diff --git a/searchindex.js b/searchindex.js index 9903212..93a4aa4 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"API Reference": [[0, "api-reference"]], "Coding guidelines": [[1, "coding-guidelines"]], "Contents:": [[2, null]], "Contributing": [[3, "contributing"]], "Contributing to cycquery": [[1, "contributing-to-cycquery"]], "Example 1. Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "Example 3. Advanced - uses ConditionRegexMatch from cycquery.ops. Get all patient encounters with diagnoses (ICD-9 long title contains schizophrenia and chronic ), in the year 2015.": [[67, "Example-3.-Advanced---uses-ConditionRegexMatch-from-cycquery.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "Example 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. Running a raw SQL string.": [[67, "Example-8.-Running-a-raw-SQL-string."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate EICUQuerier": [[64, "Imports-and-instantiate-EICUQuerier"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Installing cycquery using pip": [[3, "installing-cycquery-using-pip"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Query postgresql database": [[3, "query-postgresql-database"]], "Tutorials": [[63, "tutorials"]], "Using poetry": [[3, "using-poetry"]], "Welcome to 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"teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"API Reference": [[0, "api-reference"]], "Coding guidelines": [[1, "coding-guidelines"]], "Contents:": [[2, null]], "Contributing": [[3, "contributing"]], "Contributing to cycquery": [[1, "contributing-to-cycquery"]], "Example 1. Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "Example 3. Advanced - uses ConditionRegexMatch from cycquery.ops. Get all patient encounters with diagnoses (ICD-9 long title contains schizophrenia and chronic ), in the year 2015.": [[67, "Example-3.-Advanced---uses-ConditionRegexMatch-from-cycquery.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "Example 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. Running a raw SQL string.": [[67, "Example-8.-Running-a-raw-SQL-string."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate EICUQuerier": [[64, "Imports-and-instantiate-EICUQuerier"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Installing cycquery using pip": [[3, "installing-cycquery-using-pip"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Query postgresql database": [[3, "query-postgresql-database"]], "Tutorials": [[63, "tutorials"]], "Using poetry": [[3, "using-poetry"]], "Welcome to 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"cycquery.ops.FillNull", "cycquery.ops.GroupByAggregate", "cycquery.ops.Join", "cycquery.ops.Keep", "cycquery.ops.Limit", "cycquery.ops.Literal", "cycquery.ops.Or", "cycquery.ops.OrderBy", "cycquery.ops.QueryOp", "cycquery.ops.RandomizeOrder", "cycquery.ops.Rename", "cycquery.ops.Reorder", "cycquery.ops.ReorderAfter", "cycquery.ops.Sequential", "cycquery.ops.Substring", "cycquery.ops.Trim", "cycquery.ops.Union", "cycquery", "Tutorials", "eICU-CRD tutorial", "GEMINI tutorial", "MIMIC-III tutorial", "MIMIC-IV tutorial", "OMOP tutorial"], "titleterms": {"": 2, "1": [64, 65, 66, 67, 68], "10": 67, "100": 64, "101": 65, "1a": 65, "1b": 65, "1c": 65, "2": [64, 66, 67, 68], "20": 66, "2009": 67, "2010": 68, "2014": 64, "2015": [64, 65, 67], "2016": 65, "2020": 68, "2021": 67, "2a": 65, "3": [64, 66, 67], "31": 65, "4": [64, 66, 67], "5": 67, "6": 67, "7": 67, "8": 67, "9": [66, 67], "And": 23, "Or": 51, "aado2": 66, "abov": 65, "addcolumn": 19, "adddeltacolumn": 20, "adddeltaconst": 21, "addnumer": 22, "admiss": [65, 67], "advanc": 67, "after": 68, "all": [64, 66, 67, 68], "api": [0, 62], "appli": 24, "approx": 67, "apr": 65, "april": 65, "base": [4, 5], "batch": 67, "between": 65, "carevu": 66, "cast": 25, "chart": 66, "chronic": 67, "code": 1, "commit": 1, "conditionafterd": 26, "conditionbefored": 27, "conditionendswith": 28, "conditionequ": 29, "conditiongreaterthan": 30, "conditionin": 31, "conditioninmonth": 32, "conditioninyear": 33, "conditionlessthan": 34, "conditionlik": 35, "conditionregexmatch": [36, 67], "conditionstartswith": 37, "conditionsubstr": 38, "contain": 67, "content": 2, "contribut": [1, 3], "count": 39, "crd": 64, "creat": 65, "cycqueri": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 67], "databas": 3, "dataset": [62, 65], "datasetqueri": 5, "develop": 3, "diagnos": [64, 66, 67, 68], "diagnosisstr": 64, "discharg": [64, 65], "discharge_date_tim": 65, "distinct": 40, "document": [2, 3], "drop": 41, "dropempti": 42, "dropnul": 43, "each": 65, "eicu": [6, 7, 64], "eicuqueri": [7, 64], "encount": [64, 65, 66, 67], "end": 68, "event": 66, "exampl": [64, 65, 66, 67, 68], "extracttimestampcompon": 44, "femal": [64, 66, 67, 68], "fillnul": 45, "filter": 67, "from": [65, 67], "gastroenter": 66, "gemini": [8, 9, 65], "geminiqueri": [9, 65], "get": [3, 64, 65, 66, 67, 68], "glucos": 64, "groupbyaggreg": 46, "guidelin": 1, "have": 66, "hemoglobin": 67, "hook": 1, "hospit": [64, 65], "how": 65, "icd": [66, 67], "iii": 66, "import": [64, 65, 66, 67, 68], "index": 67, "infecti": 67, "instal": 3, "instanti": [64, 65, 66, 67, 68], "interfac": [10, 11], "iv": 67, "join": 47, "keep": [48, 65], "keyword": 67, "lab": [64, 66, 67], "later": 67, "less": 66, "limit": [49, 64], "liter": 50, "long": [66, 67], "lymphadenopathi": 67, "mai": 65, "male": 66, "mani": 65, "march": 65, "measur": 68, "medic": 64, "mimic": [66, 67], "mimiciii": [12, 13], "mimiciiiqueri": [13, 66], "mimiciv": [14, 15], "mimicivqueri": [15, 67], "mortal": [66, 68], "most": 65, "number": 65, "occur": 67, "omop": [16, 17, 68], "omopqueri": [17, 68], "one": 65, "onli": 65, "op": [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67], "orderbi": 52, "outcom": [66, 68], "partit": 67, "patient": [64, 65, 66, 67, 68], "patient_id_hash": 65, "per": 65, "pip": 3, "place": 65, "poetri": 3, "postgresql": 3, "potassium": [64, 66], "pre": 1, "queri": 3, "queryinterfac": 11, "queryop": 53, "radiologi": 67, "randomizeord": 54, "raw": 67, "recent": 65, "record": 65, "refer": 0, "renam": 55, "reorder": 56, "reorderaft": 57, "report": 67, "return": 67, "routin": 67, "row": 64, "run": 67, "schizophrenia": [64, 67], "search": 64, "sepsi": 68, "sequenti": 58, "set": 65, "sign": 67, "sodium": 65, "sort": 65, "sql": 67, "start": 3, "string": 67, "subject_id": 67, "subset": 65, "substr": [59, 64], "tabl": 65, "take": 65, "teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file diff --git a/tutorials/eicu.html b/tutorials/eicu.html index e890d4e..aa16a5f 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -615,7 +615,7 @@
-2024-10-11 12:16:16,456 INFO cycquery.orm - Database setup, ready to run queries!
+2024-11-18 13:30:52,586 INFO cycquery.orm - Database setup, ready to run queries!
@@ -679,7 +679,7 @@ Example 1. Get all female patients discharged in 2014 (limit to 100 rows).
-2024-10-11 12:16:17,526 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:30:54,052 INFO cycquery.orm - Query returned successfully!
@@ -687,7 +687,7 @@ Example 1. Get all female patients discharged in 2014 (limit to 100 rows).
-2024-10-11 12:16:17,528 INFO cycquery.utils.profile - Finished executing function run_query in 0.313798 s
+2024-11-18 13:30:54,054 INFO cycquery.utils.profile - Finished executing function run_query in 0.811666 s
@@ -722,7 +722,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-10-11 12:16:18,328 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:30:58,915 INFO cycquery.orm - Query returned successfully!
@@ -730,7 +730,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-10-11 12:16:18,330 INFO cycquery.utils.profile - Finished executing function run_query in 0.772340 s
+2024-11-18 13:30:58,918 INFO cycquery.utils.profile - Finished executing function run_query in 4.833422 s
@@ -771,7 +771,7 @@ Example 3. Get potassium lab tests for patients discharged in the year 2014,
-2024-10-11 12:16:18,812 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:30:59,552 INFO cycquery.orm - Query returned successfully!
@@ -779,7 +779,7 @@ Example 3. Get potassium lab tests for patients discharged in the year 2014,
-2024-10-11 12:16:18,814 INFO cycquery.utils.profile - Finished executing function run_query in 0.437879 s
+2024-11-18 13:30:59,554 INFO cycquery.utils.profile - Finished executing function run_query in 0.591667 s
@@ -818,7 +818,7 @@ Example 4. Get glucose medications (substring search) for female patients di
-2024-10-11 12:16:22,190 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:31:00,852 INFO cycquery.orm - Query returned successfully!
@@ -826,7 +826,7 @@ Example 4. Get glucose medications (substring search) for female patients di
-2024-10-11 12:16:22,192 INFO cycquery.utils.profile - Finished executing function run_query in 3.339489 s
+2024-11-18 13:31:00,855 INFO cycquery.utils.profile - Finished executing function run_query in 1.260199 s
diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb
index 13b51b6..5d3a327 100644
--- a/tutorials/eicu.ipynb
+++ b/tutorials/eicu.ipynb
@@ -35,10 +35,10 @@
"id": "75a140e0-fb27-4319-862f-be54397abe5c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:14.395332Z",
- "iopub.status.busy": "2024-10-11T16:16:14.394373Z",
- "iopub.status.idle": "2024-10-11T16:16:17.192986Z",
- "shell.execute_reply": "2024-10-11T16:16:17.191281Z"
+ "iopub.execute_input": "2024-11-18T18:30:47.656852Z",
+ "iopub.status.busy": "2024-11-18T18:30:47.655825Z",
+ "iopub.status.idle": "2024-11-18T18:30:53.223562Z",
+ "shell.execute_reply": "2024-11-18T18:30:53.221878Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:16,456 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-11-18 13:30:52,586 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -124,10 +124,10 @@
"id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:17.201046Z",
- "iopub.status.busy": "2024-10-11T16:16:17.199490Z",
- "iopub.status.idle": "2024-10-11T16:16:17.535427Z",
- "shell.execute_reply": "2024-10-11T16:16:17.533788Z"
+ "iopub.execute_input": "2024-11-18T18:30:53.231357Z",
+ "iopub.status.busy": "2024-11-18T18:30:53.230060Z",
+ "iopub.status.idle": "2024-11-18T18:30:54.061622Z",
+ "shell.execute_reply": "2024-11-18T18:30:54.059943Z"
},
"tags": []
},
@@ -136,14 +136,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:17,526 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:30:54,052 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:17,528 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.313798 s\n"
+ "2024-11-18 13:30:54,054 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.811666 s\n"
]
},
{
@@ -180,10 +180,10 @@
"id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:17.542086Z",
- "iopub.status.busy": "2024-10-11T16:16:17.541509Z",
- "iopub.status.idle": "2024-10-11T16:16:18.337790Z",
- "shell.execute_reply": "2024-10-11T16:16:18.336076Z"
+ "iopub.execute_input": "2024-11-18T18:30:54.069200Z",
+ "iopub.status.busy": "2024-11-18T18:30:54.067912Z",
+ "iopub.status.idle": "2024-11-18T18:30:58.925263Z",
+ "shell.execute_reply": "2024-11-18T18:30:58.923350Z"
},
"tags": []
},
@@ -192,14 +192,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:18,328 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:30:58,915 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:18,330 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.772340 s\n"
+ "2024-11-18 13:30:58,918 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.833422 s\n"
]
},
{
@@ -236,10 +236,10 @@
"id": "24043abc-1878-4e00-8229-36d4a0368b98",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:18.345835Z",
- "iopub.status.busy": "2024-10-11T16:16:18.344194Z",
- "iopub.status.idle": "2024-10-11T16:16:18.821427Z",
- "shell.execute_reply": "2024-10-11T16:16:18.819582Z"
+ "iopub.execute_input": "2024-11-18T18:30:58.932972Z",
+ "iopub.status.busy": "2024-11-18T18:30:58.931874Z",
+ "iopub.status.idle": "2024-11-18T18:30:59.561355Z",
+ "shell.execute_reply": "2024-11-18T18:30:59.559701Z"
},
"tags": []
},
@@ -248,14 +248,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:18,812 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:30:59,552 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:18,814 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.437879 s\n"
+ "2024-11-18 13:30:59,554 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.591667 s\n"
]
},
{
@@ -298,10 +298,10 @@
"id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:18.829291Z",
- "iopub.status.busy": "2024-10-11T16:16:18.827435Z",
- "iopub.status.idle": "2024-10-11T16:16:22.200132Z",
- "shell.execute_reply": "2024-10-11T16:16:22.198384Z"
+ "iopub.execute_input": "2024-11-18T18:30:59.568871Z",
+ "iopub.status.busy": "2024-11-18T18:30:59.567673Z",
+ "iopub.status.idle": "2024-11-18T18:31:00.862715Z",
+ "shell.execute_reply": "2024-11-18T18:31:00.860731Z"
},
"tags": []
},
@@ -310,14 +310,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:22,190 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:31:00,852 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:22,192 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.339489 s\n"
+ "2024-11-18 13:31:00,855 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.260199 s\n"
]
},
{
diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html
index 72d9403..2228c0a 100644
--- a/tutorials/mimiciii.html
+++ b/tutorials/mimiciii.html
@@ -615,7 +615,7 @@ Imports and instantiate
-2024-10-11 12:16:35,205 INFO cycquery.orm - Database setup, ready to run queries!
+2024-11-18 13:31:15,893 INFO cycquery.orm - Database setup, ready to run queries!
@@ -649,7 +649,7 @@ Example 1. Get all male patients with a mortality outcome.
-2024-10-11 12:16:41,589 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:31:22,132 INFO cycquery.orm - Query returned successfully!
@@ -657,7 +657,7 @@ Example 1. Get all male patients with a mortality outcome.
-2024-10-11 12:16:41,591 INFO cycquery.utils.profile - Finished executing function run_query in 0.195912 s
+2024-11-18 13:31:22,134 INFO cycquery.utils.profile - Finished executing function run_query in 0.221651 s
@@ -697,7 +697,7 @@ Example 2. Get all female patient encounters with diagnoses (
-2024-10-11 12:16:43,304 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:31:26,929 INFO cycquery.orm - Query returned successfully!
@@ -705,7 +705,7 @@ Example 2. Get all female patient encounters with diagnoses (
-2024-10-11 12:16:43,307 INFO cycquery.utils.profile - Finished executing function run_query in 1.670621 s
+2024-11-18 13:31:26,931 INFO cycquery.utils.profile - Finished executing function run_query in 4.744756 s
@@ -737,7 +737,7 @@ Example 3. Get potassium lab tests for female patients.
-2024-10-11 12:16:43,597 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:31:27,413 INFO cycquery.orm - Query returned successfully!
@@ -745,7 +745,7 @@ Example 3. Get potassium lab tests for female patients.
-2024-10-11 12:16:43,599 INFO cycquery.utils.profile - Finished executing function run_query in 0.243015 s
+2024-11-18 13:31:27,415 INFO cycquery.utils.profile - Finished executing function run_query in 0.431917 s
@@ -782,7 +782,7 @@ Example 4. Get AaDO2 carevue chart events for male patients that have a
-2024-10-11 12:26:13,416 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:56:33,762 INFO cycquery.orm - Query returned successfully!
@@ -790,7 +790,7 @@ Example 4. Get AaDO2 carevue chart events for male patients that have a
-2024-10-11 12:26:13,418 INFO cycquery.utils.profile - Finished executing function run_query in 569.750540 s
+2024-11-18 13:56:33,765 INFO cycquery.utils.profile - Finished executing function run_query in 1506.287530 s
diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb
index b0cb6a8..b04c552 100644
--- a/tutorials/mimiciii.ipynb
+++ b/tutorials/mimiciii.ipynb
@@ -35,10 +35,10 @@
"id": "75a140e0-fb27-4319-862f-be54397abe5c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:27.594684Z",
- "iopub.status.busy": "2024-10-11T16:16:27.594107Z",
- "iopub.status.idle": "2024-10-11T16:16:41.379078Z",
- "shell.execute_reply": "2024-10-11T16:16:41.377066Z"
+ "iopub.execute_input": "2024-11-18T18:31:06.641315Z",
+ "iopub.status.busy": "2024-11-18T18:31:06.639910Z",
+ "iopub.status.idle": "2024-11-18T18:31:21.895403Z",
+ "shell.execute_reply": "2024-11-18T18:31:21.893588Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:35,205 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-11-18 13:31:15,893 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -94,10 +94,10 @@
"id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:41.387034Z",
- "iopub.status.busy": "2024-10-11T16:16:41.385726Z",
- "iopub.status.idle": "2024-10-11T16:16:41.598909Z",
- "shell.execute_reply": "2024-10-11T16:16:41.597134Z"
+ "iopub.execute_input": "2024-11-18T18:31:21.904323Z",
+ "iopub.status.busy": "2024-11-18T18:31:21.902083Z",
+ "iopub.status.idle": "2024-11-18T18:31:22.142073Z",
+ "shell.execute_reply": "2024-11-18T18:31:22.140331Z"
},
"tags": []
},
@@ -106,14 +106,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:41,589 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:31:22,132 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:41,591 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.195912 s\n"
+ "2024-11-18 13:31:22,134 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.221651 s\n"
]
},
{
@@ -150,10 +150,10 @@
"id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:41.606274Z",
- "iopub.status.busy": "2024-10-11T16:16:41.605493Z",
- "iopub.status.idle": "2024-10-11T16:16:43.314273Z",
- "shell.execute_reply": "2024-10-11T16:16:43.312502Z"
+ "iopub.execute_input": "2024-11-18T18:31:22.149518Z",
+ "iopub.status.busy": "2024-11-18T18:31:22.148465Z",
+ "iopub.status.idle": "2024-11-18T18:31:26.938685Z",
+ "shell.execute_reply": "2024-11-18T18:31:26.936928Z"
},
"tags": []
},
@@ -162,14 +162,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:43,304 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:31:26,929 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:43,307 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.670621 s\n"
+ "2024-11-18 13:31:26,931 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.744756 s\n"
]
},
{
@@ -211,10 +211,10 @@
"id": "24043abc-1878-4e00-8229-36d4a0368b98",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:43.322609Z",
- "iopub.status.busy": "2024-10-11T16:16:43.321014Z",
- "iopub.status.idle": "2024-10-11T16:16:43.607302Z",
- "shell.execute_reply": "2024-10-11T16:16:43.605541Z"
+ "iopub.execute_input": "2024-11-18T18:31:26.946489Z",
+ "iopub.status.busy": "2024-11-18T18:31:26.945207Z",
+ "iopub.status.idle": "2024-11-18T18:31:27.423752Z",
+ "shell.execute_reply": "2024-11-18T18:31:27.421812Z"
},
"tags": []
},
@@ -223,14 +223,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:43,597 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:31:27,413 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:16:43,599 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.243015 s\n"
+ "2024-11-18 13:31:27,415 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.431917 s\n"
]
},
{
@@ -264,10 +264,10 @@
"id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:16:43.614733Z",
- "iopub.status.busy": "2024-10-11T16:16:43.613854Z",
- "iopub.status.idle": "2024-10-11T16:26:13.425794Z",
- "shell.execute_reply": "2024-10-11T16:26:13.424001Z"
+ "iopub.execute_input": "2024-11-18T18:31:27.431137Z",
+ "iopub.status.busy": "2024-11-18T18:31:27.430058Z",
+ "iopub.status.idle": "2024-11-18T18:56:33.773608Z",
+ "shell.execute_reply": "2024-11-18T18:56:33.771783Z"
},
"tags": []
},
@@ -276,14 +276,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:13,416 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:56:33,762 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:13,418 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 569.750540 s\n"
+ "2024-11-18 13:56:33,765 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1506.287530 s\n"
]
},
{
diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html
index 6dc89d6..3d2b200 100644
--- a/tutorials/mimiciv.html
+++ b/tutorials/mimiciv.html
@@ -615,7 +615,7 @@ Imports and instantiate
-2024-10-11 12:26:26,259 INFO cycquery.orm - Database setup, ready to run queries!
+2024-11-18 13:57:19,010 INFO cycquery.orm - Database setup, ready to run queries!
@@ -660,7 +660,7 @@ Example 1. Get all patient admissions from 2021 or later (approx year of adm
-2024-10-11 12:26:29,154 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:57:21,650 INFO cycquery.orm - Query returned successfully!
@@ -668,7 +668,7 @@ Example 1. Get all patient admissions from 2021 or later (approx year of adm
-2024-10-11 12:26:29,156 INFO cycquery.utils.profile - Finished executing function run_query in 0.515460 s
+2024-11-18 13:57:21,652 INFO cycquery.utils.profile - Finished executing function run_query in 0.341396 s
@@ -713,7 +713,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-10-11 12:26:36,327 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:57:24,496 INFO cycquery.orm - Query returned successfully!
@@ -721,7 +721,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-10-11 12:26:36,330 INFO cycquery.utils.profile - Finished executing function run_query in 7.096999 s
+2024-11-18 13:57:24,498 INFO cycquery.utils.profile - Finished executing function run_query in 2.768936 s
@@ -766,7 +766,7 @@ Example 3. Advanced - uses
-2024-10-11 12:26:40,202 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:57:28,263 INFO cycquery.orm - Query returned successfully!
@@ -774,7 +774,7 @@ Example 3. Advanced - uses
-2024-10-11 12:26:40,204 INFO cycquery.utils.profile - Finished executing function run_query in 3.800780 s
+2024-11-18 13:57:28,265 INFO cycquery.utils.profile - Finished executing function run_query in 3.694855 s
@@ -815,7 +815,7 @@ Example 4. Get routine vital signs for patients from year 2015.
-2024-10-11 12:26:44,028 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:57:32,501 INFO cycquery.orm - Query returned successfully!
@@ -823,7 +823,7 @@ Example 4. Get routine vital signs for patients from year 2015.
-2024-10-11 12:26:44,030 INFO cycquery.utils.profile - Finished executing function run_query in 3.759222 s
+2024-11-18 13:57:32,503 INFO cycquery.utils.profile - Finished executing function run_query in 4.164706 s
@@ -864,7 +864,7 @@ Example 5. Get hemoglobin lab tests for patients from year 2009.
-2024-10-11 12:26:49,580 INFO cycquery.orm - Query returned successfully!
+2024-11-18 13:57:37,054 INFO cycquery.orm - Query returned successfully!
@@ -872,7 +872,7 @@ Example 5. Get hemoglobin lab tests for patients from year 2009.
-2024-10-11 12:26:49,582 INFO cycquery.utils.profile - Finished executing function run_query in 5.479934 s
+2024-11-18 13:57:37,056 INFO cycquery.utils.profile - Finished executing function run_query in 4.479179 s
@@ -919,7 +919,7 @@ Example 6. Get radiology reports and filter on keywords
-2024-10-11 12:28:00,509 INFO cycquery.orm - Query returned successfully!
+2024-11-18 14:00:46,077 INFO cycquery.orm - Query returned successfully!
@@ -927,7 +927,7 @@ Example 6. Get radiology reports and filter on keywords
-2024-10-11 12:28:00,511 INFO cycquery.utils.profile - Finished executing function run_query in 70.867995 s
+2024-11-18 14:00:46,082 INFO cycquery.utils.profile - Finished executing function run_query in 188.960034 s
@@ -970,7 +970,7 @@ Example 7. Get all female patient encounters from year 2015, and return batc
-2024-10-11 12:28:01,742 INFO cycquery.orm - Query returned successfully!
+2024-11-18 14:00:47,284 INFO cycquery.orm - Query returned successfully!
@@ -978,7 +978,7 @@ Example 7. Get all female patient encounters from year 2015, and return batc
-2024-10-11 12:28:01,744 INFO cycquery.utils.profile - Finished executing function run_query in 1.131031 s
+2024-11-18 14:00:47,286 INFO cycquery.utils.profile - Finished executing function run_query in 1.095679 s
@@ -1006,7 +1006,7 @@ Example 8. Running a raw SQL string.
-2024-10-11 12:28:02,130 INFO cycquery.orm - Query returned successfully!
+2024-11-18 14:00:47,901 INFO cycquery.orm - Query returned successfully!
@@ -1014,7 +1014,7 @@ Example 8. Running a raw SQL string.
-2024-10-11 12:28:02,132 INFO cycquery.utils.profile - Finished executing function run_query in 0.014000 s
+2024-11-18 14:00:47,903 INFO cycquery.utils.profile - Finished executing function run_query in 0.013449 s
diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb
index fca240b..dac0749 100644
--- a/tutorials/mimiciv.ipynb
+++ b/tutorials/mimiciv.ipynb
@@ -35,10 +35,10 @@
"id": "53009e6b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:26:20.893763Z",
- "iopub.status.busy": "2024-10-11T16:26:20.892772Z",
- "iopub.status.idle": "2024-10-11T16:26:28.596124Z",
- "shell.execute_reply": "2024-10-11T16:26:28.594168Z"
+ "iopub.execute_input": "2024-11-18T18:57:05.220944Z",
+ "iopub.status.busy": "2024-11-18T18:57:05.219652Z",
+ "iopub.status.idle": "2024-11-18T18:57:21.265336Z",
+ "shell.execute_reply": "2024-11-18T18:57:21.263541Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:26,259 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-11-18 13:57:19,010 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -105,10 +105,10 @@
"id": "cdfadaa4-6fd6-4fd7-85cf-e012aa0799e1",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:26:28.603888Z",
- "iopub.status.busy": "2024-10-11T16:26:28.602564Z",
- "iopub.status.idle": "2024-10-11T16:26:29.164140Z",
- "shell.execute_reply": "2024-10-11T16:26:29.162361Z"
+ "iopub.execute_input": "2024-11-18T18:57:21.272877Z",
+ "iopub.status.busy": "2024-11-18T18:57:21.271879Z",
+ "iopub.status.idle": "2024-11-18T18:57:21.659605Z",
+ "shell.execute_reply": "2024-11-18T18:57:21.657927Z"
}
},
"outputs": [
@@ -116,14 +116,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:29,154 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:57:21,650 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:29,156 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.515460 s\n"
+ "2024-11-18 13:57:21,652 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.341396 s\n"
]
},
{
@@ -160,10 +160,10 @@
"id": "a89a9cf0",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:26:29.171233Z",
- "iopub.status.busy": "2024-10-11T16:26:29.170359Z",
- "iopub.status.idle": "2024-10-11T16:26:36.337665Z",
- "shell.execute_reply": "2024-10-11T16:26:36.335907Z"
+ "iopub.execute_input": "2024-11-18T18:57:21.666618Z",
+ "iopub.status.busy": "2024-11-18T18:57:21.665868Z",
+ "iopub.status.idle": "2024-11-18T18:57:24.504847Z",
+ "shell.execute_reply": "2024-11-18T18:57:24.503223Z"
}
},
"outputs": [
@@ -171,14 +171,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:36,327 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:57:24,496 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:36,330 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 7.096999 s\n"
+ "2024-11-18 13:57:24,498 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.768936 s\n"
]
},
{
@@ -225,10 +225,10 @@
"id": "03936cee",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:26:36.345397Z",
- "iopub.status.busy": "2024-10-11T16:26:36.344286Z",
- "iopub.status.idle": "2024-10-11T16:26:40.212468Z",
- "shell.execute_reply": "2024-10-11T16:26:40.210633Z"
+ "iopub.execute_input": "2024-11-18T18:57:24.511603Z",
+ "iopub.status.busy": "2024-11-18T18:57:24.510995Z",
+ "iopub.status.idle": "2024-11-18T18:57:28.272749Z",
+ "shell.execute_reply": "2024-11-18T18:57:28.271075Z"
}
},
"outputs": [
@@ -236,14 +236,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:40,202 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:57:28,263 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:40,204 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.800780 s\n"
+ "2024-11-18 13:57:28,265 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.694855 s\n"
]
},
{
@@ -290,10 +290,10 @@
"id": "56a72377",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:26:40.219503Z",
- "iopub.status.busy": "2024-10-11T16:26:40.218094Z",
- "iopub.status.idle": "2024-10-11T16:26:44.037378Z",
- "shell.execute_reply": "2024-10-11T16:26:44.035667Z"
+ "iopub.execute_input": "2024-11-18T18:57:28.280474Z",
+ "iopub.status.busy": "2024-11-18T18:57:28.279209Z",
+ "iopub.status.idle": "2024-11-18T18:57:32.511209Z",
+ "shell.execute_reply": "2024-11-18T18:57:32.509291Z"
}
},
"outputs": [
@@ -301,14 +301,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:44,028 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:57:32,501 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:44,030 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.759222 s\n"
+ "2024-11-18 13:57:32,503 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.164706 s\n"
]
},
{
@@ -351,10 +351,10 @@
"id": "bce11f81",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:26:44.044013Z",
- "iopub.status.busy": "2024-10-11T16:26:44.042940Z",
- "iopub.status.idle": "2024-10-11T16:26:49.589361Z",
- "shell.execute_reply": "2024-10-11T16:26:49.587659Z"
+ "iopub.execute_input": "2024-11-18T18:57:32.518840Z",
+ "iopub.status.busy": "2024-11-18T18:57:32.517548Z",
+ "iopub.status.idle": "2024-11-18T18:57:37.064960Z",
+ "shell.execute_reply": "2024-11-18T18:57:37.062867Z"
}
},
"outputs": [
@@ -362,14 +362,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:49,580 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 13:57:37,054 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:26:49,582 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.479934 s\n"
+ "2024-11-18 13:57:37,056 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.479179 s\n"
]
},
{
@@ -412,10 +412,10 @@
"id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:26:49.596516Z",
- "iopub.status.busy": "2024-10-11T16:26:49.595448Z",
- "iopub.status.idle": "2024-10-11T16:28:00.518971Z",
- "shell.execute_reply": "2024-10-11T16:28:00.517229Z"
+ "iopub.execute_input": "2024-11-18T18:57:37.072878Z",
+ "iopub.status.busy": "2024-11-18T18:57:37.071534Z",
+ "iopub.status.idle": "2024-11-18T19:00:46.090178Z",
+ "shell.execute_reply": "2024-11-18T19:00:46.088400Z"
},
"tags": []
},
@@ -424,14 +424,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:00,509 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 14:00:46,077 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:00,511 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 70.867995 s\n"
+ "2024-11-18 14:00:46,082 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 188.960034 s\n"
]
},
{
@@ -480,10 +480,10 @@
"id": "28683d70-376e-4d9b-883d-1a7de634e455",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:28:00.526105Z",
- "iopub.status.busy": "2024-10-11T16:28:00.525303Z",
- "iopub.status.idle": "2024-10-11T16:28:02.108507Z",
- "shell.execute_reply": "2024-10-11T16:28:02.106665Z"
+ "iopub.execute_input": "2024-11-18T19:00:46.098516Z",
+ "iopub.status.busy": "2024-11-18T19:00:46.097415Z",
+ "iopub.status.idle": "2024-11-18T19:00:47.879618Z",
+ "shell.execute_reply": "2024-11-18T19:00:47.877919Z"
}
},
"outputs": [
@@ -491,14 +491,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:01,742 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 14:00:47,284 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:01,744 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.131031 s\n"
+ "2024-11-18 14:00:47,286 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.095679 s\n"
]
},
{
@@ -543,10 +543,10 @@
"id": "a853deec",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:28:02.116016Z",
- "iopub.status.busy": "2024-10-11T16:28:02.114890Z",
- "iopub.status.idle": "2024-10-11T16:28:02.139558Z",
- "shell.execute_reply": "2024-10-11T16:28:02.137899Z"
+ "iopub.execute_input": "2024-11-18T19:00:47.887307Z",
+ "iopub.status.busy": "2024-11-18T19:00:47.886022Z",
+ "iopub.status.idle": "2024-11-18T19:00:47.910074Z",
+ "shell.execute_reply": "2024-11-18T19:00:47.908472Z"
},
"tags": []
},
@@ -555,14 +555,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:02,130 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 14:00:47,901 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:02,132 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.014000 s\n"
+ "2024-11-18 14:00:47,903 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013449 s\n"
]
},
{
diff --git a/tutorials/omop.html b/tutorials/omop.html
index 50cf19c..17a528e 100644
--- a/tutorials/omop.html
+++ b/tutorials/omop.html
@@ -623,7 +623,7 @@ Imports and instantiate
-2024-10-11 12:28:11,217 INFO cycquery.orm - Database setup, ready to run queries!
+2024-11-18 14:00:56,667 INFO cycquery.orm - Database setup, ready to run queries!
@@ -698,7 +698,7 @@ Example 1. Get all patient visits in or after 2010.
-2024-10-11 12:28:12,837 INFO cycquery.orm - Query returned successfully!
+2024-11-18 14:00:59,409 INFO cycquery.orm - Query returned successfully!
@@ -706,7 +706,7 @@ Example 1. Get all patient visits in or after 2010.
-2024-10-11 12:28:12,838 INFO cycquery.utils.profile - Finished executing function run_query in 0.328618 s
+2024-11-18 14:00:59,411 INFO cycquery.utils.profile - Finished executing function run_query in 1.546872 s
@@ -764,7 +764,7 @@ Example 2. Get measurements for all visits in or after 2020.
-2024-10-11 12:28:13,854 INFO cycquery.orm - Query returned successfully!
+2024-11-18 14:01:01,867 INFO cycquery.orm - Query returned successfully!
@@ -772,7 +772,7 @@ Example 2. Get measurements for all visits in or after 2020.
-2024-10-11 12:28:13,856 INFO cycquery.utils.profile - Finished executing function run_query in 0.691309 s
+2024-11-18 14:01:01,868 INFO cycquery.utils.profile - Finished executing function run_query in 1.683107 s
@@ -818,7 +818,7 @@ Imports and instantiate
-2024-10-11 12:28:21,190 INFO cycquery.orm - Database setup, ready to run queries!
+2024-11-18 14:01:10,962 INFO cycquery.orm - Database setup, ready to run queries!
@@ -858,7 +858,7 @@ Example 1. Get all patient visits that ended in a mortality outcome in or af
-2024-10-11 12:28:28,979 INFO cycquery.orm - Query returned successfully!
+2024-11-18 14:01:19,696 INFO cycquery.orm - Query returned successfully!
@@ -866,7 +866,7 @@ Example 1. Get all patient visits that ended in a mortality outcome in or af
-2024-10-11 12:28:28,981 INFO cycquery.utils.profile - Finished executing function run_query in 1.169106 s
+2024-11-18 14:01:19,698 INFO cycquery.utils.profile - Finished executing function run_query in 2.550324 s
@@ -922,7 +922,7 @@ Example 2. Get all measurements for female patient visits with
-2024-10-11 12:32:34,822 INFO cycquery.orm - Query returned successfully!
+2024-11-18 14:08:02,342 INFO cycquery.orm - Query returned successfully!
@@ -930,7 +930,7 @@ Example 2. Get all measurements for female patient visits with
-2024-10-11 12:32:34,824 INFO cycquery.utils.profile - Finished executing function run_query in 245.573900 s
+2024-11-18 14:08:02,344 INFO cycquery.utils.profile - Finished executing function run_query in 402.379286 s
@@ -956,8 +956,10 @@ Example 2. Get all measurements for female patient visits with
measurement_concept_name
-Body weight 51
-No matching concept 49
+Urine output 78
+No matching concept 13
+Output.stool [Volume] 6
+Fluid output.nasogastric tube Measured 3
Name: count, dtype: int64[pyarrow]
diff --git a/tutorials/omop.ipynb b/tutorials/omop.ipynb
index 4c10e06..d5d0d6b 100644
--- a/tutorials/omop.ipynb
+++ b/tutorials/omop.ipynb
@@ -45,10 +45,10 @@
"id": "53009e6b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:28:06.720179Z",
- "iopub.status.busy": "2024-10-11T16:28:06.719099Z",
- "iopub.status.idle": "2024-10-11T16:28:12.458670Z",
- "shell.execute_reply": "2024-10-11T16:28:12.456929Z"
+ "iopub.execute_input": "2024-11-18T19:00:53.149077Z",
+ "iopub.status.busy": "2024-11-18T19:00:53.147768Z",
+ "iopub.status.idle": "2024-11-18T19:00:57.813070Z",
+ "shell.execute_reply": "2024-11-18T19:00:57.811248Z"
}
},
"outputs": [
@@ -56,7 +56,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:11,217 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-11-18 14:00:56,667 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -151,10 +151,10 @@
"id": "3a3d9cb9-fe40-45b8-ba2f-8de52a3b7f4f",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:28:12.466027Z",
- "iopub.status.busy": "2024-10-11T16:28:12.464963Z",
- "iopub.status.idle": "2024-10-11T16:28:13.052933Z",
- "shell.execute_reply": "2024-10-11T16:28:13.051255Z"
+ "iopub.execute_input": "2024-11-18T19:00:57.820866Z",
+ "iopub.status.busy": "2024-11-18T19:00:57.819381Z",
+ "iopub.status.idle": "2024-11-18T19:01:00.072645Z",
+ "shell.execute_reply": "2024-11-18T19:01:00.070783Z"
}
},
"outputs": [
@@ -162,14 +162,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:12,837 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 14:00:59,409 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:12,838 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.328618 s\n"
+ "2024-11-18 14:00:59,411 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.546872 s\n"
]
},
{
@@ -227,10 +227,10 @@
"id": "030e2491-a7cc-42f3-a1ca-618212b3524c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:28:13.061057Z",
- "iopub.status.busy": "2024-10-11T16:28:13.059349Z",
- "iopub.status.idle": "2024-10-11T16:28:13.864072Z",
- "shell.execute_reply": "2024-10-11T16:28:13.862151Z"
+ "iopub.execute_input": "2024-11-18T19:01:00.080672Z",
+ "iopub.status.busy": "2024-11-18T19:01:00.079089Z",
+ "iopub.status.idle": "2024-11-18T19:01:01.876163Z",
+ "shell.execute_reply": "2024-11-18T19:01:01.874483Z"
}
},
"outputs": [
@@ -238,14 +238,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:13,854 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 14:01:01,867 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:13,856 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.691309 s\n"
+ "2024-11-18 14:01:01,868 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.683107 s\n"
]
},
{
@@ -303,10 +303,10 @@
"id": "0622b3df-2864-4f32-bd98-806019f59c50",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:28:13.872091Z",
- "iopub.status.busy": "2024-10-11T16:28:13.870966Z",
- "iopub.status.idle": "2024-10-11T16:28:27.736614Z",
- "shell.execute_reply": "2024-10-11T16:28:27.734703Z"
+ "iopub.execute_input": "2024-11-18T19:01:01.883993Z",
+ "iopub.status.busy": "2024-11-18T19:01:01.882742Z",
+ "iopub.status.idle": "2024-11-18T19:01:17.074689Z",
+ "shell.execute_reply": "2024-11-18T19:01:17.072995Z"
},
"tags": []
},
@@ -315,7 +315,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:21,190 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-11-18 14:01:10,962 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -357,10 +357,10 @@
"id": "40ff2e83-75e4-4119-aa33-26f95e63ddaa",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:28:27.744630Z",
- "iopub.status.busy": "2024-10-11T16:28:27.743292Z",
- "iopub.status.idle": "2024-10-11T16:28:28.988318Z",
- "shell.execute_reply": "2024-10-11T16:28:28.986570Z"
+ "iopub.execute_input": "2024-11-18T19:01:17.082310Z",
+ "iopub.status.busy": "2024-11-18T19:01:17.080926Z",
+ "iopub.status.idle": "2024-11-18T19:01:19.706517Z",
+ "shell.execute_reply": "2024-11-18T19:01:19.704618Z"
},
"tags": []
},
@@ -369,14 +369,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:28,979 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 14:01:19,696 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:28:28,981 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.169106 s\n"
+ "2024-11-18 14:01:19,698 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.550324 s\n"
]
},
{
@@ -419,10 +419,10 @@
"id": "46fd771c-5da7-4bce-aec7-08a5210a069b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:28:28.995249Z",
- "iopub.status.busy": "2024-10-11T16:28:28.994611Z",
- "iopub.status.idle": "2024-10-11T16:32:34.833022Z",
- "shell.execute_reply": "2024-10-11T16:32:34.830972Z"
+ "iopub.execute_input": "2024-11-18T19:01:19.714573Z",
+ "iopub.status.busy": "2024-11-18T19:01:19.713010Z",
+ "iopub.status.idle": "2024-11-18T19:08:02.352671Z",
+ "shell.execute_reply": "2024-11-18T19:08:02.350900Z"
},
"tags": []
},
@@ -431,14 +431,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:32:34,822 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-11-18 14:08:02,342 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-10-11 12:32:34,824 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 245.573900 s\n"
+ "2024-11-18 14:08:02,344 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 402.379286 s\n"
]
},
{
@@ -488,10 +488,10 @@
"id": "d20a2581-f613-4ab8-9feb-3e84b8835db1",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-10-11T16:32:34.852201Z",
- "iopub.status.busy": "2024-10-11T16:32:34.851356Z",
- "iopub.status.idle": "2024-10-11T16:32:35.021791Z",
- "shell.execute_reply": "2024-10-11T16:32:35.019701Z"
+ "iopub.execute_input": "2024-11-18T19:08:02.360216Z",
+ "iopub.status.busy": "2024-11-18T19:08:02.359176Z",
+ "iopub.status.idle": "2024-11-18T19:08:02.582276Z",
+ "shell.execute_reply": "2024-11-18T19:08:02.580609Z"
},
"tags": []
},
@@ -500,8 +500,10 @@
"data": {
"text/plain": [
"measurement_concept_name\n",
- "Body weight 51\n",
- "No matching concept 49\n",
+ "Urine output 78\n",
+ "No matching concept 13\n",
+ "Output.stool [Volume] 6\n",
+ "Fluid output.nasogastric tube Measured 3\n",
"Name: count, dtype: int64[pyarrow]"
]
},