMPC_BWT_003_001': '',
'IMPC_BWT_004_001': '',
'IMPC_BWT_005_001': '',
'IMPC_BWT_007_001': '',
'IMPC_CBC_001_001': '',
'IMPC_CBC_002_001': '',
'IMPC_CBC_003_001': '',
'IMPC_CBC_004_001': '',
'IMPC_CBC_005_001': '',
'IMPC_CBC_006_001': '',
'IMPC_CBC_007_001': '',
'IMPC_CBC_008_001': '',
'IMPC_CBC_009_001': '',
'IMPC_CBC_010_001': '',
'IMPC_CBC_011_001': '',
'IMPC_CBC_012_001': '',
'IMPC_CBC_013_001': '',
'IMPC_CBC_014_001': '',
'IMPC_CBC_015_001': '',
'IMPC_CBC_016_001': '',
'IMPC_CBC_017_001': '',
'IMPC_CBC_018_001': '',
'IMPC_CBC_026_001': '',
'IMPC_CBC_033_001': '',
'IMPC_CBC_034_001': '',
'IMPC_CBC_035_001': '',
'IMPC_CBC_036_001': '',
'IMPC_CBC_037_001': '',
'IMPC_CBC_038_001': '',
'IMPC_CBC_039_001': '',
'IMPC_CBC_040_001': '',
'IMPC_CBC_041_001': '',
'IMPC_CBC_042_001': '',
'IMPC_CBC_043_001': '',
'IMPC_CBC_044_001': '',
'IMPC_CBC_045_001': '',
'IMPC_CBC_046_001': '',
'IMPC_CBC_047_001': '',
'IMPC_CBC_048_001': '',
'IMPC_CBC_049_001': '',
'IMPC_CBC_051_001': '',
'IMPC_CBC_056_001': '',
'IMPC_CBC_057_001': '',
'IMPC_CBC_059_001': '',
'IMPC_CSD_001_001': '',
'IMPC_CSD_002_001': '',
'IMPC_CSD_003_001': '',
'IMPC_CSD_004_001': '',
'IMPC_CSD_005_001': '',
'IMPC_CSD_006_001': '',
'IMPC_CSD_007_001': '',
'IMPC_CSD_008_001': '',
'IMPC_CSD_009_001': '',
'IMPC_CSD_010_001': '',
'IMPC_CSD_011_001': '',
'IMPC_CSD_012_001': '',
'IMPC_CSD_013_001': '',
'IMPC_CSD_014_001': '',
'IMPC_CSD_015_001': '',
'IMPC_CSD_016_001': '',
'IMPC_CSD_017_001': '',
'IMPC_CSD_018_001': '',
'IMPC_CSD_019_001': '',
'IMPC_CSD_020_001': '',
'IMPC_CSD_021_001': '',
'IMPC_CSD_022_001': '',
'IMPC_CSD_023_001': '',
'IMPC_CSD_024_001': '',
'IMPC_CSD_025_001': '',
'IMPC_CSD_026_001': '',
'IMPC_CSD_027_001': '',
'IMPC_CSD_028_001': '',
'IMPC_CSD_029_001': '',
'IMPC_CSD_030_001': '',
'IMPC_CSD_031_001': '',
'IMPC_CSD_032_001': '',
'IMPC_CSD_033_001': '',
'IMPC_CSD_034_001': '',
'IMPC_CSD_035_001': '',
'IMPC_CSD_036_001': '',
'IMPC_CSD_037_001': '',
'IMPC_CSD_038_001': '',
'IMPC_CSD_039_001': '',
'IMPC_CSD_040_001': '',
'IMPC_CSD_040_002': '',
'IMPC_CSD_041_001': '',
'IMPC_CSD_041_002': '',
'IMPC_CSD_042_001': '',
'IMPC_CSD_042_002': '',
'IMPC_CSD_043_001': '',
'IMPC_CSD_043_002': '',
'IMPC_CSD_044_001': '',
'IMPC_CSD_044_002': '',
'IMPC_CSD_045_001': '',
'IMPC_CSD_045_002': '',
'IMPC_CSD_046_001': '',
'IMPC_CSD_047_001': '',
'IMPC_CSD_048_001': '',
'IMPC_CSD_048_002': '',
'IMPC_CSD_049_001': '',
'IMPC_CSD_049_002': '',
'IMPC_CSD_050_001': '',
'IMPC_CSD_050_002': '',
'IMPC_CSD_051_001': '',
'IMPC_CSD_051_002': '',
'IMPC_CSD_052_001': '',
'IMPC_CSD_052_002': '',
'IMPC_CSD_053_001': '',
'IMPC_CSD_053_002': '',
'IMPC_CSD_054_001': '',
'IMPC_CSD_054_002': '',
'IMPC_CSD_055_001': '',
'IMPC_CSD_055_002': '',
'IMPC_CSD_056_001': '',
'IMPC_CSD_057_001': '',
'IMPC_CSD_058_001': '',
'IMPC_CSD_059_001': '',
'IMPC_CSD_060_001': '',
'IMPC_CSD_061_001': '',
'IMPC_CSD_062_001': '',
'IMPC_CSD_063_001': '',
'IMPC_CSD_064_001': '',
'IMPC_CSD_065_001': '',
'IMPC_CSD_066_001': '',
'IMPC_CSD_067_001': '',
'IMPC_CSD_068_001': '',
'IMPC_CSD_069_001': '',
'IMPC_CSD_070_001': '',
'IMPC_CSD_071_001': '',
'IMPC_CSD_072_001': '',
'IMPC_CSD_073_001': '',
'IMPC_CSD_074_001': '',
'IMPC_CSD_075_001': '',
'IMPC_CSD_076_001': '',
'IMPC_CSD_077_001': '',
'IMPC_CSD_078_001': '',
'IMPC_CSD_079_001': '',
'IMPC_CSD_080_001': '',
'IMPC_CSD_081_001': '',
'IMPC_CSD_082_001': '',
'IMPC_CSD_083_001': '',
'IMPC_CSD_084_001': '',
'IMPC_CSD_085_001': '',
'IMPC_CSD_086_001': '',
'IMPC_DXA_001_001': '',
'IMPC_DXA_002_001': '',
'IMPC_DXA_003_001': '',
'IMPC_DXA_004_001': '',
'IMPC_DXA_005_001': '',
'IMPC_DXA_006_001': '',
'IMPC_DXA_007_001': '',
'IMPC_DXA_008_001': '',
'IMPC_DXA_009_001': '',
'IMPC_DXA_010_001': '',
'IMPC_DXA_011_001': '',
'IMPC_DXA_012_001': '',
'IMPC_DXA_013_001': '',
'IMPC_DXA_014_001': '',
'IMPC_DXA_015_001': '',
'IMPC_DXA_016_001': '',
'IMPC_ECG_001_001': '',
'IMPC_ECG_002_001': '',
'IMPC_ECG_003_001': '',
'IMPC_ECG_004_001': '',
'IMPC_ECG_005_001': '',
'IMPC_ECG_006_001': '',
'IMPC_ECG_007_001': '',
'IMPC_ECG_008_001': '',
'IMPC_ECG_009_001': '',
'IMPC_ECG_009_002': '',
'IMPC_ECG_010_001': '',
'IMPC_ECG_011_001': '',
'IMPC_ECG_012_001': '',
'IMPC_ECG_013_001': '',
'IMPC_ECG_014_001': '',
'IMPC_ECG_015_001': '',
'IMPC_ECG_016_001': '',
'IMPC_ECG_017_001': '',
'IMPC_ECG_018_001': '',
'IMPC_ECG_019_001': '',
'IMPC_ECG_020_001': '',
'IMPC_ECG_025_001': '',
'IMPC_ECG_026_001': '',
'IMPC_ECG_028_001': '',
'IMPC_ECG_030_001': '',
'IMPC_ECG_031_001': '',
'IMPC_EYE_001_001': '',
'IMPC_EYE_002_001': '',
'IMPC_EYE_003_001': '',
'IMPC_EYE_004_001': '',
'IMPC_EYE_005_001': '',
'IMPC_EYE_006_001': '',
'IMPC_EYE_007_001': '',
'IMPC_EYE_008_001': '',
'IMPC_EYE_009_001': '',
'IMPC_EYE_010_001': '',
'IMPC_EYE_011_001': '',
'IMPC_EYE_012_001': '',
'IMPC_EYE_013_001': '',
'IMPC_EYE_014_001': '',
'IMPC_EYE_015_001': '',
'IMPC_EYE_016_001': '',
'IMPC_EYE_017_001': '',
'IMPC_EYE_018_001': '',
'IMPC_EYE_019_001': '',
'IMPC_EYE_020_001': '',
'IMPC_EYE_021_001': '',
'IMPC_EYE_022_001': '',
'IMPC_EYE_023_001': '',
'IMPC_EYE_024_001': '',
'IMPC_EYE_025_001': '',
'IMPC_EYE_026_001': '',
'IMPC_EYE_027_001': '',
'IMPC_EYE_028_001': '',
'IMPC_EYE_029_001': '',
'IMPC_EYE_030_001': '',
'IMPC_EYE_031_001': '',
'IMPC_EYE_032_001': '',
'IMPC_EYE_033_001': '',
'IMPC_EYE_034_001': '',
'IMPC_EYE_035_001': '',
'IMPC_EYE_036_001': '',
'IMPC_EYE_043_001': '',
'IMPC_EYE_044_001': '',
'IMPC_EYE_045_001': '',
'IMPC_EYE_046_001': '',
'IMPC_EYE_047_001': '',
'IMPC_EYE_050_001': '',
'IMPC_EYE_051_001': '',
'IMPC_EYE_080_001': '',
'IMPC_EYE_081_001': '',
'IMPC_EYE_082_001': '',
'IMPC_EYE_083_001': '',
'IMPC_GRS_001_001': '',
'IMPC_GRS_002_001': '',
'IMPC_GRS_003_001': '',
'IMPC_GRS_004_001': '',
'IMPC_GRS_005_001': '',
'IMPC_GRS_006_001': '',
'IMPC_GRS_007_001': '',
'IMPC_GRS_008_001': '',
'IMPC_GRS_009_001': '',
'IMPC_GRS_010_001': '',
'IMPC_GRS_011_001': '',
'IMPC_GRS_012_001': '',
'IMPC_GRS_013_001': '',
'IMPC_GRS_014_001': '',
'IMPC_HEM_001_001': '',
'IMPC_HEM_002_001': '',
'IMPC_HEM_003_001': '',
'IMPC_HEM_004_001': '',
'IMPC_HEM_005_001': '',
'IMPC_HEM_006_001': '',
'IMPC_HEM_007_001': '',
'IMPC_HEM_008_001': '',
'IMPC_HEM_009_001': '',
'IMPC_HEM_010_001': '',
'IMPC_HEM_011_001': '',
'IMPC_HEM_012_001': '',
'IMPC_HEM_013_001': '',
'IMPC_HEM_014_001': '',
'IMPC_HEM_015_001': '',
'IMPC_HEM_016_001': '',
'IMPC_HEM_017_001': '',
'IMPC_HEM_018_001': '',
'IMPC_HEM_020_001': '',
'IMPC_HEM_021_001': '',
'IMPC_HEM_022_001': '',
'IMPC_HEM_024_001': '',
'IMPC_HEM_026_001': '',
'IMPC_HWT_001_001': '',
'IMPC_HWT_003_001': '',
'IMPC_HWT_005_001': '',
'IMPC_HWT_006_001': '',
'IMPC_HWT_007_001': '',
'IMPC_HWT_008_001': '',
'IMPC_HWT_010_001': '',
'IMPC_HWT_011_001': '',
'IMPC_IPG_001_001': '',
'IMPC_IPG_002_001': '',
'IMPC_IPG_003_001': '',
'IMPC_IPG_004_001': '',
'IMPC_IPG_005_001': '',
'IMPC_IPG_006_001': '',
'IMPC_IPG_007_001': '',
'IMPC_IPG_008_001': '',
'IMPC_IPG_013_001': '',
'JAX_ERG_001_001': '',
'JAX_ERG_002_001': '',
'JAX_ERG_003_001': '',
'JAX_ERG_004_001': '',
'JAX_ERG_005_001': '',
'JAX_ERG_006_001': '',
'JAX_ERG_007_001': '',
'JAX_ERG_008_001': '',
'JAX_ERG_009_001': '',
'JAX_ERG_010_001': '',
'JAX_ERG_011_001': '',
'JAX_ERG_012_001': '',
'JAX_ERG_013_001': '',
'JAX_ERG_014_001': '',
'JAX_ERG_015_001': '',
'JAX_ERG_016_001': '',
'JAX_ERG_017_001': '',
'JAX_ERG_018_001': '',
'JAX_ERG_019_001': '',
'JAX_ERG_020_001': '',
'JAX_ERG_021_001': '',
'JAX_ERG_022_001': '',
'JAX_ERG_023_001': '',
'JAX_ERG_024_001': '',
'JAX_ERG_025_001': '',
'JAX_ERG_026_001': '',
'JAX_ERG_027_001': '',
'JAX_ERG_028_001': '',
'JAX_ERG_029_001': '',
'JAX_ERG_030_001': '',
'JAX_ERG_031_001': '',
'JAX_ERG_032_001': '',
'JAX_ERG_033_001': '',
'JAX_ERG_034_001': '',
'JAX_ERG_035_001': '',
'JAX_ERG_036_001': '',
'JAX_ERG_037_001': '',
'JAX_ERG_038_001': '',
'JAX_ERG_039_001': '',
'JAX_ERG_040_001': '',
'JAX_ERG_041_001': '',
'JAX_ERG_042_001': '',
'JAX_ERG_044_001': '',
'JAX_ERG_045_001': '',
'JAX_ERG_046_001': '',
'JAX_ERG_047_001': '',
'JAX_ERG_048_001': '',
'JAX_ERG_049_001': '',
'JAX_ERG_050_001': '',
'JAX_ERG_051_001': '',
'JAX_ERG_052_001': '',
'JAX_ERG_053_001': '',
'JAX_ERG_054_001': '',
'JAX_ERG_055_001': '',
'JAX_ERG_056_001': '',
'JAX_ERG_057_001': '',
'JAX_ERG_058_001': '',
'JAX_ERG_059_001': '',
'JAX_HBD_001_001': '',
'JAX_HBD_002_001': '',
'JAX_HBD_003_001': '',
'JAX_HBD_004_001': '',
'JAX_HBD_005_001': '',
'JAX_HBD_006_001': '',
'JAX_HBD_007_001': '',
'JAX_HBD_008_001': '',
'JAX_HBD_009_001': '',
'JAX_HBD_010_001': '',
'JAX_LDT_001_001': '',
'JAX_LDT_002_001': '',
'JAX_LDT_003_001': '',
'JAX_LDT_004_001': '',
'JAX_LDT_005_001': '',
'JAX_LDT_006_001': '',
'JAX_LDT_007_001': '',
'JAX_LDT_008_001': '',
'JAX_LDT_009_001': '',
'JAX_LDT_010_001': '',
'JAX_LDT_011_001': '',
'JAX_LDT_012_001': '',
'JAX_LDT_013_001': '',
'JAX_LDT_014_001': '',
'JAX_LDT_015_001': '',
'JAX_LDT_016_001': '',
'JAX_LDT_017_001': '',
'JAX_LDT_018_001': '',
'JAX_LDT_019_001': '',
'JAX_OFD_005_001': '',
'JAX_OFD_006_001': '',
'JAX_OFD_007_001': '',
'JAX_OFD_008_001': '',
'JAX_OFD_009_001': '',
'JAX_OFD_010_001': '',
'JAX_OFD_011_001': '',
'JAX_OFD_012_001': '',
'JAX_OFD_013_001': '',
'JAX_OFD_014_001': '',
'JAX_OFD_015_001': '',
'JAX_OFD_016_001': '',
'JAX_OFD_017_001': '',
'JAX_OFD_018_001': '',
'JAX_OFD_019_001': '',
'JAX_OFD_020_001': '',
'JAX_OFD_021_001': '',
'JAX_OFD_022_001': '',
'JAX_OFD_023_001': '',
'JAX_OFD_024_001': '',
'JAX_OFD_025_001': '',
'JAX_OFD_026_001': '',
'JAX_OFD_027_001': '',
'JAX_OFD_028_001': '',
'JAX_OFD_029_001': '',
'JAX_OFD_030_001': '',
'JAX_OFD_031_001': '',
'JAX_OFD_032_001': '',
'JAX_OFD_033_001': '',
'JAX_OFD_034_001': '',
'JAX_OFD_035_001': '',
'JAX_OFD_036_001': '',
'JAX_OFD_037_001': '',
'JAX_OFD_038_001': '',
'JAX_OFD_039_001': '',
'JAX_OFD_041_001': '',
'JAX_OFD_051_001': '',
'JAX_OFD_052_001': ''
}
kompExperimentNames = [
"BODY_WEIGHT",
"AUDITORY_BRAINSTEM_RESPONSE",
"BODY_COMPOSITION",
"CLINICAL_BLOOD_CHEMISTRY",
"ELECTROCARDIOGRAM",
"ELECTRORETINOGRAPHY",
"EYE_MORPHOLOGY",
"FUNDUS_IMAGING",
"GLUCOSE_TOLERANCE_TEST",
"GRIP_STRENGTH",
"HEART_WEIGHT",
"HEMATOLOGY",
"HOLEBOARD",
"LIGHT_DARK_BOX",
"OPEN_FIELD",
"SHIRPA_DYSMORPHOLOGY",
"STARTLE_PPI"
]
# Constants
DCC_SIMPLE_TYPE = 1
DCC_MEDIA_TYPE = 3
DCC_SERIES_TYPE = 4
DCC_SERIES_MEDIA_TYPE = 5
DCC_METADATA_TYPE = 7
FIRST_GTT_SERIES = 'IMPC_IPG_002_001_T0' # t0, t15, t30, t60, t120
FIRST_OFD_DISTANCE_TRAVELLED_SERIES = 'JAX_OFD_005_001_1ST5' # 1st5, 2nd5, 3rd5, 4th5
FIRST_GRS_FORELIMB_SERIES = 'IMPC_GRS_001_001_T1' #t1, t2, t3
FIRST_GRS_FOREHINDLIMB_SERIES = 'IMPC_GRS_002_001_T1' #t1, t2, t3
FIRST_HBD_HOLEPOKE_SEQUENCE_SERIES = 'JAX_HBD_002_001' # Comes in as a single string. Needs to be converted into a series.
FIRST_SHIRPA_DYS_IMAGE_SERIES = 'IMPC_CSD_051_001_1'
FIRST_EYE_SLITLAMP_IMAGE_SERIES = 'IMPC_EYE_051_001_1'
FIRST_EYE_FUNDUS_IMAGE_SERIES = 'IMPC_EYE_050_001_1'
FIRST_ECG_IMAGE_SERIES = 'IMPC_ECG_025_001_f1'
"""
IMPC_GRS_001_001
IMPC_GRS_002_001
IMPC_IPG_002_001
JAX_HBD_002_001
JAX_OFD_005_001 Distance travelled
JAX_OFD_006_001 ??? Number of rears - not colllected
"""
seriesImpcCodes = [
FIRST_GTT_SERIES,
FIRST_OFD_DISTANCE_TRAVELLED_SERIES,
FIRST_GRS_FORELIMB_SERIES,
FIRST_GRS_FOREHINDLIMB_SERIES,
FIRST_HBD_HOLEPOKE_SEQUENCE_SERIES
]
"""
IMPC_CSD_085_001
IMPC_ECG_025_001
IMPC_EYE_050_001
IMPC_EYE_051_001
"""
# TODO Get from PFS
seriesMediaImpcCodes = [
FIRST_SHIRPA_DYS_IMAGE_SERIES,
FIRST_EYE_SLITLAMP_IMAGE_SERIES,
FIRST_EYE_FUNDUS_IMAGE_SERIES,
FIRST_ECG_IMAGE_SERIES
]
############################# MICE/SAMPLES #################
def getKompMice():
mycfg = cfg.parse_config(path="config.yml")
# Setup credentials for database
baseURL = mycfg['corepfs_database']['baseURL']
mouseEndpoint = mycfg['corepfs_database']['mouseEndpoint']
username = mycfg['corepfs_database']['username']
password = mycfg['corepfs_database']['password']
try:
my_auth = HTTPBasicAuth(username, password)
query = baseURL + mouseEndpoint
result = requests.get(query, auth=my_auth,headers = {"Prefer": "odata.maxpagesize=5000"})
wgJson = result.json()
#Get list of values
valueLs = wgJson.get('value')
# Make sure we got all the mice
totalCount = wgJson.get('@odata.count')
return totalCount,valueLs
except requests.exceptions.Timeout as e:
print(repr(e))
my_logger.info(repr(e))
raise
except requests.exceptions.InvalidHeader as e:
print(repr(e))
my_logger.info(repr(e))
raise
except requests.exceptions.InvalidURL as e:
print(repr(e))
my_logger.info(repr(e))
raise
except requests.exceptions.RequestException as e: # All others
print(repr(e))
my_logger.info(repr(e))
raise
pass
# This function returns a list of animalInfo.
# Each element in the list is animal dictional, a line dictionary and a genotypes list of dictionaries.
# Ex:
#{
# "animal": {
# "animalName": "A-560",
# "dateBorn": "2022-02-21T05:00:00",
# "sex": "Male",
# "generation": "E18.5",
# },
# "line": {
# "stock": "034083",
# "litter": {
# "birthID": null,
# },
# "genotypes": [
# {
# "genotype": "-/-",
# }
# ]
#},
#
def getSampleList(kompRequestlist):
# Give "value": [ <blah>, REV_MOUSESAMPLELOT_KOMPREQUEST [ { "EntityTypeName": "MOUSE_SAMPLE_LOT", ... "SAMPLE": { <the good stuff> }]
# TODO Can I filter out previously uploaded mice?
sampleDictls = []
for kompRequest in kompRequestlist:
mouseSampleLotList = kompRequest["REV_MOUSESAMPLELOT_KOMPREQUEST"]
for mouseSampleLot in mouseSampleLotList:
if mouseSampleLot["SAMPLE"] is None:
continue
sampleDict = mouseSampleLot["SAMPLE"]
# TEMP - filter out garbage from test env
#if sampleDict["JAX_MOUSESAMPLE_ALLELE"] == None or "(JR0" not in sampleDict["JAX_MOUSESAMPLE_ALLELE"]:
# continue
# End of TEMP
tmpDict = {}
animalDict = {}
lineDict = {}
litterDict = {}
genotypesLs = []
genotypeDict = {}
animalDict["animalName"] = sampleDict["JAX_SAMPLE_EXTERNALID"]
animalDict["dateBorn"] = sampleDict["JAX_MOUSESAMPLE_DATEOFBIRTH"]
sex =''
if sampleDict["JAX_MOUSESAMPLE_SEX"] == 'M':
sex = 'Male'
else:
sex = 'Female'
animalDict["sex"] = sex
animalDict["generation"] = "F1" # Is this OK
tmpDict["animal"] = animalDict
lineDict["stock"] = jaxstrainToStocknumber(sampleDict["JAX_MOUSESAMPLE_ALLELE"])
tmpDict["line"] = lineDict
litterDict["birthID"] = sampleDict["JAX_MOUSESAMPLE_LITTERNUMBER"]
tmpDict["litter"] = litterDict
genotypeDict["genotype"] = sampleDict["JAX_MOUSESAMPLE_GENOTYPE"]
genotypeDict["assay"] = sampleDict["JAX_MOUSESAMPLE_ALLELE"]
genotypesLs.append(genotypeDict)
tmpDict["genotypes"] = genotypesLs #list of dict ; each dict has one element { "genotype: "}
sampleDictls.append(tmpDict)
return sampleDictls
def updateAssayWithFailReason(expName,assayBarcode,failreason,failcomments):
# Update the assay failed reason and comments
put_data = getAssay(expName,assayBarcode)
put_data['Barcode'] = assayBarcode
put_data['JAX_ASSAY_ASSAYFAILREASON'] = failreason
put_data['JAX_ASSAY_ASSAYFAILCOMMENTS'] = failcomments
mycfg = cfg.parse_config(path="config.yml")
baseURL = mycfg['corepfs_database']['baseURL']
username = mycfg['corepfs_database']['username']
password = mycfg['corepfs_database']['password']
my_auth = HTTPBasicAuth(username, password)
query = baseURL + "KOMP_{0}_ASSAY_DATA('{1}')".format(expName,assayBarcode) # expName is like BODY_WEIGHT
#print(put_data)
my_logger.info(put_data)
result = requests.put(query, data=json.dumps(put_data), auth=my_auth,headers = {"Content-Type": "application/json", "If-Match": "*" })
#print(result.text)
my_logger.info(result.text)
# Did it work? Chekc for code 200
return 200
def updateExperimentStatus(expName,expBarcode,status='Data Sent to DCC',comments=''):
put_data = getExperiment(expName,expBarcode)
put_data['Barcode'] = expBarcode
put_data['JAX_EXPERIMENT_STATUS'] = status
put_data['JAX_EXPERIMENT_COMMENTS'] = comments
my_logger.info("PUT data:" + str(put_data))
s = f"Name: {expName} Barcode: {expBarcode} Status: {status} Comments: {comments}"
my_logger.info(s)
mycfg = cfg.parse_config(path="config.yml")
baseURL = mycfg['corepfs_database']['baseURL']
username = mycfg['corepfs_database']['username']
password = mycfg['corepfs_database']['password']
my_auth = HTTPBasicAuth(username, password)
query = baseURL + "{0}('{1}')".format(expName,expBarcode) # expName is like KOMP_BODY_WEIGHT_EXPERIMENT
result = requests.put(query, data=json.dumps(put_data), auth=my_auth,headers = {"Content-Type": "application/json", "If-Match": "*" })
my_logger.info(result.text)
# Did it work? Chekc for code 200
if result.status_code == 200 or result.status_code == 5000: # CORE bug : returns error 5000 but PUT works
my_logger.info("BARCODE " + expBarcode + " succesfully update to " + status)
else:
#print("BARCODE " + expBarcode + " failed to update to " + status)
my_logger.info("BARCODE " + expBarcode + " failed to update to " + status + ". Return code: " + str(result.status_code))
def getExperiment(expName:str, expBarcode:str) -> dict:
# Get the experiment from the barcode and return it as a dict
try:
mycfg = cfg.parse_config(path="config.yml")
baseURL = mycfg['corepfs_database']['baseURL']
username = mycfg['corepfs_database']['username']
password = mycfg['corepfs_database']['password']
my_auth = HTTPBasicAuth(username, password)
query = baseURL + "{0}('{1}')".format(expName, expBarcode) # expName is like BODY_WEIGHT
result = requests.get(query, auth=my_auth,headers = {"Content-Type": "application/json", "If-Match": "*" })
cont = result.content
if cont == None:
my_logger.info("No content returned for {0} {1}".format(expName,expBarcode))
return {}
d = json.loads(cont.decode('utf-8'))
d.pop("@odata.context", None)
except Exception as e:
my_logger.info(repr(e))
return {}
return d
def getAssay(expName:str, assayBarcode:str) -> dict:
# Get the experiment from the barcode and return it as a dict
mycfg = cfg.parse_config(path="config.yml")
baseURL = mycfg['corepfs_database']['baseURL']
username = mycfg['corepfs_database']['username']
password = mycfg['corepfs_database']['password']
my_auth = HTTPBasicAuth(username, password)
query = baseURL + "KOMP_{0}_ASSAY_DATA('{1}')".format(expName, assayBarcode) # expName is like BODY_WEIGHT
result = requests.get(query, auth=my_auth,headers = {"Content-Type": "application/json", "If-Match": "*" })
cont = result.content
d = json.loads(cont.decode('utf-8'))
d.pop("@odata.context", None)
return d
def jaxstrainToStocknumber(jaxstrain):
# Find last occurance of "JR"
# Copy the next 6 characters
index = jaxstrain.rfind('JR')
if index != -1:
return jaxstrain[index+2:index+8]
else:
return jaxstrain
def jaxstrainToAssay(jaxstrain):
# Find last occurance of "JR"
# Copy the next 6 characters
index = jaxstrain.rfind('JR')
if index != -1:
return jaxstrain[0:index]
else:
return jaxstrain
def getPfsAnimalInfo():
# Return a list of animal info
numberOfKompRequest, valuelist = getKompMice()
return getSampleList(valuelist)
def getExperimentData(experimentname):
try:
mycfg = cfg.parse_config(path="config.yml")
baseURL = mycfg['corepfs_database']['baseURL']
username = mycfg['corepfs_database']['username']
password = mycfg['corepfs_database']['password']
experimentEndpointTemplate = mycfg['corepfs_database']['experimentEndpointTemplate']
experimentEndpoint = experimentEndpointTemplate.format(exp=experimentname)
my_auth = HTTPBasicAuth(username, password)
query = baseURL + experimentEndpoint
result = requests.get(query, auth=my_auth,headers = {"Prefer": "odata.maxpagesize=5000"})
wgJson = result.json()
#Get list of values
valueLs = []
totalCount = 0
if 'value' in wgJson.keys(): # A list of dicts
valueLs = wgJson.get('value')
totalCount = wgJson.get('@odata.count')
else: # A single dict
valueLs.append(wgJson)
totalCount = 1
my_logger.info("Number of requests for {0}:".format(experimentname) + str(totalCount))
if valueLs != None:
return len(valueLs),valueLs
else:
return 0, []
except requests.exceptions.Timeout as e:
print(repr(e))
my_logger.info(repr(e))
raise
except requests.exceptions.InvalidHeader as e:
print(repr(e))
my_logger.info(repr(e))
raise
except requests.exceptions.InvalidURL as e:
print(repr(e))
my_logger.info(repr(e))
raise
except requests.exceptions.RequestException as e: # All others
print(repr(e))
my_logger.info(repr(e))
raise
# The results will be taskInfo [ animal [], taskInstance [ inputs [] , outputs [] ] ]
def buildTaskInfoList(expDataLs):
# Return a list of dictionaries where each element is a list of dictionaries.
taskInfoLs = []
for procedure in expDataLs:
animal = []
animalInfo = {}
taskInfo = {}
inputs = getInputs(procedure) # We get the inputs from the procedure (experiment)
# Remove? dateStr = procedure['JAX_EXPERIMENT_STARTDATE']
for expSample in procedure['EXPERIMENT_SAMPLES']:
taskInfo = {}
animal = []
animalInfo = {}
# Yuck.
dateStr = ""
if 'JAX_ASSAY_TEST_DATE' in expSample['ASSAY_DATA'].keys():
dateStr = expSample['ASSAY_DATA']['JAX_ASSAY_TEST_DATE']
elif 'JAX_ASSAY_TESTDATE' in expSample['ASSAY_DATA'].keys():
dateStr = expSample['ASSAY_DATA']['JAX_ASSAY_TESTDATE']
elif 'IMPC_CBC_046_001' in expSample['ASSAY_DATA'].keys():
dateStr = expSample['ASSAY_DATA']['IMPC_CBC_046_001']
sampleEntity = expSample['ENTITY']
animalInfo["animalName"] = sampleEntity['SAMPLE']['JAX_SAMPLE_EXTERNALID']
assayData = expSample['ASSAY_DATA']
if 'JAX_ASSAY_STRAINNAME' not in assayData.keys(): # Some CSD seems to be missing these...
my_logger.info("No JAX_ASSAY_STRAINNAME in " + str(assayData))
continue # Skip it
animalInfo['stock'] = assayData['JAX_ASSAY_STRAINNAME']
animal.append(animalInfo)
taskInfo['animal'] = animal
taskInfo['taskInstance'] = getTaskInfo(procedure,expSample['Id'])
taskInfo['taskInstance'][0]['dateComplete'] = dateStr # from the ASSAY
taskInfo['taskInstance'][0]['inputs'] = inputs # from the EXPERIMENT - not the ASSAY
taskInfo['taskInstance'][0]['outputs'] = getOutputs(expSample['ASSAY_DATA'],dateStr) # dateStr unneeded
taskInfo["taskInstance"][0]["taskStatus"] = expSample['ASSAY_DATA']['JAX_ASSAY_ASSAYFAILREASON'] # Is dash OK?
taskInfoLs.append(taskInfo)
return taskInfoLs
def getTaskInfo(procedure,taskInstanceKey):
# Extract experiment data into inputs and assay data into outputs
taskInstanceLs = [] # List of one dict the dict is some procedure data followed by a list of inputs followed by a list of outputs
taskInstanceInfo = {}
taskInstanceInfo['taskInstanceKey'] = taskInstanceKey
taskInstanceInfo['workflowTaskName'] = procedure['EntityTypeName']
# TODO - remove taskInstanceInfo['dateComplete'] = procedure['JAX_EXPERIMENT_STARTDATE']
taskInstanceInfo['reviewedBy'] = 'Ame Willett'
taskInstanceInfo['dateReviewed'] = procedure['JAX_EXPERIMENT_STARTDATE']
# Cancelled at the ASSAY level. Not at experiment
taskInstanceInfo['taskStatus'] = "Complete" # The default. Assume complete until proven otherwise
taskInstanceInfo['barcode'] = procedure['Barcode']
taskInstanceLs.append(taskInstanceInfo)
return taskInstanceLs
def getInputs(procedure):
inputLs = []
# If the name of the input can be found in KOMP.DCCPARAMETERDETAILS then include it.
keyList = list(procedure.keys())
for keystr in keyList:
inputDict = {}
inputKey = db.getKeyFromImpcCode(keystr)
if inputKey > 0:
inputDict['name']= keystr
inputDict['inputValue'] = procedure[keystr]
inputDict['inputKey'] = inputKey
inputLs.append(inputDict)
return inputLs
def removeUnderscoresFromCvValue(key, outputvalue):
# The jerks at Thermo Fisher can't handle commas in their CVs.
if isinstance(outputvalue,str):
if 'EYE' in key:
return outputvalue.replace('_',',')
if 'CSD' in key:
return outputvalue.replace('_',',')
return outputvalue
def getOutputs(expSample,dateStr):
outputLs = []
keyList = list(expSample.keys())
for keystr in keyList:
outputDict = {}
# Check for failed output
if (keystr+'_QC') in expSample:
outputDict['statusCode'] = expSample[(keystr+'_QC')]
if outputDict['statusCode'] == '-':
outputDict['statusCode'] = '' # Status code of '-' means no qc issue
else:
outputDict['statusCode'] = ''
if isSeries(keystr): # We must construct it
outputDict = getSeriesOutput(expSample,keystr,dateStr)
if outputDict != None:
outputLs.append(outputDict)
else:
continue # Skip it??
elif isMediaSeries(keystr):# We must construct it
outputDict = getMediaSeriesOutput(expSample,keystr,dateStr)
if outputDict != None:
outputLs.append(outputDict)
else: # Simple type or ignore
if 'JAX_' in keystr or 'IMPC_' in keystr:
outputKey = db.getKeyFromImpcCode(keystr)
if outputKey > 0:
outputDict['name']= keystr
outputDict['outputValue'] = removeUnderscoresFromCvValue(keystr,expSample[keystr])
outputDict['outputKey'] = outputKey
outputDict['collectedBy'] = expSample["JAX_ASSAY_TESTER"]
if 'JAX_ASSAY_TEST_DATE' in expSample.keys():
outputDict['collectedDate'] = expSample["JAX_ASSAY_TEST_DATE"]
elif 'JAX_ASSAY_TESTDATE' in expSample.keys():
outputDict['collectedDate'] = expSample["JAX_ASSAY_TESTDATE"]
elif 'IMPC_CBC_046_001' in expSample.keys(): # "Date-Time Collection"
outputDict['collectedDate'] = expSample["IMPC_CBC_046_001"]
else:
outputDict['collectedDate'] = ""
outputLs.append(outputDict)
return outputLs
def getSeriesOutput(expSample,keystr,dateStr):
outputDictValue = {}
outputDict = {}
idx=15 # For "JAX_"
# Build up the series. A dictionary. Key is increment value is value