def test_deleteRows(self):
DBUtil.runDBScript(self.SCRIPT_FILE, False)
query = "select count(*) from TestTypes;"
# Insert some test data to delete
tableName = "TestTypes"
columnNames = self.DATA_COLS.split()
idFile = StringIO()
DBUtil.insertFile(self.DATA_FILE, tableName, columnNames, None, idFile)
idValues = idFile.getvalue().split()
# Count up rows before and after delete
initialCount = DBUtil.execute(query)[0][0]
DBUtil.deleteRows("TestTypes", idValues)
afterCount = DBUtil.execute(query)[0][0]
self.assertEqual(initialCount - len(idValues), afterCount)
# Reinsert the test data to try deleting them by a non-default Id column
idFile = StringIO()
DBUtil.insertFile(self.DATA_FILE, tableName, columnNames, None, idFile)
nonDefaultIds = [100, 200]
initialCount = DBUtil.execute(query)[0][0]
DBUtil.deleteRows("TestTypes", nonDefaultIds, "MyInteger")
afterCount = DBUtil.execute(query)[0][0]
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self);
self.manager = SimManager(); # Instance to test on
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader;
ClinicalItemDataLoader.build_clinical_item_psql_schemata();
self.manager.buildCPOESimSchema();
log.info("Populate the database with test data")
#### Basically import a bunch of rigged CSV or TSV files that have realistic simulating case and grading data
# Get that data into the test database
dataTextStr = \
"""sim_result_id;name;description;group_string;priority
-10;Temp;Temperature (F);Flowsheet>Vitals;10
-20;Pulse;Pulse / Heart Rate (HR);Flowsheet>Vitals;20
-30;SBP;Blood Pressure, Systolic (SBP);Flowsheet>Vitals;30
-40;DBP;Blood Pressure, Diastolic (DBP);Flowsheet>Vitals;40
-50;Resp;Respirations (RR);Flowsheet>Vitals;50
-60;FiO2;Fraction Inspired Oxygen;Flowsheet>Vitals;60
-70;Urine;Urine Output (UOP);Flowsheet>Vitals;70
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_result", delim=";");
def test_insertFile_escapeStrings(self):
# Create a test data file to insert, and verify no errors
DBUtil.runDBScript(
self.SCRIPT_FILE,
False) # Assume this works based on test_runDBScript method
tableName = "TestTypes"
columnNames = ["MyInteger", "MyText"]
dataFile = StringIO()
dataFile.write('''-1\t"A"\n''')
dataFile.write('''-2\t"B\xaeb"\n''')
dataFile.write('''-3\t"C"\n''')
dataFile.write('''-4\tD\n''')
dataFile = StringIO(dataFile.getvalue())
DBUtil.insertFile(dataFile, tableName, columnNames, escapeStrings=True)
verifyQuery = \
"""select MyInteger, MyText
from TestTypes
where MyInteger < 0
order by MyInteger desc
"""
expectedData = \
[ [ -1, "A"],
[ -2, u"B\\xaeb"],
[ -3, "C"],
[ -4, "D"],
]
# Verify rows inserted with properly parsed dates
results = DBUtil.execute(verifyQuery)
self.assertEqual(expectedData, results)
def test_insertFile_dateParsing(self):
# Create a test data file to insert, and verify no errors
DBUtil.runDBScript( self.SCRIPT_FILE, False ) # Assume this works based on test_runDBScript method
tableName = "TestTypes"
columnNames = ["MyInteger","MyText","MyDateTime"]
dataFile = StringIO()
dataFile.write('''-1\t"12/11/2010"\t"12/11/2010"\n''');
dataFile.write('''-2\t"2013-04-15 13:45:21"\t"2013-04-15 13:45:21"\n''');
dataFile.write('''-3\t"2003-04-15 10:45:21"\t"2003-04-15 10:45:21"\n''');
dataFile.write('''-4\t"4/11/12 6:20"\t"4/11/12 6:20"\n''');
dataFile = StringIO(dataFile.getvalue())
dateColFormats = {"myDateTime":None} # Deliberately change capitalization to ensure robustness
DBUtil.insertFile( dataFile, tableName, columnNames, dateColFormats=dateColFormats)
verifyQuery = \
"""select MyInteger, MyText, MyDateTime
from TestTypes
where MyInteger < 0
order by MyInteger desc
""";
expectedData = \
[ [ -1, "12/11/2010", datetime(2010,12,11) ],
[ -2, "2013-04-15 13:45:21", datetime(2013,4,15,13,45,21) ],
[ -3, "2003-04-15 10:45:21", datetime(2003,4,15,10,45,21) ],
[ -4, "4/11/12 6:20", datetime(2012,4,11,6,20) ],
];
# Verify rows inserted with properly parsed dates
results = DBUtil.execute(verifyQuery);
self.assertEqual( expectedData, results );
def test_insertFile(self):
# Create a test data file to insert, and verify no errors
DBUtil.runDBScript( self.SCRIPT_FILE, False ) # Assume this works based on test_runDBScript method
tableName = "TestTypes"
idFile = StringIO()
DBUtil.insertFile( self.MULTI_LINE_DATA_FILE, tableName, None, "\t", idFile ); # Assume column names extracted from first row of data file
# Verify number rows inserted
self.assertEqual( len(self.MULTI_LINE_DATA_ROWS), idFile.getvalue().count("\n") )
results = DBUtil.execute( self.DATA_QUERY );
self.assertEqual( self.MULTI_LINE_DATA_ROWS, results );
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
log.info("Populate the database with test data")
StrideLoader.build_stride_psql_schemata()
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
###### PREPARE SOME FAKE INPUT DATA TO BE CONVERTED ##############
###### PREPARE SOME FAKE INPUT DATA TO BE CONVERTED ##############
###### PREPARE SOME FAKE INPUT DATA TO BE CONVERTED ##############
###### PREPARE SOME FAKE INPUT DATA TO BE CONVERTED ##############
###### PREPARE SOME FAKE INPUT DATA TO BE CONVERTED ##############
dataTextStr = \
"""order_proc_anon_id,pat_anon_id,pat_enc_csn_anon_id,proc_code,organism_name,antibiotic_name,suseptibility,shifted_result_time
-10,1,2,LABBLC,BACTEROIDES FRAGILIS,Clindamycin,Intermediate,9/10/2111 13:15
-11,2,3,LABBLC,COAG NEGATIVE STAPHYLOCOCCUS,Vancomycin,Susceptible,4/26/2109 9:49
-12,3,4,LABBLC,COAG NEGATIVE STAPHYLOCOCCUS,Oxacillin,Resistant,4/18/2109 4:48
-13,4,5,LABBLC,COAG NEGATIVE STAPHYLOCOCCUS,Vancomycin,Susceptible,3/28/2109 23:21
-14,5,6,LABBLC,ENTEROCOCCUS FAECALIS,Amoxicillin/Clavulanic Acid,Susceptible,6/3/2109 17:07
-14,5,6,LABBLC,ENTEROCOCCUS FAECALIS,Amoxicillin/Clavulanic Acid,Susceptible,6/3/2109 17:07
-20,10,11,LABBLC,ENTEROCOCCUS FAECALIS,Method,,6/10/2109 17:07
-15,6,7,LABBLC2,,,,6/4/2109 17:07
-16,7,8,LABBLC2,,,,
-17,10,10,LABBLC2,ENTEROCOCCUS FAECALIS,Penicillin,,6/8/2109 17:07
-17,10,10,LABBLC2,ENTEROCOCCUS FAECALIS,,Intermediate,6/11/2109 17:07
-18,11,11,LABBLC2,ENTEROCOCCUS FAECALIS,Amikacin,Positive,6/11/2111 18:07
"""
# Parse into DB insertion object
# DBUtil.insertFile( StringIO(dataTextStr), "stride_culture_micro", delim=" ", dateColFormats={"trtmnt_tm_begin_date": None, "trtmnt_tm_end_date": None} );
DBUtil.insertFile(StringIO(dataTextStr),
"stride_culture_micro",
delim=",",
dateColFormats={"shifted_result_time": None})
self.converter = STRIDECultureMicroConversion()
def _insertTestRecords(self):
"""Populate database for with patient data."""
# clinical_item_category
testRecords = ED_TEST_INPUT_TABLES.get("clinical_item_category")
DBUtil.insertFile(StringIO(testRecords), "clinical_item_category", \
delim="\t")
# clinical_item
testRecords = ED_TEST_INPUT_TABLES.get("clinical_item")
DBUtil.insertFile(StringIO(testRecords), "clinical_item", delim="\t")
# patient_item
testRecords = ED_TEST_INPUT_TABLES.get("patient_item")
DBUtil.insertFile(StringIO(testRecords), "patient_item", delim="\t")
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
self.manager = SimManager() # Instance to test on
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
self.manager.buildCPOESimSchema()
log.info("Populate the database with test data")
# Basically import a bunch of rigged CSV or TSV files that have realistic simulating case and grading data
# Get that data into the test database
clinical_item_category_str = \
"""clinical_item_category_id;source_table
1;source_table
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_category_str),
"clinical_item_category",
delim=";")
clinical_item_str = \
"""clinical_item_id;clinical_item_category_id;name
1;1;Clinical item 1
2;1;Clinical item 2
3;1;Clinical item 3
4;1;Clinical item 4
5;1;Clinical item 5
6;1;Clinical item 6
7;1;Clinical item 7
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_str),
"clinical_item",
delim=";")
clinical_item_str = \
"""sim_user_id;name
0;Default user
1;Jonathan Chen
2;User 2
3;User 3
4;User 4
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_str), "sim_user", delim=";")
sim_patient_str = \
"""sim_patient_id;name;age_years;gender
1;Patient One;40;Male
2;Patient Two;50;Female
3;Patient Three;60;Male
4;Patient Four;70;Female
5;Patient Five;80;Male
6;Patient Six;90;Female
7;Patient Seven;100;Male
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_patient_str), "sim_patient", delim=";")
sim_state_str = \
"""sim_state_id;name
1;Sim state 1
2;Sim state 2
3;Sim state 3
4;Sim state 4
5;Sim state 5
6;Sim state 6
7;Sim state 7
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_state_str), "sim_state", delim=";")
sim_patient_order_str = \
"""sim_patient_order_id;sim_user_id;sim_patient_id;clinical_item_id;relative_time_start;sim_state_id
1;0;1;1;1;1
2;1;1;2;2;2
3;1;1;3;3;3
4;1;1;4;4;4
5;1;1;5;5;5
6;1;1;6;6;6
7;1;1;7;7;7
8;2;2;1;1;1
9;3;2;2;2;1
10;3;2;3;3;2
11;2;3;1;1;1
12;3;3;2;2;2
13;3;3;3;3;3
14;1;4;1;1;2
15;1;4;2;2;3
16;2;5;1;1;3
17;2;5;2;2;4
18;3;6;4;1;1
19;3;6;4;2;2
20;3;6;4;3;3
21;4;7;5;1;1
22;4;7;5;2;2
23;4;7;5;3;3
24;4;7;5;4;4
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_patient_order_str),
"sim_patient_order",
delim=";")
sim_grading_key_str = \
"""sim_grader_id;sim_state_id;clinical_item_id;score;group_name
Jonathan Chen;1;1;1;g1
Jonathan Chen;2;2;1;g2
Jonathan Chen;3;3;1;g3
Jonathan Chen;4;4;1;
Jonathan Chen;5;5;1;g5
Jonathan Chen;6;6;1;
Jonathan Chen;7;7;1;g7
Jonathan Chen;3;1;1;g8
Jonathan Chen;4;2;1;g8
Jonathan Chen;1;4;-1000;
Jonathan Chen;2;4;10;
Jonathan Chen;3;4;2000;
Jonathan Chen;1;5;-1000;g9
Jonathan Chen;2;5;-1;
Jonathan Chen;3;5;0;g10
Jonathan Chen;3;5;-500;
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_grading_key_str),
"sim_grading_key",
delim=";")
self.expected_grades_by_patient_id = [
{
"total_score":
6, # Default user (id = 0) is ignored and NULL group_names are counted separately
"sim_patient_id": 1,
"most_graded_user_id": 1,
"most_active_user_id": 1,
"sim_grader_id": "Jonathan Chen"
},
{
"total_score":
1, # Ungraded (clinical_item_id, sim_state_id) keys are omitted from summation
"sim_patient_id": 2,
"most_graded_user_id":
2, # Most graded user is User 2 (even though most active is User 3)
"most_active_user_id": 3,
"sim_grader_id": "Jonathan Chen"
},
{
"total_score": 3,
"sim_patient_id": 3,
"most_graded_user_id":
3, # Most graded user is the most active one
"most_active_user_id": 3,
"sim_grader_id": "Jonathan Chen"
},
# 4: No grading available for the existing case
{
"total_score":
1, # Scores in the same group g8 are counted only once
"sim_patient_id": 5,
"most_graded_user_id": 2,
"most_active_user_id": 2,
"sim_grader_id": "Jonathan Chen"
},
{
"total_score":
1010, # Non-uniform scores (i.e., not all scores = 1)
"sim_patient_id": 6,
"most_graded_user_id": 3,
"most_active_user_id": 3,
"sim_grader_id": "Jonathan Chen"
},
{
"total_score":
-1501, # All negative and one 0 score results in negative score
"sim_patient_id": 7,
"most_graded_user_id": 4,
"most_active_user_id": 4,
"sim_grader_id": "Jonathan Chen"
}
# 8: Case doesn't exist
]
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self);
self.manager = SimManager(); # Instance to test on
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader;
ClinicalItemDataLoader.build_clinical_item_psql_schemata();
self.manager.buildCPOESimSchema();
self.testPatientId = None;
self.purgeTestRecords();
log.info("Populate the database with test data")
self.clinicalItemCategoryIdStrList = list();
headers = ["clinical_item_category_id","source_table"];
dataModels = \
[
RowItemModel( [-1, "Labs"], headers ),
RowItemModel( [-2, "Imaging"], headers ),
RowItemModel( [-3, "Meds"], headers ),
RowItemModel( [-4, "Nursing"], headers ),
RowItemModel( [-5, "Problems"], headers ),
RowItemModel( [-6, "Lab Results"], headers ),
];
for dataModel in dataModels:
(dataItemId, isNew) = DBUtil.findOrInsertItem("clinical_item_category", dataModel );
self.clinicalItemCategoryIdStrList.append( str(dataItemId) );
headers = ["clinical_item_id","clinical_item_category_id","name","analysis_status"];
dataModels = \
[
RowItemModel( [-1, -1, "CBC",1], headers ),
RowItemModel( [-2, -1, "BMP",1], headers ),
RowItemModel( [-3, -1, "Hepatic Panel",1], headers ),
RowItemModel( [-4, -1, "Cardiac Enzymes",1], headers ),
RowItemModel( [-5, -2, "CXR",1], headers ),
RowItemModel( [-6, -2, "RUQ Ultrasound",1], headers ),
RowItemModel( [-7, -2, "CT Abdomen/Pelvis",1], headers ),
RowItemModel( [-8, -2, "CT PE Thorax",1], headers ),
RowItemModel( [-9, -3, "Acetaminophen",1], headers ),
RowItemModel( [-10, -3, "Carvedilol",1], headers ),
RowItemModel( [-11, -3, "Enoxaparin",1], headers ),
RowItemModel( [-12, -3, "Warfarin",1], headers ),
RowItemModel( [-13, -3, "Ceftriaxone",1], headers ),
RowItemModel( [-14, -4, "Foley Catheter",1], headers ),
RowItemModel( [-15, -4, "Vital Signs",1], headers ),
RowItemModel( [-16, -4, "Fall Precautions",1], headers ),
];
for dataModel in dataModels:
(dataItemId, isNew) = DBUtil.findOrInsertItem("clinical_item", dataModel );
dataTextStr = \
"""sim_user_id;name
-1;Test User
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_user", delim=";");
dataTextStr = \
"""sim_patient_id;age_years;gender;name
-1;60;Female;Test Female Patient
-2;55;Male;Test Male Patient
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_patient", delim=";");
dataTextStr = \
"""sim_result_id;name;description;group_string;priority
-10;Temp;Temperature (F);Flowsheet>Vitals;10
-20;Pulse;Pulse / Heart Rate (HR);Flowsheet>Vitals;20
-30;SBP;Blood Pressure, Systolic (SBP);Flowsheet>Vitals;30
-40;DBP;Blood Pressure, Diastolic (DBP);Flowsheet>Vitals;40
-50;Resp;Respirations (RR);Flowsheet>Vitals;50
-60;FiO2;Fraction Inspired Oxygen;Flowsheet>Vitals;60
-70;Urine;Urine Output (UOP);Flowsheet>Vitals;70
-11000;WBC;WBC;LAB BLOOD ORDERABLES>Hematology>Automated Blood Count;11000
-11010;HGB;HEMOGLOBIN;LAB BLOOD ORDERABLES>Hematology>Automated Blood Count;11010
-11020;HCT;HEMATOCRIT;LAB BLOOD ORDERABLES>Hematology>Automated Blood Count;11020
-11030;PLT;PLATELET COUNT;LAB BLOOD ORDERABLES>Hematology>Automated Blood Count;11030
-13010;NA;SODIUM, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13010
-13020;K;POTASSIUM, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13020
-13030;CL;CHLORIDE, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13030
-13040;CO2;CO2, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13040
-13050;BUN;UREA NITROGEN,SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13050
-13060;CR;CREATININE, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13060
-13070;GLU;GLUCOSE, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13070
-13090;CA;CALCIUM, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13090
-13110;MG;MAGNESIUM, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13110
-13120;PHOS;PHOSPHORUS, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13120
-13210;TBIL;TOTAL BILIRUBIN;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13210
-13220;DBIL;CONJUGATED BILI;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13220
-13230;IBIL;UNCONJUGATED BILIRUBIN;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13230
-13240;AST;AST (SGOT), SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13240
-13250;ALT;ALT (SGPT), SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13250
-13260;ALKP;ALK P'TASE, TOTAL, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13260
-13270;ALB;ALBUMIN, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13270
-13280;TP;PROTEIN, TOTAL, SER/PLAS;LAB BLOOD ORDERABLES>Chemistry>General Chemistry;13280
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_result", delim=";");
# Map orders to expected results.
# Simplify expect vital signs to result in 5 minutes. Basic chemistry labs in 10 minutes, CBC in 15 minutes
dataTextStr = \
"""sim_order_result_map_id;clinical_item_id;sim_result_id;turnaround_time
-1;-15;-10;300
-2;-15;-20;300
-3;-15;-30;300
-4;-15;-40;300
-5;-15;-50;300
-6;-1;-11000;900
-7;-1;-11010;900
-8;-1;-11020;900
-9;-1;-11030;900
-10;-2;-13010;600
-11;-2;-13020;600
-12;-2;-13030;600
-13;-2;-13040;600
-14;-2;-13050;600
-15;-2;-13060;600
-16;-2;-13070;600
-17;-2;-13090;600
-18;-3;-13210;600
-19;-3;-13240;600
-20;-3;-13250;600
-21;-3;-13260;600
-22;-3;-13270;600
-23;-3;-13280;600
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_order_result_map", delim=";");
dataTextStr = \
"""sim_state_id;name;description
0;Test 0; Test State 0
-1;Test 1;Test State 1
-2;Test 2;Test State 2
-3;Test 3;Test State 3
-4;Test 4;Test State 4
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_state", delim=";");
dataTextStr = \
"""sim_state_transition_id;pre_state_id;post_state_id;clinical_item_id;time_trigger;description
-1;-1;-2;None;9000;Passive time from 1 to 2
-2;-2;-3;-11;None;Transition 2 to 3 if order for 11 (Enoxaparin)
-3;-2;-3;-12;None;Transition 2 to 3 if order for 12 (Warfarin) (don't need both anti-coagulants. One adequate to trigger transition)
-4;-2;-4;-13;None;Transition 2 to 4 if order for 13 (Ceftriaxone)
-5;-3;-1;-10;9000;Transition 3 back to 1 if order for 10 (Carvedilol) OR 9000 seconds pass
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_state_transition", delim=";");
dataTextStr = \
"""sim_patient_state_id;sim_patient_id;sim_state_id;relative_time_start;relative_time_end
-1;-1;-1;-7200;0
-3;-1;-1;0;1800
-2;-1;-2;1800;None
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_patient_state", delim=";");
# Order Vital Signs at time 0, then basic labs (CBC, BMP, LFTs) at 10 minutes (600 seconds)
dataTextStr = \
"""sim_patient_order_id;sim_user_id;sim_patient_id;sim_state_id;clinical_item_id;relative_time_start;relative_time_end
-1;-1;-1;-1;-15;0;None
-2;-1;-1;-1;-1;600;None
-3;-1;-1;-1;-2;600;None
-4;-1;-1;-1;-3;600;None
-5;-1;-1;-2;-15;1800;None
-6;-1;-1;-2;-1;1800;None
-7;-1;-1;-2;-2;1800;None
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_patient_order", delim=";");
dataTextStr = \
"""sim_state_result_id;sim_result_id;sim_state_id;num_value;num_value_noise;text_value;result_flag
-1;-10;0;98.7;0.2;;
-2;-20;0;75;3;;
-3;-30;0;130;4;;
-4;-40;0;85;2;;
-5;-50;0;12;1;;
-6;-60;0;0.21;0;;
-7;-70;0;500;100;;
-8;-11000;0;7;1;;
-9;-11010;0;13;0.5;;
-10;-11020;0;40;1;;
-11;-11030;0;300;25;;
-12;-13010;0;140;4;;
-13;-13020;0;4.5;0.4;;
-14;-13030;0;95;3;;
-15;-13040;0;24;1;;
-16;-13050;0;12;3;;
-17;-13060;0;0.7;0.2;;
-18;-13070;0;140;12;;
-19;-13090;0;9;0.4;;
-20;-13110;0;2;0.3;;
-21;-13120;0;3;0.5;;
-22;-13210;0;0.2;0.1;;
-23;-13240;0;29;5;;
-24;-13250;0;20;4;;
-25;-13260;0;85;8;;
-26;-13270;0;4;0.4;;
-27;-13280;0;6;0.5;;
-28;-10;-1;101.4;0.4;Fever;H
-29;-20;-1;115;4;Tachycardia;H
-30;-30;-1;92;5;Hypotension;L
-31;-40;-1;55;3;Hypotension;L
-32;-70;-1;50;10;Low UOP;L
-33;-11000;-1;12;1;Leukocytosis;H
-34;-13060;-1;2.4;0.3;AKI;H
-35;-20;-2;105;4;Tachycardia;H
-36;-11000;-2;10;1;;
-37;-13060;-2;1.9;0.3;AKI;H
-38;-13070;-2;250;13;;H
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_state_result", delim=";");
dataTextStr = \
"""sim_note_id;sim_state_id;relative_state_time;content
-1;-1;7200;Initial Note
-2;-2;0;Later Note
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "sim_note", delim=";");
DBUtil.execute \
( """
-- Delete reference or diagnosis linking items
delete
from item_collection_item as ici
where collection_type_id in (1,2,3,5);
-- Delete the resultant orphaned parent collection records
delete
from item_collection
where item_collection_id not in
(
select item_collection_id
from item_collection_item
);
""",
conn=conn
)
# Populate the database with updates to the item_collection and item_collection_item tables to add more reference collections
DBUtil.insertFile(open("item_collection.update.tab"), "item_collection")
DBUtil.insertFile(open("item_collection_item.diagnosisLink.update.tab"),
"item_collection_item")
DBUtil.insertFile(open("item_collection_item.referenceOrders.update.tab"),
"item_collection_item")
conn.commit()
finally:
conn.close()
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
log.info("Populate the database with test data")
StrideLoader.build_stride_psql_schemata()
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
dataTextStr = \
"""pat_id\tdeath_date\tbirth_year\tgender\trace\tethnicity
-100\tNone\t1958\tMALE\tAMERICAN INDIAN OR ALASKA NATIVE\tNON-HISPANIC/NON-LATINO
-200\tNone\t1992\tMALE\tAMERICAN INDIAN OR ALASKA NATIVE\tHISPANIC/LATINO
-300\tNone\t1993\tFEMALE\tASIAN\tNON-HISPANIC/NON-LATINO
-400\t2011-09-28\t1997\tFEMALE\tASIAN\tHISPANIC/LATINO
-500\tNone\t1952\tMALE\tASIAN\tPATIENT REFUSED
-600\tNone\t1984\tMALE\tASIAN\tUNKNOWN
-700\tNone\t1991\tFEMALE\tASIAN - HISTORICAL CONV\tNON-HISPANIC/NON-LATINO
-800\tNone\t1962\tMALE\tASIAN, HISPANIC\tUNKNOWN
-900\tNone\t1972\tMALE\tASIAN, HISPANIC\tHISPANIC/LATINO
-1000\tNone\t1970\tMALE\tASIAN, NON-HISPANIC\tNON-HISPANIC/NON-LATINO
-1100\tNone\t2001\tFEMALE\tASIAN, NON-HISPANIC\tUNKNOWN
-1200\tNone\t1969\tFEMALE\tBLACK OR AFRICAN AMERICAN\tNON-HISPANIC/NON-LATINO
-1300\tNone\t1945\tFEMALE\tBLACK OR AFRICAN AMERICAN\tHISPANIC/LATINO
-1400\tNone\t1945\tFEMALE\tBLACK OR AFRICAN AMERICAN\tUNKNOWN
-1500\t2012-05-02\t1956\tMALE\tBLACK OR AFRICAN AMERICAN\tPATIENT REFUSED
-1600\tNone\t1981\tFEMALE\tBLACK, HISPANIC\tHISPANIC/LATINO
-1700\tNone\t1985\tFEMALE\tBLACK, HISPANIC\tUNKNOWN
-1800\tNone\t1932\tMALE\tBLACK, NON-HISPANIC\tNON-HISPANIC/NON-LATINO
-1900\tNone\t1954\tMALE\tBLACK, NON-HISPANIC\tUNKNOWN
-2000\tNone\t1932\tMALE\tNATIVE AMERICAN, HISPANIC\tHISPANIC/LATINO
-2100\tNone\t1961\tFEMALE\tNATIVE AMERICAN, NON-HISPANIC\tUNKNOWN
-2200\tNone\t1974\tMALE\tNATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER \tNON-HISPANIC/NON-LATINO
-2300\tNone\t1953\tFEMALE\tNATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER \tHISPANIC/LATINO
-2400\tNone\t1943\tFEMALE\tNATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER \tUNKNOWN
-2500\tNone\t1963\tFEMALE\tOTHER\tHISPANIC/LATINO
-2600\tNone\t1974\tMALE\tOTHER\tNON-HISPANIC/NON-LATINO
-2700\tNone\t1963\tFEMALE\tOTHER\tPATIENT REFUSED
-2800\tNone\t2005\tFEMALE\tOTHER\tUNKNOWN
-2900\tNone\t1996\tMALE\tOTHER, HISPANIC\tUNKNOWN
-3000\tNone\t1952\tMALE\tOTHER, HISPANIC\tHISPANIC/LATINO
-3100\tNone\t1983\tFEMALE\tOTHER, HISPANIC\tNON-HISPANIC/NON-LATINO
-3200\tNone\t1971\tFEMALE\tOTHER, NON-HISPANIC\tNON-HISPANIC/NON-LATINO
-3300\tNone\t1976\tMALE\tOTHER, NON-HISPANIC\tUNKNOWN
-3400\tNone\t1995\tFEMALE\tOTHER, NON-HISPANIC\tHISPANIC/LATINO
-3500\tNone\t1982\tMALE\tPACIFIC ISLANDER, NON-HISPANIC\tNON-HISPANIC/NON-LATINO
-3600\tNone\t1940\tMALE\tPACIFIC ISLANDER, NON-HISPANIC\tUNKNOWN
-3700\tNone\t1934\tMALE\tPATIENT REFUSED\tPATIENT REFUSED
-3800\tNone\t1981\tFEMALE\tPATIENT REFUSED\tNON-HISPANIC/NON-LATINO
-3900\tNone\t1998\tMALE\tPATIENT REFUSED\tHISPANIC/LATINO
-4000\tNone\t1978\tMALE\tRACE AND ETHNICITY UNKNOWN\tUNKNOWN
-4100\tNone\t1933\tFEMALE\tRACE AND ETHNICITY UNKNOWN\tNON-HISPANIC/NON-LATINO
-4200\tNone\t1997\tFEMALE\tUNKNOWN\tUNKNOWN
-4300\tNone\t1932\tMALE\tUNKNOWN\tNON-HISPANIC/NON-LATINO
-4400\t2012-11-13\t1947\tFEMALE\tUNKNOWN\tHISPANIC/LATINO
-4500\tNone\t1932\tMALE\tUNKNOWN\tPATIENT REFUSED
-4600\tNone\t1936\tMALE\tUNKNOWN\t
-4700\tNone\t1993\tFEMALE\tWHITE\tNON-HISPANIC/NON-LATINO
-4800\tNone\t1948\tMALE\tWHITE\tHISPANIC/LATINO
-4900\tNone\t1968\tMALE\tWHITE\tUNKNOWN
-5000\tNone\t2003\tFEMALE\tWHITE\tPATIENT REFUSED
-5100\tNone\t1970\tMALE\tWHITE\t
-5200\tNone\t1998\tMALE\tWHITE, HISPANIC\tHISPANIC/LATINO
-5300\tNone\t1986\tMALE\tWHITE, HISPANIC\tUNKNOWN
-5400\tNone\t1997\tFEMALE\tWHITE, HISPANIC\tNON-HISPANIC/NON-LATINO
-5500\tNone\t1964\tMALE\tWHITE, NON-HISPANIC\tNON-HISPANIC/NON-LATINO
-5600\tNone\t1940\tMALE\tWHITE, NON-HISPANIC\tUNKNOWN
-5700\tNone\t1962\tMALE\tWHITE, NON-HISPANIC\tHISPANIC/LATINO
-5800\tNone\t1931\tFEMALE\tNone\tNone
-5900\tNone\t1991\tFEMALE\tNone\tNON-HISPANIC/NON-LATINO
-6000\tNone\t1973\tFEMALE\tNone\tUNKNOWN
-6050\tNone\tNone\tNone\tNone\tNone
-6100\tNone\t1953\tFEMALE\tNone\tHISPANIC/LATINO
"""
self.patientIds = [
"-100", "-200", "-300", "-400", "-500", "-600", "-700", "-800",
"-900", "-1000", "-1100", "-1200", "-1300", "-1400", "-1500",
"-1600", "-1700", "-1800", "-1900", "-2000", "-2100", "-2200",
"-2300", "-2400", "-2500", "-2600", "-2700", "-2800", "-2900",
"-3000", "-3100", "-3200", "-3300", "-3400", "-3500", "-3600",
"-3700", "-3800", "-3900", "-4000", "-4100", "-4200", "-4300",
"-4400", "-4500", "-4600", "-4700", "-4800", "-4900", "-5000",
"-5100", "-5200", "-5300", "-5400", "-5500", "-5600", "-5700",
"-5800", "-5900", "-6000", "-6050", "-6100"
]
# Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr),
"stride_patient",
delim="\t",
dateColFormats={"death_date": None})
self.converter = STRIDEDemographicsConversion()
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
self.manager = SimManager() # Instance to test on
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
self.manager.buildCPOESimSchema()
log.info("Populate the database with test data")
# Basically import a bunch of rigged CSV or TSV files that have realistic simulating case and grading data
# Get that data into the test database
clinical_item_category_str = \
"""clinical_item_category_id;source_table
1;source_table
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_category_str), "clinical_item_category", delim=";")
clinical_item_str = \
"""clinical_item_id;clinical_item_category_id;name
1;1;Clinical item 1
2;1;Clinical item 2
3;1;Clinical item 3
4;1;Clinical item 4
5;1;Clinical item 5
6;1;Clinical item 6
7;1;Clinical item 7
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_str), "clinical_item", delim=";")
clinical_item_str = \
"""sim_user_id;name
0;Default user
1;Jonathan Chen
2;User 2
3;User 3
4;User 4
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_str), "sim_user", delim=";")
sim_patient_str = \
"""sim_patient_id;name;age_years;gender
1;Patient One;40;Male
2;Patient Two;50;Female
3;Patient Three;60;Male
4;Patient Four;70;Female
5;Patient Five;80;Male
6;Patient Six;90;Female
7;Patient Seven;100;Male
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_patient_str), "sim_patient", delim=";")
sim_state_str = \
"""sim_state_id;name
1;Sim state 1
2;Sim state 2
3;Sim state 3
4;Sim state 4
5;Sim state 5
6;Sim state 6
7;Sim state 7
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_state_str), "sim_state", delim=";")
sim_patient_order_str = \
"""sim_patient_order_id;sim_user_id;sim_patient_id;clinical_item_id;relative_time_start;sim_state_id
1;0;1;1;1;1
2;1;1;2;2;2
3;1;1;3;3;3
4;1;1;4;4;4
5;1;1;5;5;5
6;1;1;6;6;6
7;1;1;7;7;7
8;2;2;1;1;1
9;3;2;2;2;1
10;3;2;3;3;2
11;2;3;1;1;1
12;3;3;2;2;2
13;3;3;3;3;3
14;1;4;1;1;2
15;1;4;2;2;3
16;2;5;1;1;3
17;2;5;2;2;4
18;3;6;4;1;1
19;3;6;4;2;2
20;3;6;4;3;3
21;4;7;5;1;1
22;4;7;5;2;2
23;4;7;5;3;3
24;4;7;5;4;4
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_patient_order_str), "sim_patient_order", delim=";")
sim_grading_key_str = \
"""sim_grader_id;sim_state_id;clinical_item_id;score;group_name
Jonathan Chen;1;1;1;g1
Jonathan Chen;2;2;1;g2
Jonathan Chen;3;3;1;g3
Jonathan Chen;4;4;1;
Jonathan Chen;5;5;1;g5
Jonathan Chen;6;6;1;
Jonathan Chen;7;7;1;g7
Jonathan Chen;3;1;1;g8
Jonathan Chen;4;2;1;g8
Jonathan Chen;1;4;-1000;
Jonathan Chen;2;4;10;
Jonathan Chen;3;4;2000;
Jonathan Chen;1;5;-1000;g9
Jonathan Chen;2;5;-1;
Jonathan Chen;3;5;0;g10
Jonathan Chen;3;5;-500;
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_grading_key_str), "sim_grading_key", delim=";")
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
log.info("Populate the database with test data")
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
#self.purgeTestRecords();
self.clinicalItemCategoryIdStrList = list()
headers = [
"clinical_item_category_id", "default_recommend", "source_table"
]
dataModels = \
[
RowItemModel( [-1, 1, "Labs"], headers ),
RowItemModel( [-2, 1, "Imaging"], headers ),
RowItemModel( [-3, 1, "Meds"], headers ),
RowItemModel( [-4, 1, "Nursing"], headers ),
RowItemModel( [-5, 0, "Problems"], headers ),
RowItemModel( [-6, 1, "Lab Results"], headers ),
RowItemModel( [-7, 1, "Admit Dx"], headers ),
RowItemModel( [-8, 0, "Demographics"], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("clinical_item_category",
dataModel)
self.clinicalItemCategoryIdStrList.append(str(dataItemId))
headers = [
"clinical_item_id", "clinical_item_category_id", "analysis_status",
"default_recommend", "name"
]
dataModels = \
[
RowItemModel( [-1, -1, 1, 1, "CBC"], headers ),
RowItemModel( [-2, -1, 1, 1, "BMP"], headers ),
RowItemModel( [-3, -1, 1, 1, "Hepatic Panel"], headers ),
RowItemModel( [-4, -1, 1, 1, "Cardiac Enzymes"], headers ),
RowItemModel( [-5, -2, 1, 1, "CXR"], headers ),
RowItemModel( [-6, -2, 1, 1, "RUQ Ultrasound"], headers ),
RowItemModel( [-7, -2, 1, 1, "CT Abdomen/Pelvis"], headers ),
RowItemModel( [-8, -2, 1, 1, "CT PE Thorax"], headers ),
RowItemModel( [-9, -3, 1, 1, "Acetaminophen"], headers ),
RowItemModel( [-10, -3, 1, 1, "Carvedilol"], headers ),
RowItemModel( [-11, -3, 1, 1, "Enoxaparin"], headers ),
RowItemModel( [-12, -3, 1, 1, "Warfarin"], headers ),
RowItemModel( [-13, -3, 1, 0, "Ceftriaxone"], headers ),
RowItemModel( [-14, -4, 1, 1, "Foley Catheter"], headers ),
RowItemModel( [-15, -4, 1, 1, "Strict I&O"], headers ),
RowItemModel( [-16, -4, 1, 1, "Fall Precautions"], headers ),
RowItemModel( [-22, -5, 1, 1, "Diagnosis 2"], headers ),
RowItemModel( [-23, -5, 1, 1, "Diagnosis 3"], headers ),
RowItemModel( [-24, -5, 1, 1, "Diagnosis 4"], headers ),
RowItemModel( [-21, -7, 0, 1, "Diagnosis 1 (Admit)"], headers ),
RowItemModel( [-25, -7, 1, 1, "Diagnosis 2 (Admit)"], headers ),
RowItemModel( [-30, -6, 1, 1, "Troponin (High)"], headers ),
RowItemModel( [-31, -6, 1, 1, "BNP (High)"], headers ),
RowItemModel( [-32, -6, 1, 1, "Creatinine (High)"], headers ),
RowItemModel( [-33, -6, 1, 1, "ESR (High)"], headers ), # Default exclude from recommendations
RowItemModel( [-41, -8, 1, 1, "Male"], headers ),
RowItemModel( [-42, -8, 1, 1, "Female"], headers ),
RowItemModel( [-43, -8, 1, 1, "Birth"], headers ),
RowItemModel( [-44, -8, 1, 1, "Birth1980s"], headers ),
RowItemModel( [-45, -8, 1, 1, "Birth1970s"], headers ),
RowItemModel( [-46, -8, 1, 1, "RaceWhite"], headers ),
RowItemModel( [-47, -8, 1, 1, "RaceBlack"], headers ),
RowItemModel( [-49, -8, 1, 1, "Death"], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("clinical_item", dataModel)
headers = [
"patient_item_id", "patient_id", "clinical_item_id", "item_date",
"analyze_date"
]
dataModels = \
[
RowItemModel( [-101,-11111, -43, datetime(1972, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-102,-11111, -45, datetime(1972, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-103,-11111, -41, datetime(1972, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-104,-11111, -46, datetime(1972, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-52, -11111, -23, datetime(1999, 9, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-51, -11111, -21, datetime(2000, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-1, -11111, -4, datetime(2000, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-2, -11111, -10, datetime(2000, 1, 1, 1), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-3, -11111, -8, datetime(2000, 1, 1, 2), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-4, -11111, -4, datetime(2000, 1, 1, 3), datetime(2010, 1, 1, 0)], headers ), # Repeat item
RowItemModel( [-60, -11111, -32, datetime(2000, 1, 1, 4), datetime(2010, 1, 1, 0)], headers ), # Within query time
RowItemModel( [-61, -11111, -30, datetime(2000, 1, 4, 0), datetime(2010, 1, 1, 0)], headers ), # Within 1 week
RowItemModel( [-63, -11111, -13, datetime(2000, 1, 4, 5), datetime(2010, 1, 1, 0)], headers ), # Exclude item
RowItemModel( [-64, -11111, -24, datetime(2000, 1, 4,10), datetime(2010, 1, 1, 0)], headers ), # Exclude category
RowItemModel( [-62, -11111, -31, datetime(2000, 1,10, 0), datetime(2010, 1, 1, 0)], headers ), # Beyond 1 week
RowItemModel( [-71, -11111, -8, datetime(2000, 1, 4, 1), datetime(2010, 1, 1, 0)], headers ), # Repeat query item within 1 week verify period, don't use as a verify item
RowItemModel( [-201, -11111,-49, datetime(2009, 1, 1, 1), datetime(2010, 1, 1, 0)], headers ), # Death date in far future
RowItemModel( [-5, -11111, -12, datetime(2000, 2, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-121,-22222, -43, datetime(1983, 5, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-122,-22222, -44, datetime(1983, 5, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-123,-22222, -42, datetime(1983, 5, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-124,-22222, -47, datetime(1983, 5, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-10, -22222, -7, datetime(2000, 1, 5, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-12, -22222, -6, datetime(2000, 1, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-13, -22222, -11, datetime(2000, 1, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-131,-33333, -43, datetime(1983, 5, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-132,-33333, -44, datetime(1983, 5, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-133,-33333, -42, datetime(1983, 5, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-134,-33333, -46, datetime(1983, 5, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-14, -33333, -6, datetime(2000, 2, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-15, -33333, -2, datetime(2000, 2,11, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-141,-44444, -43, datetime(1975, 3, 3, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-142,-44444, -45, datetime(1975, 3, 3, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-143,-44444, -42, datetime(1975, 3, 3, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-144,-44444, -46, datetime(1975, 3, 3, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-20, -44444, -21, datetime(2000, 1, 5, 0), datetime(2010, 1, 1, 0)], headers ), # Admit diagnosis
RowItemModel( [-22, -44444, -6, datetime(2000, 1, 5, 0), datetime(2010, 1, 1, 0)], headers ), # Items recorded with date level precision, not time
RowItemModel( [-23, -44444, -12, datetime(2000, 1, 5, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-24, -44444, -11, datetime(2000, 1, 6, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-25, -44444, -8, datetime(2000, 1, 6, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-204,-44444,-49, datetime(2000, 2, 1, 1), datetime(2010, 1, 1, 0)], headers ), # Death date within 1 month
# Order Set Usage example
RowItemModel( [-5002,-55555, -3, datetime(2000,10, 1, 0, 0), datetime(2010, 1, 1, 0)], headers ), # Very old item, not relevant to current query
RowItemModel( [-5040,-55555, -25, datetime(2000,10,10, 0, 0), datetime(2010, 1, 1, 0)], headers ), # Admit diagnosis (coded at date level precision before time-level order data)
RowItemModel( [-5005,-55555, -2, datetime(2000,10,10,10, 0), datetime(2010, 1, 1, 0)], headers ), # Non-order set item before
RowItemModel( [-5010,-55555, -1, datetime(2000,10,10,10, 5), datetime(2010, 1, 1, 0)], headers ), # Order Set 1
RowItemModel( [-5020,-55555, -9, datetime(2000,10,10,10, 5), datetime(2010, 1, 1, 0)], headers ), # Order Set 1
RowItemModel( [-5030,-55555, -5, datetime(2000,10,10,10,10), datetime(2010, 1, 1, 0)], headers ), # Ad-hoc within 1 hour
RowItemModel( [-5050,-55555, -8, datetime(2000,10,10,10,30), datetime(2010, 1, 1, 0)], headers ), # Order Set 2
RowItemModel( [-5060,-55555, -11, datetime(2000,10,10,10,30), datetime(2010, 1, 1, 0)], headers ), # Order Set 2
RowItemModel( [-5070,-55555, -12, datetime(2000,10,10,10,30), datetime(2010, 1, 1, 0)], headers ), # Ad-hoc Within 1 hour
RowItemModel( [-5080,-55555, -10, datetime(2000,10,10,20, 0), datetime(2010, 1, 1, 0)], headers ), # Ad-hoc 10 hours later
RowItemModel( [-5090,-55555, -1, datetime(2000,10,10,20, 0), datetime(2010, 1, 1, 0)], headers ), # Order Set 1 again (ignore repeats)
RowItemModel( [-5100,-55555, -2, datetime(2000,10,10,20, 0), datetime(2010, 1, 1, 0)], headers ), # Order Set 1 again
RowItemModel( [-5110,-55555, -3, datetime(2000,10,10,20, 0), datetime(2010, 1, 1, 0)], headers ), # Ad-hoc 10 hours later
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("patient_item", dataModel)
dataTextStr = \
"""item_collection_id;external_id;name;section;subgroup
-1;-1;Test Order Set - 1;Meds;TreatmentMeds
-2;-1;Test Order Set - 1;Meds;SymptomsMeds
-3;-1;Test Order Set - 1;Labs;GeneralLabs
-4;-2;Test Order Set - 2;Labs;GeneralLabs
-5;-2;Test Order Set - 2;Imaging;Xrays
-6;-2;Test Order Set - 2;Imaging;AdvancedImaging
-7;-3;Test Order Set - 3;Imaging;GeneralImaging
-8;-3;Test Order Set - 3;Nursing;GeneralNursing
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr), "item_collection", delim=";")
dataTextStr = \
"""item_collection_item_id;item_collection_id;clinical_item_id;collection_type_id
-1;-1;-11;4
-2;-1;-12;4
-3;-1;-13;4
-4;-2;-9;4
-5;-2;-10;4
-6;-3;-1;4
-7;-3;-2;4
-8;-3;-3;4
-100;-3;-4;4
-9;-4;-1;4
-10;-4;-2;4
-11;-4;-3;4
-101;-4;-11;4
-12;-5;-5;4
-74;-6;-6;4
-77;-6;-7;4
-13;-6;-8;4
-14;-7;-5;4
-15;-7;-6;4
-16;-7;-7;4
-17;-7;-8;4
-18;-8;-14;4
-19;-8;-15;4
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr),
"item_collection_item",
delim=";")
dataTextStr = \
"""patient_item_collection_link_id;patient_item_id;item_collection_item_id
-1;-5010;-6
-2;-5020;-4
-3;-5050;-13
-4;-5060;-101
-5;-5090;-6
-6;-5100;-7
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr),
"patient_item_collection_link",
delim=";")
# Instance to test on
self.analyzer = PreparePatientItems()
def _insertTestRecords(self):
"""Populate database for with patient data."""
# Populate clinical_item_category.
testRecords = FM_TEST_INPUT_TABLES.get("clinical_item_category")
DBUtil.insertFile(StringIO(testRecords), "clinical_item_category", \
delim="\t")
# Populate clinical_item.
testRecords = FM_TEST_INPUT_TABLES.get("clinical_item")
DBUtil.insertFile(StringIO(testRecords), "clinical_item", delim="\t")
# Populate patient_item.
testRecords = FM_TEST_INPUT_TABLES.get("patient_item")
DBUtil.insertFile(StringIO(testRecords), "patient_item", delim="\t", \
dateColFormats={"item_date": None})
# Populate stride_order_proc.
testRecords = FM_TEST_INPUT_TABLES.get("stride_order_proc")
DBUtil.insertFile(StringIO(testRecords), "stride_order_proc", \
delim="\t", \
dateColFormats={"item_date": None})
# Populate stride_order_results.
testRecords = FM_TEST_INPUT_TABLES.get("stride_order_results")
DBUtil.insertFile(StringIO(testRecords), "stride_order_results", \
delim="\t", dateColFormats={"result_time": None})
# Populate stride_flowsheet.
testRecords = FM_TEST_INPUT_TABLES.get("stride_flowsheet")
DBUtil.insertFile(StringIO(testRecords), "stride_flowsheet", \
delim="\t", \
dateColFormats={"shifted_record_dt_tm": None})
# Populate stride_order_med.
testRecords = FM_TEST_INPUT_TABLES.get("stride_order_med")
DBUtil.insertFile(StringIO(testRecords), "stride_order_med", \
delim="\t", dateColFormats = {"start_taking_time": None, \
"end_taking_time": None})
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
log.info("Populate the database with test data")
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
#self.purgeTestRecords();
headers = [
"clinical_item_category_id", "default_recommend", "source_table"
]
dataModels = \
[
RowItemModel( [-1, 1, "Labs"], headers ),
RowItemModel( [-2, 1, "Imaging"], headers ),
RowItemModel( [-3, 1, "Meds"], headers ),
RowItemModel( [-4, 1, "Nursing"], headers ),
RowItemModel( [-5, 1, "Problems"], headers ),
RowItemModel( [-6, 1, "Lab Results"], headers ),
RowItemModel( [-7, 0, "No Rec Category"], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("clinical_item_category",
dataModel)
headers = [
"clinical_item_id", "clinical_item_category_id", "patient_count",
"name", "analysis_status"
]
dataModels = \
[
RowItemModel( [-1, -1, 100, "CBC",1], headers ),
RowItemModel( [-2, -1, 200, "BMP",0], headers ), # Clear analysis status, so this will be ignored unless changed
RowItemModel( [-3, -1, 300, "Hepatic Panel",1], headers ),
RowItemModel( [-4, -1, 400, "Cardiac Enzymes",1], headers ),
RowItemModel( [-5, -2, 500, "CXR",1], headers ),
RowItemModel( [-6, -2, 600, "RUQ Ultrasound",1], headers ),
RowItemModel( [-7, -2, 700, "CT Abdomen/Pelvis",1], headers ),
RowItemModel( [-8, -2, 800, "CT PE Thorax",1], headers ),
RowItemModel( [-9, -3, 900, "Acetaminophen",1], headers ),
RowItemModel( [-10, -3, 1000, "Carvedilol",1], headers ),
RowItemModel( [-11, -3, 100, "Enoxaparin",1], headers ),
RowItemModel( [-12, -3, 200, "Warfarin",1], headers ),
RowItemModel( [-13, -3, 300, "Ceftriaxone",1], headers ),
RowItemModel( [-14, -4, 400, "Foley Catheter",1], headers ),
RowItemModel( [-15, -4, 500, "Strict I&O",1], headers ),
RowItemModel( [-16, -4, 600, "Fall Precautions",1], headers ),
RowItemModel( [-77, -7, 700, "No Rec Item",1], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("clinical_item", dataModel)
dataTextStr = \
"""patient_item_id;patient_id;clinical_item_id;item_date
-1;-123;-6;3/11/2012 10:57
-2;-123;-7;3/11/2012 10:57
-3;-123;-1;4/11/2012 10:57
-4;-123;-2;4/11/2012 10:57
-5;-123;-3;4/11/2012 10:57
-6;-123;-4;4/11/2012 10:57
-8;-123;-8;4/11/2012 10:57
-9;-123;-9;4/11/2012 10:57
-10;-123;-10;4/11/2012 0:00
-11;-123;-11;4/11/2012 10:57
-12;-123;-12;4/11/2012 10:57
-13;-123;-13;4/11/2012 10:57
-14;-123;-12;4/12/2012 3:57
-15;-123;-14;4/12/2012 3:57
-16;-123;-15;4/12/2012 3:57
-17;-123;-16;4/12/2012 3:57
-18;-123;-13;5/12/2012 8:57
-19;-123;-5;5/12/2012 8:57
-21;-456;-4;12/24/2013 6:50
-22;-456;-4;12/24/2013 7:50
-24;-456;-77;12/24/2013 8:50
-25;-456;-10;12/24/2013 0:00
-26;-456;-12;12/24/2013 6:50
-27;-456;-12;12/24/2013 6:55
-28;-456;-12;12/24/2013 6:59
-29;-456;-12;12/24/2013 18:50
-30;-456;-12;12/24/2013 19:50
-31;-456;-14;12/24/2013 18:50
-32;-456;-8;12/24/2013 18:50
-33;-456;-8;12/24/2013 20:50
-34;-456;-8;12/24/2013 18:30
-35;-789;-1;8/19/2011 11:12
-36;-789;-3;8/19/2011 11:12
-37;-789;-3;8/19/2011 0:12
-38;-789;-3;8/19/2011 0:52
-39;-789;-5;8/19/2011 11:12
-40;-789;-9;8/19/2011 11:12
-41;-789;-9;8/19/2011 0:12
-42;-789;-9;8/19/2011 13:12
-43;-789;-10;8/19/2011 0:00
-44;-789;-11;8/19/2011 11:12
-45;-789;-13;8/19/2011 19:12
-46;-789;-15;8/19/2011 19:12
-47;-789;-15;8/19/2011 19:14
-48;-789;-15;8/19/2011 19:22
-49;-789;-15;8/19/2011 19:32
-50;-789;-15;8/19/2011 19:42
-1001;-321;-6;3/11/2012 10:57
-1002;-321;-7;3/11/2012 10:57
-1010;-321;-10;4/11/2012 0:00
-1003;-321;-1;4/11/2012 10:57
-1004;-321;-2;4/11/2012 10:57
-1005;-321;-3;4/11/2012 10:57
-1006;-321;-4;4/11/2012 10:57
-1008;-321;-8;4/11/2012 10:57
-1009;-321;-9;4/11/2012 10:57
-1011;-321;-11;4/11/2012 10:57
-1012;-321;-12;4/11/2012 10:57
-1013;-321;-13;4/11/2012 10:57
-1014;-321;-12;4/12/2012 3:57
-1015;-321;-14;4/12/2012 3:57
-1016;-321;-15;4/12/2012 3:57
-1017;-321;-16;4/12/2012 3:57
-1018;-321;-13;4/12/2012 8:57
-1019;-321;-5;4/12/2012 8:57
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr), "patient_item", delim=";")
dataTextStr = \
"""item_collection_id;external_id;name;section;subgroup
-1;-1;Test Order Set - 1;Meds;TreatmentMeds
-2;-1;Test Order Set - 1;Meds;SymptomsMeds
-3;-1;Test Order Set - 1;Labs;GeneralLabs
-4;-2;Test Order Set - 2;Labs;GeneralLabs
-5;-2;Test Order Set - 2;Imaging;Xrays
-6;-2;Test Order Set - 2;Imaging;AdvancedImaging
-7;-3;Test Order Set - 3;Imaging;GeneralImaging
-8;-3;Test Order Set - 3;Nursing;GeneralNursing
-9;-4;Test Order Set - 4;Ad-hoc Orders;Ad-hoc Orders
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr), "item_collection", delim=";")
dataTextStr = \
"""item_collection_item_id;item_collection_id;clinical_item_id;collection_type_id
-1;-1;-12;4
-2;-1;-13;4
-3;-2;-11;4
-4;-2;-10;4
-5;-3;-1;4
-6;-3;-2;4
-7;-4;-2;4
-8;-4;-3;4
-9;-5;-5;4
-10;-6;-6;4
-11;-6;-7;4
-12;-6;-8;4
-74;-6;-4;4
-77;-6;-77;4
-13;-7;-5;4
-14;-7;-6;4
-15;-8;-14;4
-16;-8;-15;4
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr),
"item_collection_item",
delim=";")
dataTextStr = \
"""patient_item_collection_link_id;patient_item_id;item_collection_item_id
-1;-3;-5
-2;-4;-6
-3;-15;-15
-4;-32;-12
-1001;-1003;-5
-1002;-1004;-6
-1003;-1015;-15
-1004;-1019;-9
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr),
"patient_item_collection_link",
delim=";")
# Sample Prepared Validation File
self.validationFileStr = \
"""patient_id\tqueryItemCountByIdJSON\tverifyItemCountByIdJSON\tbaseItemId\tbaseItemDate\tqueryStartTime\tqueryEndTime\tverifyEndTime\toutcome.7
-123\t{"-1": 1, "-2": 1, "-3": 1, "-4": 1, "-8": 1, "-9": 1, "-10": 1, "-11": 1, "-12": 1, "-13": 1}\t{"-12": 1, "-14": 1, "-15": 1, "-16": 1}\t10\t2012-04-11 00:00:00\t2012-04-11 10:57:00\t2012-04-11 14:57:00\t2012-04-12 10:57:00\t0
-456\t{"-4": 2, "-77": 1, "-10": 1, "-12": 3}\t{"-12": 2, "-14": 1, "-8": 3}\t10\t2013-12-24 00:00:00\t2013-12-24 06:50:00\t2013-12-24 10:50:00\t2013-12-25 06:50:00\t1
-789\t{"-1": 1, "-3": 3, "-5": 1, "-9": 3, "-10": 1, "-11": 1}\t{"-13": 1, "-15": 5}\t10\t2011-08-19 00:00:00\t2011-08-19 11:12:00\t2011-08-19 15:12:00\t2011-08-20 11:12:00\t0
-321\t{"-1": 1, "-2": 1, "-3": 1, "-4": 1, "-8": 1, "-9": 1, "-10": 1, "-11": 1, "-12": 1, "-13": 1}\t{"-12": 1, "-14": 1, "-15": 1, "-16": 1}\t10\t2012-04-11 00:00:00\t2012-04-11 10:57:00\t2012-04-11 14:57:00\t2012-04-12 10:57:00\t0
"""
# Another Sample Prepared Validation File, with key Order Set triggers
self.orderSetValidationFileStr = \
"""patient_id\tqueryItemCountByIdJSON\tverifyItemCountByIdJSON\tbaseItemId\tbaseItemDate\tqueryStartTime\tqueryEndTime\tverifyEndTime\toutcome.7\torder_set_id
-123\t{"-10": 1}\t{"-1": 1, "-2": 1, "-3": 1, "-4": 1, "-8": 1, "-9": 1, "-11": 1, "-12": 1, "-13": 1}\t10\t2012-04-11 00:00:00\t2012-04-11 10:57:00\t2012-04-11 10:57:00\t2012-04-11 11:57:00\t0\t-1
-456\t{"-10": 1, "-4": 2, "-77": 1, "-12": 4, "-14": 1, "-8": 1}\t{"-12": 1, "-8": 2}\t10\t2013-12-24 00:00:00\t2013-12-24 06:50:00\t2013-12-24 18:50:00\t2013-12-24 19:50:00\t1\t-2
-789\t{"-1": 1, "-3": 3, "-5": 1, "-9": 3, "-10": 1, "-11": 1}\t{"-13": 1, "-15": 5}\t10\t2011-08-19 00:00:00\t2011-08-19 11:12:00\t2011-08-19 15:12:00\t2011-08-20 11:12:00\t0\t-4
-321\t{"-10": 1}\t{"-1": 1, "-2": 1, "-3": 1, "-4": 1, "-8": 1, "-9": 1, "-11": 1, "-12": 1, "-13": 1}\t10\t2012-04-11 00:00:00\t2012-04-11 10:57:00\t2012-04-11 10:57:00\t2012-04-11 11:57:00\t0\t-1
-321\t{"-10": 1, "-1": 1, "-2": 1, "-3": 1, "-4": 1, "-8": 1, "-9": 1, "-11": 1, "-12": 1, "-13": 1}\t{"-12": 1,"-14": 1, "-15": 1, "-16": 1}\t10\t2012-04-11 00:00:00\t2012-04-11 10:57:00\t2012-04-12 3:57:00\t2012-04-12 4:57:00\t0\t-3
"""
self.analyzer = OrderSetUsageAnalysis()
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
log.info("Populate the database with test data")
self.clinicalItemCategoryIdStrList = list()
headers = ["clinical_item_category_id", "source_table"]
dataModels = \
[
RowItemModel( [-1, "Labs"], headers ),
RowItemModel( [-2, "Imaging"], headers ),
RowItemModel( [-3, "Meds"], headers ),
RowItemModel( [-4, "Nursing"], headers ),
RowItemModel( [-5, "Problems"], headers ),
RowItemModel( [-6, "Lab Results"], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("clinical_item_category",
dataModel)
self.clinicalItemCategoryIdStrList.append(str(dataItemId))
headers = ["clinical_item_id", "clinical_item_category_id", "name"]
dataModels = \
[
RowItemModel( [-1, -1, "CBC"], headers ),
RowItemModel( [-2, -1, "BMP"], headers ),
RowItemModel( [-3, -1, "Hepatic Panel"], headers ),
RowItemModel( [-4, -1, "Cardiac Enzymes"], headers ),
RowItemModel( [-5, -2, "CXR"], headers ),
RowItemModel( [-6, -2, "RUQ Ultrasound"], headers ),
RowItemModel( [-7, -2, "CT Abdomen/Pelvis"], headers ),
RowItemModel( [-8, -2, "CT PE Thorax"], headers ),
RowItemModel( [-9, -3, "Acetaminophen"], headers ),
RowItemModel( [-10, -3, "Carvedilol"], headers ),
RowItemModel( [-11, -3, "Enoxaparin"], headers ),
RowItemModel( [-12, -3, "Warfarin"], headers ),
RowItemModel( [-13, -3, "Ceftriaxone"], headers ),
RowItemModel( [-14, -4, "Foley Catheter"], headers ),
RowItemModel( [-15, -4, "Strict I&O"], headers ),
RowItemModel( [-16, -4, "Fall Precautions"], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("clinical_item", dataModel)
headers = [
"patient_item_id", "patient_id", "clinical_item_id", "item_date",
"analyze_date"
]
dataModels = \
[
RowItemModel( [-1, -11111, -4, datetime(2000, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-2, -11111, -10, datetime(2000, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-3, -11111, -8, datetime(2000, 1, 1, 2), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-4, -11111, -10, datetime(2000, 1, 2, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-5, -11111, -12, datetime(2000, 2, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-10, -22222, -7, datetime(2000, 1, 5, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-12, -22222, -6, datetime(2000, 1, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-13, -22222, -11, datetime(2000, 1, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-14, -33333, -6, datetime(2000, 2, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-15, -33333, -2, datetime(2000, 2,11, 0), datetime(2010, 1, 1, 0)], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("patient_item", dataModel)
dataTextStr = \
"""item_collection_id;external_id;name;section;subgroup
-1;-1;Test Order Set - 1;Meds;TreatmentMeds
-2;-1;Test Order Set - 1;Meds;SymptomsMeds
-3;-1;Test Order Set - 1;Labs;GeneralLabs
-4;-2;Test Order Set - 2;Labs;GeneralLabs
-5;-2;Test Order Set - 2;Imaging;Xrays
-6;-2;Test Order Set - 2;Imaging;AdvancedImaging
-7;-3;Test Order Set - 3;Imaging;GeneralImaging
-8;-3;Test Order Set - 3;Nursing;GeneralNursing
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr), "item_collection", delim=";")
dataTextStr = \
"""item_collection_item_id;item_collection_id;clinical_item_id;collection_type_id
-1;-1;-12;4
-2;-1;-13;4
-3;-2;-11;4
-4;-2;-10;4
-5;-3;-1;4
-6;-3;-2;4
-7;-4;-2;4
-8;-4;-3;4
-9;-5;-5;4
-10;-6;-6;4
-11;-6;-7;4
-12;-6;-8;4
-13;-7;-5;4
-14;-7;-6;4
-15;-8;-14;4
-16;-8;-15;4
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr),
"item_collection_item",
delim=";")
self.recommender = OrderSetRecommender()
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
self.usage_reporter = SimManager()
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
self.usage_reporter.buildCPOESimSchema()
log.info("Populate the database with test data")
# Basically import a bunch of rigged CSV or TSV files that have realistic simulating case and grading data
# Get that data into the test database
clinical_item_category_str = \
"""clinical_item_category_id;source_table
1;source_table
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_category_str), "clinical_item_category", delim=";")
clinical_item_str = \
"""clinical_item_id;clinical_item_category_id;name
1;1;Clinical item 1
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_str), "clinical_item", delim=";")
clinical_item_str = \
"""sim_user_id;name
1;Jonathan Chen
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(clinical_item_str), "sim_user", delim=";")
sim_patient_str = \
"""sim_patient_id;name;age_years;gender
1;Patient One;40;Male
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_patient_str), "sim_patient", delim=";")
sim_state_str = \
"""sim_state_id;name
1;Sim state 1
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_state_str), "sim_state", delim=";")
sim_patient_order_str = \
"""sim_patient_order_id;sim_user_id;sim_patient_id;clinical_item_id;relative_time_start;sim_state_id
1;1;1;1;1;1
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_patient_order_str), "sim_patient_order", delim=";")
sim_grading_key_str = \
"""sim_grader_id;sim_state_id;clinical_item_id;score;group_name;sim_case_name
Jonathan Chen;1;1;1;g1;case_name
Andre Kumar;1;1;2;g1;case_name
"""
# Parse into DB insertion object
DBUtil.insertFile(StringIO(sim_grading_key_str), "sim_grading_key", delim=";")
# Prepare survey file
self.survey_csv = tempfile.NamedTemporaryFile(mode='w+', delete=False)
self.survey_csv.write("Physician User Name,resident" + os.linesep +
"Jonathan Chen,1")
self.survey_csv.flush()
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self);
log.info("Populate the database with test data")
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader;
ClinicalItemDataLoader.build_clinical_item_psql_schemata();
self.clinicalItemCategoryIdStrList = list();
headers = ["clinical_item_category_id","default_recommend","source_table"];
dataModels = \
[
RowItemModel( [-1, 1, "Labs"], headers ),
RowItemModel( [-2, 1, "Imaging"], headers ),
RowItemModel( [-3, 1, "Meds"], headers ),
RowItemModel( [-4, 0, "Nursing"], headers ), # Disable default recommend to allow for checks
RowItemModel( [-5, 0, "Problems"], headers ),
RowItemModel( [-6, 1, "Lab Results"], headers ),
RowItemModel( [-7, 1, "Admit Dx"], headers ),
RowItemModel( [-8, 0, "Demographics"], headers ),
];
for dataModel in dataModels:
(dataItemId, isNew) = DBUtil.findOrInsertItem("clinical_item_category", dataModel );
self.clinicalItemCategoryIdStrList.append( str(dataItemId) );
headers = ["clinical_item_id","clinical_item_category_id","default_recommend","item_count","name"];
dataModels = \
[
RowItemModel( [-1, -1, 1, 30, "CBC"], headers ),
RowItemModel( [-2, -1, 1, 30, "BMP"], headers ),
RowItemModel( [-3, -1, 1, 95, "Hepatic Panel"], headers ),
RowItemModel( [-4, -1, 1, 40, "Cardiac Enzymes"], headers ),
RowItemModel( [-5, -2, 1, 40, "CXR"], headers ),
RowItemModel( [-6, -2, 1, 70, "RUQ Ultrasound"], headers ),
RowItemModel( [-7, -2, 1, 70, "CT Abdomen/Pelvis"], headers ),
RowItemModel( [-8, -2, 1, 35, "CT PE Thorax"], headers ),
RowItemModel( [-9, -3, 1, 0, "Acetaminophen"], headers ),
RowItemModel( [-10, -3, 1, 45, "Carvedilol"], headers ),
RowItemModel( [-11, -3, 1, 50, "Enoxaparin"], headers ),
RowItemModel( [-12, -3, 1, 75, "Warfarin"], headers ),
RowItemModel( [-13, -3, 0, 0, "Ceftriaxone"], headers ), # Disable default recommend to allow for checks
RowItemModel( [-14, -4, 1, 0, "Foley Catheter"], headers ),
RowItemModel( [-15, -4, 1, 0, "Strict I&O"], headers ),
RowItemModel( [-16, -4, 1, 0, "Fall Precautions"], headers ),
];
for dataModel in dataModels:
(dataItemId, isNew) = DBUtil.findOrInsertItem("clinical_item", dataModel );
headers = ["patient_item_id","patient_id","clinical_item_id","item_date","analyze_date"];
dataModels = \
[
RowItemModel( [-1, -11111, -4, datetime(2000, 1, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-2, -11111, -10, datetime(2000, 1, 1, 1), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-3, -11111, -8, datetime(2000, 1, 1, 2), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-5, -11111, -12, datetime(2000, 2, 1, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-6, -11111, -6, datetime(2000, 2, 1, 1), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-10, -22222, -7, datetime(2000, 1, 5, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-12, -22222, -6, datetime(2000, 1, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-13, -22222, -11, datetime(2000, 1, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-14, -33333, -6, datetime(2000, 2, 9, 0), datetime(2010, 1, 1, 0)], headers ),
RowItemModel( [-15, -33333, -2, datetime(2000, 2,11, 0), datetime(2010, 1, 1, 0)], headers ),
];
for dataModel in dataModels:
(dataItemId, isNew) = DBUtil.findOrInsertItem("patient_item", dataModel );
headers = \
[ "clinical_item_id","subsequent_item_id",
"count_0","count_3600","count_86400","count_604800","count_any",
"time_diff_sum", "time_diff_sum_squares",
];
dataModels = \
[
RowItemModel( [ -1, -1, 30, 30, 30, 30, 30, 0.0, 0.0], headers ),
RowItemModel( [ -2, -2, 30, 30, 30, 30, 30, 0.0, 0.0], headers ),
RowItemModel( [ -3, -3, 95, 95, 97, 97, 97, 0.0, 0.0], headers ),
RowItemModel( [ -4, -4, 40, 40, 40, 40, 40, 0.0, 0.0], headers ),
RowItemModel( [ -5, -5, 40, 40, 50, 50, 50, 0.0, 0.0], headers ),
RowItemModel( [ -6, -6, 70, 70, 70, 70, 70, 0.0, 0.0], headers ),
RowItemModel( [ -7, -7, 70, 70, 70, 70, 70, 0.0, 0.0], headers ),
RowItemModel( [ -8, -8, 35, 35, 35, 50, 80, 0.0, 0.0], headers ),
RowItemModel( [-10,-10, 45, 45, 55, 60, 90, 0.0, 0.0], headers ),
RowItemModel( [-11,-11, 50, 50, 50, 80, 90, 0.0, 0.0], headers ),
RowItemModel( [-12,-12, 75, 75, 75, 80, 90, 0.0, 0.0], headers ),
RowItemModel( [ -2, -4, 0, 2, 3, 3, 3, 200.0, 50000.0], headers ),
RowItemModel( [ -2, -6, 2, 2, 5, 5, 5, 300.0, 11990.0], headers ),
RowItemModel( [ -3, -1, 20, 23, 23, 23, 23, 400.0, 344990.0], headers ),
RowItemModel( [ -4, -5, 3, 3, 13, 43, 43, 340.0, 343110.0], headers ),
RowItemModel( [ -4, -6, 23, 33, 33, 33, 63, 420.0, 245220.0], headers ),
RowItemModel( [ -4, -7, 27, 33, 33, 33, 63, 40.0, 5420.0], headers ),
RowItemModel( [ -4,-10, 25, 35, 40, 45, 63, 47.0, 5420.0], headers ),
RowItemModel( [ -5, -4, 0, 0, 20, 20, 20, 540.0, 54250.0], headers ),
RowItemModel( [ -8,-12, 15,15, 15, 15, 15, 25.0, 520.0], headers ),
RowItemModel( [ -10,-11, 12,12, 16, 16, 20, 20.0, 220.0], headers ),
RowItemModel( [ -10,-12, 10,10, 10, 10, 10, 20.0, 120.0], headers ),
];
for dataModel in dataModels:
(dataItemId, isNew) = DBUtil.findOrInsertItem("clinical_item_association", dataModel );
dataTextStr = \
"""item_collection_id;external_id;name;section;subgroup
-1;-1;Test Order Set - 1;Meds;TreatmentMeds
-2;-1;Test Order Set - 1;Meds;SymptomsMeds
-3;-1;Test Order Set - 1;Labs;GeneralLabs
-4;-2;Test Order Set - 2;Labs;GeneralLabs
-5;-2;Test Order Set - 2;Imaging;Xrays
-6;-2;Test Order Set - 2;Imaging;AdvancedImaging
-7;-3;Test Order Set - 3;Imaging;GeneralImaging
-8;-3;Test Order Set - 3;Nursing;GeneralNursing
-9;-3;Test Order Set - 3;Meds;RandomMeds
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "item_collection", delim=";");
dataTextStr = \
"""item_collection_item_id;item_collection_id;clinical_item_id;collection_type_id
-1;-1;-11;4
-2;-1;-12;4
-3;-1;-13;4
-4;-2;-9;4
-5;-2;-10;4
-6;-3;-1;4
-7;-3;-2;4
-8;-3;-3;4
-100;-3;-4;4
-9;-4;-1;4
-10;-4;-2;4
-11;-4;-3;4
-101;-4;-11;4
-12;-5;-5;4
-74;-6;-6;4
-77;-6;-7;4
-13;-6;-8;4
-14;-7;-5;4
-15;-7;-6;4
-16;-7;-7;4
-17;-7;-8;4
-18;-8;-14;4
-19;-8;-15;4
-20;-9;-11;4
-21;-9;-12;4
-22;-9;-13;4
""" # Parse into DB insertion object
DBUtil.insertFile( StringIO(dataTextStr), "item_collection_item", delim=";");
# Instance to test on
self.analyzer = RecommendationClassificationAnalysis();
self.preparer = PreparePatientItems();
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
log.info("Populate the database with test data")
StrideLoader.build_stride_psql_schemata()
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
dataTextStr = """order_proc_id\tpat_id\tpat_enc_csn_id\torder_type\tproc_id\tproc_code\tdescription
-30560253\t-7803\t-1772\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-31300455\t-2168\t-261\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-29501223\t-9860\t-1772\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-31823670\t-2130\t-3897\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-31237072\t-124\t-8391\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-29966444\t-5690\t-1150\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-33197720\t-9926\t-4898\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-36668349\t-9815\t-3658\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-33280031\t-3858\t-6463\tLab\t471521\tLABACETA\tACETAMINOPHEN, SERUM
-38543619\t-6562\t-4489\tLab\t898794\tLABCSMP\tCANCER SOMATIC MUTATION PANEL
-35954787\t-7074\t-6965\tLab\t898794\tLABCSMP\tCANCER SOMATIC MUTATION PANEL
-22793877\t-3261\t-4837\tLab\t471944\tLABCBCD\tCBC WITH DIFF
-40604146\t-7480\t-8730\tLab\t896082\t10355R\tHLA - MONITORING BY IGG
-33765278\t-4255\t-622\tLab\t896082\t10355R\tHLA - MONITORING BY IGG
-39004110\t-5750\t-4953\tLab\t472748\tLABYLEPTN\tLEPTIN
-22910018\t-1862\t-621\tLab\t472785\tLABMGN\tMAGNESIUM, SERUM/PLASMA
-22840955\t-9532\t-639\tLab\t472837\tLABTNI\tTROPONIN I
-21479311\t-9844\t-5135\tLab\t473684\tLABMETB\tMETABOLIC PANEL, BASIC
-19231504\t-1518\t-3744\tLab\t473684\tLABMETB\tMETABOLIC PANEL, BASIC
-19007449\t-9542\t-4105\tLab\t473684\tLABMETB\tMETABOLIC PANEL, BASIC
-1748206\t-1099\t-9890\tLab\t473766\tLABY25VD\tVITAMIN D, 25-HYDROXY
-2794591\t-4038\t-6687\tLab\t473766\tLABY25VD\tVITAMIN D, 25-HYDROXY
-3580354\t-2795\t-752\tLab\t473766\tLABY25VD\tVITAMIN D, 25-HYDROXY
-3347071\t-6139\t-7104\tLab\t473766\tLABY25VD\tVITAMIN D, 25-HYDROXY
-4464954\t-4591\t-1383\tLab\t473766\tLABY25VD\tVITAMIN D, 25-HYDROXY
-3393444\t-5157\t-5537\tLab\t473766\tLABY25VD\tVITAMIN D, 25-HYDROXY
-2658433\t-6894\t-211\tLab\t473766\tLABY25VD\tVITAMIN D, 25-HYDROXY
"""
DBUtil.insertFile(StringIO(dataTextStr),
"stride_order_proc",
delim="\t")
# Deliberately design dates in far future to facilitate isolated testing
dataTextStr = \
"""order_proc_id\tline\tresult_time\tcommon_name\tbase_name\tord_num_value\tresult_flag\tresult_in_range_yn
-4464954\t2\t5/28/2113 23:28\t25-HYDROXY D3\t25OHD3\t55\tNone\tNone
-3580354\t2\t12/17/2113 0:40\t25-HYDROXY D3\t25OHD3\t49\tNone\tNone
-3393444\t2\t10/9/2113 5:03\t25-HYDROXY D3\t25OHD3\t65\tNone\tNone
-3347071\t2\t9/8/2113 22:10\t25-HYDROXY D3\t25OHD3\t2\tNone\tNone
-2794591\t2\t3/19/2113 19:26\t25-HYDROXY D3\t25OHD3\t70\tNone\tNone
-2658433\t2\t7/5/2111 0:28\t25-HYDROXY D3\t25OHD3\t45\tNone\tNone
-1748206\t2\t7/3/2111 14:21\t25-HYDROXY D3\t25OHD3\t50\tNone\tNone
-36668349\t1\t10/30/2111 7:23\tACETAMINOPHEN(ACETA)\tACETA\t7.7\tNone\tNone
-33280031\t1\t11/29/2111 7:41\tACETAMINOPHEN(ACETA)\tACETA\t9999999\tNone\tNone
-33197720\t1\t11/29/2111 15:22\tACETAMINOPHEN(ACETA)\tACETA\tNone\tNone\tNone
-31823670\t1\t11/29/2111 14:08\tACETAMINOPHEN(ACETA)\tACETA\t5.4\tNone\tNone
-31300455\t1\t11/29/2111 18:58\tACETAMINOPHEN(ACETA)\tACETA\t270.7\tNone\tNone
-31237072\t1\t11/29/2111 5:45\tACETAMINOPHEN(ACETA)\tACETA\t50.6\tNone\tNone
-30560253\t1\t11/29/2111 16:13\tACETAMINOPHEN(ACETA)\tACETA\t2.6\tNone\tNone
-29966444\t1\t11/29/2111 2:27\tACETAMINOPHEN(ACETA)\tACETA\t4.2\tNone\tNone
-29501223\t1\t11/29/2111 0:15\tACETAMINOPHEN(ACETA)\tACETA\t5.1\tNone\tNone
-22793877\t4\t11/29/2111 14:36\tHEMATOCRIT(HCT)\tHCT\t19.7\tLow Panic\tNone
-22793877\t3\t11/30/2111 7:36\tHEMOGLOBIN(HGB)\tHGB\t7\tLow Panic\tNone
-40604146\t15\t12/13/2111 18:12\tINTERPRETATION/ COMMENTS CLASS II 9374R\t9374R\tNone\tNone\tNone
-33765278\t10\t9/22/2112 20:26\tINTERPRETATION/ COMMENTS CLASS II 9374R\t9374R\t9999999\tNone\tNone
-39004110\t1\t8/26/2112 15:07\tLEPTIN\tYLEPT1\t20\tNone\tNone
-22910018\t1\t11/13/2112 8:18\tMAGNESIUM, SER/PLAS(MGN)\tMG\t2.1\tNone\tY
-22793877\t6\t10/17/2112 1:09\tMCH(MCH)\tMCH\t31.7\tNone\tY
-22793877\t7\t12/13/2112 2:54\tMCHC(MCHC)\tMCHC\t35.4\tNone\tY
-22793877\t5\t11/11/2112 2:54\tMCV(MCV)\tMCV\t89.7\tNone\tY
-22793877\t9\t1/30/2113 13:28\tPLATELET COUNT(PLT)\tPLT\t11\tLow\tNone
-22793877\t2\t7/11/2113 23:24\tRBC(RBC)\tRBC\t2.2\tLow\tNone
-22793877\t8\t1/27/2113 14:44\tRDW(RDW)\tRDW\t33.3\tHigh\tNone
-21479311\t1\t8/31/2109 15:42\tSODIUM, SER/PLAS\tNA\t142\tNone\tNone
-19231504\t1\t8/20/2109 12:22\tSODIUM, SER/PLAS\tNA\t134\tLow\tNone
-19007449\t1\t9/13/2109 11:55\tSODIUM, SER/PLAS\tNA\t157\tHigh\tNone
-38543619\t15\t10/23/2109 14:30\tTP53(GTP53)\tGTP53\t9999999\tNone\tNone
-35954787\t15\t8/19/2109 16:39\tTP53(GTP53)\tGTP53\t9999999\tNone\tNone
-22793877\t1\t9/25/2109 16:10\tWBC(WBC)\tWBC\t0.2\tLow Panic\tNone
"""
DBUtil.insertFile(StringIO(dataTextStr),
"stride_order_results",
delim="\t",
dateColFormats={"result_time": None})
self.converter = STRIDEOrderResultsConversion()
def setUp(self):
"""Prepare state for test cases"""
DBTestCase.setUp(self)
log.info("Populate the database with test data")
from stride.clinical_item.ClinicalItemDataLoader import ClinicalItemDataLoader
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
self.clinicalItemCategoryIdStrList = list()
headers = ["clinical_item_category_id", "source_table"]
dataModels = \
[
RowItemModel( [-1, "Labs"], headers ),
RowItemModel( [-2, "Imaging"], headers ),
RowItemModel( [-3, "Meds"], headers ),
RowItemModel( [-4, "Nursing"], headers ),
RowItemModel( [-5, "Problems"], headers ),
RowItemModel( [-6, "Lab Results"], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("clinical_item_category",
dataModel)
self.clinicalItemCategoryIdStrList.append(str(dataItemId))
headers = [
"clinical_item_id", "clinical_item_category_id", "name",
"analysis_status"
]
dataModels = \
[
RowItemModel( [-1, -1, "CBC",1], headers ),
RowItemModel( [-2, -1, "BMP",0], headers ), # Clear analysis status, so this will be ignored unless changed
RowItemModel( [-3, -1, "Hepatic Panel",1], headers ),
RowItemModel( [-4, -1, "Cardiac Enzymes",1], headers ),
RowItemModel( [-5, -2, "CXR",1], headers ),
RowItemModel( [-6, -2, "RUQ Ultrasound",1], headers ),
RowItemModel( [-7, -2, "CT Abdomen/Pelvis",1], headers ),
RowItemModel( [-8, -2, "CT PE Thorax",1], headers ),
RowItemModel( [-9, -3, "Acetaminophen",1], headers ),
RowItemModel( [-10, -3, "Carvedilol",1], headers ),
RowItemModel( [-11, -3, "Enoxaparin",1], headers ),
RowItemModel( [-12, -3, "Warfarin",1], headers ),
RowItemModel( [-13, -3, "Ceftriaxone",1], headers ),
RowItemModel( [-14, -4, "Foley Catheter",1], headers ),
RowItemModel( [-15, -4, "Strict I&O",1], headers ),
RowItemModel( [-16, -4, "Fall Precautions",1], headers ),
]
for dataModel in dataModels:
(dataItemId,
isNew) = DBUtil.findOrInsertItem("clinical_item", dataModel)
dataTextStr = \
"""item_collection_id;external_id;name;section;subgroup
-1;-1;Test Order Set - 1;Meds;TreatmentMeds
-2;-1;Test Order Set - 1;Meds;SymptomsMeds
-3;-1;Test Order Set - 1;Labs;GeneralLabs
-4;-2;Test Order Set - 2;Labs;GeneralLabs
-5;-2;Test Order Set - 2;Imaging;Xrays
-6;-2;Test Order Set - 2;Imaging;AdvancedImaging
-7;-3;Test Order Set - 3;Imaging;GeneralImaging
-8;-3;Test Order Set - 3;Nursing;GeneralNursing
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr), "item_collection", delim=";")
dataTextStr = \
"""item_collection_item_id;item_collection_id;clinical_item_id;collection_type_id
-1;-1;-12;4
-2;-1;-13;4
-3;-2;-11;4
-4;-2;-10;4
-5;-3;-1;4
-6;-3;-2;4
-7;-4;-2;4
-8;-4;-3;4
-9;-5;-5;4
-10;-6;-6;4
-11;-6;-7;4
-12;-6;-8;4
-13;-7;-5;4
-14;-7;-6;4
-15;-8;-14;4
-16;-8;-15;4
""" # Parse into DB insertion object
DBUtil.insertFile(StringIO(dataTextStr),
"item_collection_item",
delim=";")
# Sample Prepared Validation File
self.validationFileStr = \
"""patient_id\tqueryItemCountByIdJSON\tverifyItemCountByIdJSON\tbaseItemId\tbaseItemDate\tqueryStartTime\tqueryEndTime\tverifyEndTime\toutcome.7
123\t{"-1": 1, "-2": 1, "-3": 1, "-4": 1, "-5": 1, "-8": 1, "-9": 1, "-10": 1, "-11": 1, "-12": 1, "-13": 1}\t{"-12": 1, "-14": 1, "-15": 1, "-16": 1}\t10\t2012-04-11 00:00:00\t2012-04-11 10:57:00\t2012-04-11 14:57:00\t2012-04-12 10:57:00\t0
456\t{"-2": 1, "-4": 2, "-8": 4, "-10": 1, "-12": 6}\t{"-12": 6, "-14": 7, "-16": 8}\t10\t2013-12-24 00:00:00\t2013-12-24 06:50:00\t2013-12-24 10:50:00\t2013-12-25 06:50:00\t1
789\t{"-1": 1, "-3": 3, "-5": 5, "-9": 9, "-10": 1, "-11": 11}\t{"-13": 13, "-15": 15}\t10\t2011-08-19 00:00:00\t2011-08-19 11:12:00\t2011-08-19 15:12:00\t2011-08-20 11:12:00\t0
"""
self.analyzer = OrderSetRecommenderClassificationAnalysis()