diff --git a/searchindex.js b/searchindex.js index 2b8486b..d29b553 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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[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 +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.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 e9e5966..4f1fbcc 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -615,7 +615,7 @@
-2024-04-18 11:27:55,239 INFO cycquery.orm - Database setup, ready to run queries!
+2024-04-18 11:49:57,728 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).
-2024-04-18 11:27:56,249 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:49:58,725 INFO cycquery.orm - Query returned successfully!
@@ -687,7 +687,7 @@ Example 1. Get all female patients discharged in 2014 (limit to 100 rows).
-2024-04-18 11:27:56,250 INFO cycquery.utils.profile - Finished executing function run_query in 0.267212 s
+2024-04-18 11:49:58,727 INFO cycquery.utils.profile - Finished executing function run_query in 0.158988 s
@@ -722,7 +722,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-04-18 11:27:57,101 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:50:00,239 INFO cycquery.orm - Query returned successfully!
@@ -730,7 +730,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-04-18 11:27:57,103 INFO cycquery.utils.profile - Finished executing function run_query in 0.820597 s
+2024-04-18 11:50:00,242 INFO cycquery.utils.profile - Finished executing function run_query in 1.481393 s
@@ -771,7 +771,7 @@ Example 3. Get potassium lab tests for patients discharged in the year 2014,
-2024-04-18 11:27:57,416 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:50:00,623 INFO cycquery.orm - Query returned successfully!
@@ -779,7 +779,7 @@ Example 3. Get potassium lab tests for patients discharged in the year 2014,
-2024-04-18 11:27:57,418 INFO cycquery.utils.profile - Finished executing function run_query in 0.270279 s
+2024-04-18 11:50:00,624 INFO cycquery.utils.profile - Finished executing function run_query in 0.336015 s
@@ -818,7 +818,7 @@ Example 4. Get glucose medications (substring search) for female patients di
-2024-04-18 11:27:58,060 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:50:01,613 INFO cycquery.orm - Query returned successfully!
@@ -826,7 +826,7 @@ Example 4. Get glucose medications (substring search) for female patients di
-2024-04-18 11:27:58,062 INFO cycquery.utils.profile - Finished executing function run_query in 0.605530 s
+2024-04-18 11:50:01,615 INFO cycquery.utils.profile - Finished executing function run_query in 0.951092 s
diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb
index b5c3ce5..e638c89 100644
--- a/tutorials/eicu.ipynb
+++ b/tutorials/eicu.ipynb
@@ -35,10 +35,10 @@
"id": "75a140e0-fb27-4319-862f-be54397abe5c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:27:51.905530Z",
- "iopub.status.busy": "2024-04-18T15:27:51.904077Z",
- "iopub.status.idle": "2024-04-18T15:27:55.962358Z",
- "shell.execute_reply": "2024-04-18T15:27:55.960477Z"
+ "iopub.execute_input": "2024-04-18T15:49:55.705840Z",
+ "iopub.status.busy": "2024-04-18T15:49:55.704785Z",
+ "iopub.status.idle": "2024-04-18T15:49:58.544771Z",
+ "shell.execute_reply": "2024-04-18T15:49:58.542771Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:55,239 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-04-18 11:49:57,728 \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": "2024-04-18T15:27:55.970164Z",
- "iopub.status.busy": "2024-04-18T15:27:55.968863Z",
- "iopub.status.idle": "2024-04-18T15:27:56.258692Z",
- "shell.execute_reply": "2024-04-18T15:27:56.256831Z"
+ "iopub.execute_input": "2024-04-18T15:49:58.553316Z",
+ "iopub.status.busy": "2024-04-18T15:49:58.551443Z",
+ "iopub.status.idle": "2024-04-18T15:49:58.735570Z",
+ "shell.execute_reply": "2024-04-18T15:49:58.733602Z"
},
"tags": []
},
@@ -136,14 +136,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:56,249 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:49:58,725 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:56,250 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.267212 s\n"
+ "2024-04-18 11:49:58,727 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.158988 s\n"
]
},
{
@@ -180,10 +180,10 @@
"id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:27:56.266700Z",
- "iopub.status.busy": "2024-04-18T15:27:56.265227Z",
- "iopub.status.idle": "2024-04-18T15:27:57.110670Z",
- "shell.execute_reply": "2024-04-18T15:27:57.108809Z"
+ "iopub.execute_input": "2024-04-18T15:49:58.743169Z",
+ "iopub.status.busy": "2024-04-18T15:49:58.741993Z",
+ "iopub.status.idle": "2024-04-18T15:50:00.249238Z",
+ "shell.execute_reply": "2024-04-18T15:50:00.247357Z"
},
"tags": []
},
@@ -192,14 +192,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:57,101 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:50:00,239 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:57,103 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.820597 s\n"
+ "2024-04-18 11:50:00,242 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.481393 s\n"
]
},
{
@@ -236,10 +236,10 @@
"id": "24043abc-1878-4e00-8229-36d4a0368b98",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:27:57.118196Z",
- "iopub.status.busy": "2024-04-18T15:27:57.117110Z",
- "iopub.status.idle": "2024-04-18T15:27:57.425866Z",
- "shell.execute_reply": "2024-04-18T15:27:57.423990Z"
+ "iopub.execute_input": "2024-04-18T15:50:00.257242Z",
+ "iopub.status.busy": "2024-04-18T15:50:00.255696Z",
+ "iopub.status.idle": "2024-04-18T15:50:00.631685Z",
+ "shell.execute_reply": "2024-04-18T15:50:00.630022Z"
},
"tags": []
},
@@ -248,14 +248,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:57,416 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:50:00,623 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:57,418 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.270279 s\n"
+ "2024-04-18 11:50:00,624 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.336015 s\n"
]
},
{
@@ -298,10 +298,10 @@
"id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:27:57.433326Z",
- "iopub.status.busy": "2024-04-18T15:27:57.432264Z",
- "iopub.status.idle": "2024-04-18T15:27:58.070042Z",
- "shell.execute_reply": "2024-04-18T15:27:58.068146Z"
+ "iopub.execute_input": "2024-04-18T15:50:00.639305Z",
+ "iopub.status.busy": "2024-04-18T15:50:00.638032Z",
+ "iopub.status.idle": "2024-04-18T15:50:01.622558Z",
+ "shell.execute_reply": "2024-04-18T15:50:01.620823Z"
},
"tags": []
},
@@ -310,14 +310,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:58,060 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:50:01,613 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:27:58,062 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.605530 s\n"
+ "2024-04-18 11:50:01,615 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.951092 s\n"
]
},
{
diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html
index 509bc0b..a0fcb12 100644
--- a/tutorials/mimiciii.html
+++ b/tutorials/mimiciii.html
@@ -615,7 +615,7 @@ Imports and instantiate
-2024-04-18 11:28:10,924 INFO cycquery.orm - Database setup, ready to run queries!
+2024-04-18 11:50:14,867 INFO cycquery.orm - Database setup, ready to run queries!
@@ -649,7 +649,7 @@ Example 1. Get all male patients with a mortality outcome.
-2024-04-18 11:28:17,118 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:50:20,952 INFO cycquery.orm - Query returned successfully!
@@ -657,7 +657,7 @@ Example 1. Get all male patients with a mortality outcome.
-2024-04-18 11:28:17,120 INFO cycquery.utils.profile - Finished executing function run_query in 0.144103 s
+2024-04-18 11:50:20,954 INFO cycquery.utils.profile - Finished executing function run_query in 0.108410 s
@@ -697,7 +697,7 @@ Example 2. Get all female patient encounters with diagnoses (
-2024-04-18 11:28:19,416 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:50:22,359 INFO cycquery.orm - Query returned successfully!
@@ -705,7 +705,7 @@ Example 2. Get all female patient encounters with diagnoses (
-2024-04-18 11:28:19,419 INFO cycquery.utils.profile - Finished executing function run_query in 2.245811 s
+2024-04-18 11:50:22,361 INFO cycquery.utils.profile - Finished executing function run_query in 1.356768 s
@@ -737,7 +737,7 @@ Example 3. Get potassium lab tests for female patients.
-2024-04-18 11:28:19,820 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:50:22,596 INFO cycquery.orm - Query returned successfully!
@@ -745,7 +745,7 @@ Example 3. Get potassium lab tests for female patients.
-2024-04-18 11:28:19,821 INFO cycquery.utils.profile - Finished executing function run_query in 0.355687 s
+2024-04-18 11:50:22,598 INFO cycquery.utils.profile - Finished executing function run_query in 0.187926 s
@@ -782,7 +782,7 @@ Example 4. Get AaDO2 carevue chart events for male patients that have a
-2024-04-18 11:39:53,732 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:57:40,475 INFO cycquery.orm - Query returned successfully!
@@ -790,7 +790,7 @@ Example 4. Get AaDO2 carevue chart events for male patients that have a
-2024-04-18 11:39:53,734 INFO cycquery.utils.profile - Finished executing function run_query in 693.847932 s
+2024-04-18 11:57:40,477 INFO cycquery.utils.profile - Finished executing function run_query in 437.809877 s
diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb
index c5b688f..313b814 100644
--- a/tutorials/mimiciii.ipynb
+++ b/tutorials/mimiciii.ipynb
@@ -35,10 +35,10 @@
"id": "75a140e0-fb27-4319-862f-be54397abe5c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:28:03.644795Z",
- "iopub.status.busy": "2024-04-18T15:28:03.643680Z",
- "iopub.status.idle": "2024-04-18T15:28:16.958728Z",
- "shell.execute_reply": "2024-04-18T15:28:16.956835Z"
+ "iopub.execute_input": "2024-04-18T15:50:07.333083Z",
+ "iopub.status.busy": "2024-04-18T15:50:07.331982Z",
+ "iopub.status.idle": "2024-04-18T15:50:20.828781Z",
+ "shell.execute_reply": "2024-04-18T15:50:20.826850Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:28:10,924 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-04-18 11:50:14,867 \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": "2024-04-18T15:28:16.967253Z",
- "iopub.status.busy": "2024-04-18T15:28:16.965511Z",
- "iopub.status.idle": "2024-04-18T15:28:17.127541Z",
- "shell.execute_reply": "2024-04-18T15:28:17.125745Z"
+ "iopub.execute_input": "2024-04-18T15:50:20.836500Z",
+ "iopub.status.busy": "2024-04-18T15:50:20.835504Z",
+ "iopub.status.idle": "2024-04-18T15:50:20.961645Z",
+ "shell.execute_reply": "2024-04-18T15:50:20.959787Z"
},
"tags": []
},
@@ -106,14 +106,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:28:17,118 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:50:20,952 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:28:17,120 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.144103 s\n"
+ "2024-04-18 11:50:20,954 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.108410 s\n"
]
},
{
@@ -150,10 +150,10 @@
"id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:28:17.134933Z",
- "iopub.status.busy": "2024-04-18T15:28:17.133791Z",
- "iopub.status.idle": "2024-04-18T15:28:19.425873Z",
- "shell.execute_reply": "2024-04-18T15:28:19.424225Z"
+ "iopub.execute_input": "2024-04-18T15:50:20.968679Z",
+ "iopub.status.busy": "2024-04-18T15:50:20.967640Z",
+ "iopub.status.idle": "2024-04-18T15:50:22.369500Z",
+ "shell.execute_reply": "2024-04-18T15:50:22.367644Z"
},
"tags": []
},
@@ -162,14 +162,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:28:19,416 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:50:22,359 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:28:19,419 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.245811 s\n"
+ "2024-04-18 11:50:22,361 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.356768 s\n"
]
},
{
@@ -211,10 +211,10 @@
"id": "24043abc-1878-4e00-8229-36d4a0368b98",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:28:19.432708Z",
- "iopub.status.busy": "2024-04-18T15:28:19.431747Z",
- "iopub.status.idle": "2024-04-18T15:28:19.829082Z",
- "shell.execute_reply": "2024-04-18T15:28:19.827438Z"
+ "iopub.execute_input": "2024-04-18T15:50:22.376446Z",
+ "iopub.status.busy": "2024-04-18T15:50:22.375532Z",
+ "iopub.status.idle": "2024-04-18T15:50:22.605722Z",
+ "shell.execute_reply": "2024-04-18T15:50:22.603842Z"
},
"tags": []
},
@@ -223,14 +223,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:28:19,820 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:50:22,596 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:28:19,821 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.355687 s\n"
+ "2024-04-18 11:50:22,598 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.187926 s\n"
]
},
{
@@ -264,10 +264,10 @@
"id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:28:19.836150Z",
- "iopub.status.busy": "2024-04-18T15:28:19.835162Z",
- "iopub.status.idle": "2024-04-18T15:39:53.742670Z",
- "shell.execute_reply": "2024-04-18T15:39:53.740900Z"
+ "iopub.execute_input": "2024-04-18T15:50:22.612709Z",
+ "iopub.status.busy": "2024-04-18T15:50:22.611797Z",
+ "iopub.status.idle": "2024-04-18T15:57:40.485339Z",
+ "shell.execute_reply": "2024-04-18T15:57:40.483565Z"
},
"tags": []
},
@@ -276,14 +276,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:39:53,732 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:57:40,475 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:39:53,734 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 693.847932 s\n"
+ "2024-04-18 11:57:40,477 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 437.809877 s\n"
]
},
{
diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html
index be65abc..562d405 100644
--- a/tutorials/mimiciv.html
+++ b/tutorials/mimiciv.html
@@ -615,7 +615,7 @@ Imports and instantiate
-2024-04-18 11:40:03,490 INFO cycquery.orm - Database setup, ready to run queries!
+2024-04-18 11:57:49,853 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
-2024-04-18 11:40:05,988 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:57:52,390 INFO cycquery.orm - Query returned successfully!
@@ -668,7 +668,7 @@ Example 1. Get all patient admissions from 2021 or later (approx year of adm
-2024-04-18 11:40:05,989 INFO cycquery.utils.profile - Finished executing function run_query in 0.282214 s
+2024-04-18 11:57:52,392 INFO cycquery.utils.profile - Finished executing function run_query in 0.305880 s
@@ -713,7 +713,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-04-18 11:40:09,010 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:57:54,717 INFO cycquery.orm - Query returned successfully!
@@ -721,7 +721,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-04-18 11:40:09,012 INFO cycquery.utils.profile - Finished executing function run_query in 2.946522 s
+2024-04-18 11:57:54,719 INFO cycquery.utils.profile - Finished executing function run_query in 2.251988 s
@@ -766,7 +766,7 @@ Example 3. Advanced - uses
-2024-04-18 11:40:13,018 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:57:58,465 INFO cycquery.orm - Query returned successfully!
@@ -774,7 +774,7 @@ Example 3. Advanced - uses
-2024-04-18 11:40:13,020 INFO cycquery.utils.profile - Finished executing function run_query in 3.936798 s
+2024-04-18 11:57:58,466 INFO cycquery.utils.profile - Finished executing function run_query in 3.676533 s
@@ -815,7 +815,7 @@ Example 4. Get routine vital signs for patients from year 2015.
-2024-04-18 11:40:17,679 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:58:02,071 INFO cycquery.orm - Query returned successfully!
@@ -823,7 +823,7 @@ Example 4. Get routine vital signs for patients from year 2015.
-2024-04-18 11:40:17,681 INFO cycquery.utils.profile - Finished executing function run_query in 4.587958 s
+2024-04-18 11:58:02,072 INFO cycquery.utils.profile - Finished executing function run_query in 3.533433 s
@@ -864,7 +864,7 @@ Example 5. Get hemoglobin lab tests for patients from year 2009.
-2024-04-18 11:40:21,795 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:58:06,669 INFO cycquery.orm - Query returned successfully!
@@ -872,7 +872,7 @@ Example 5. Get hemoglobin lab tests for patients from year 2009.
-2024-04-18 11:40:21,797 INFO cycquery.utils.profile - Finished executing function run_query in 4.043617 s
+2024-04-18 11:58:06,671 INFO cycquery.utils.profile - Finished executing function run_query in 4.522759 s
@@ -919,7 +919,7 @@ Example 6. Get radiology reports and filter on keywords
-2024-04-18 11:40:33,180 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:58:18,062 INFO cycquery.orm - Query returned successfully!
@@ -927,7 +927,7 @@ Example 6. Get radiology reports and filter on keywords
-2024-04-18 11:40:33,182 INFO cycquery.utils.profile - Finished executing function run_query in 11.322607 s
+2024-04-18 11:58:18,063 INFO cycquery.utils.profile - Finished executing function run_query in 11.330467 s
@@ -970,7 +970,7 @@ Example 7. Get all female patient encounters from year 2015, and return batc
-2024-04-18 11:40:34,314 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:58:19,146 INFO cycquery.orm - Query returned successfully!
@@ -978,7 +978,7 @@ Example 7. Get all female patient encounters from year 2015, and return batc
-2024-04-18 11:40:34,317 INFO cycquery.utils.profile - Finished executing function run_query in 1.030955 s
+2024-04-18 11:58:19,147 INFO cycquery.utils.profile - Finished executing function run_query in 0.983342 s
@@ -1006,7 +1006,7 @@ Example 8. Running a raw SQL string.
-2024-04-18 11:40:34,690 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:58:19,505 INFO cycquery.orm - Query returned successfully!
@@ -1014,7 +1014,7 @@ Example 8. Running a raw SQL string.
-2024-04-18 11:40:34,692 INFO cycquery.utils.profile - Finished executing function run_query in 0.013542 s
+2024-04-18 11:58:19,506 INFO cycquery.utils.profile - Finished executing function run_query in 0.012544 s
diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb
index 3c163ab..a0d592e 100644
--- a/tutorials/mimiciv.ipynb
+++ b/tutorials/mimiciv.ipynb
@@ -35,10 +35,10 @@
"id": "53009e6b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:39:58.323475Z",
- "iopub.status.busy": "2024-04-18T15:39:58.322223Z",
- "iopub.status.idle": "2024-04-18T15:40:05.663901Z",
- "shell.execute_reply": "2024-04-18T15:40:05.662249Z"
+ "iopub.execute_input": "2024-04-18T15:57:45.701081Z",
+ "iopub.status.busy": "2024-04-18T15:57:45.700105Z",
+ "iopub.status.idle": "2024-04-18T15:57:52.041768Z",
+ "shell.execute_reply": "2024-04-18T15:57:52.040031Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:03,490 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-04-18 11:57:49,853 \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": "2024-04-18T15:40:05.671417Z",
- "iopub.status.busy": "2024-04-18T15:40:05.669944Z",
- "iopub.status.idle": "2024-04-18T15:40:05.996760Z",
- "shell.execute_reply": "2024-04-18T15:40:05.995088Z"
+ "iopub.execute_input": "2024-04-18T15:57:52.049607Z",
+ "iopub.status.busy": "2024-04-18T15:57:52.048050Z",
+ "iopub.status.idle": "2024-04-18T15:57:52.399337Z",
+ "shell.execute_reply": "2024-04-18T15:57:52.397697Z"
}
},
"outputs": [
@@ -116,14 +116,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:05,988 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:57:52,390 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:05,989 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.282214 s\n"
+ "2024-04-18 11:57:52,392 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.305880 s\n"
]
},
{
@@ -160,10 +160,10 @@
"id": "a89a9cf0",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:06.003930Z",
- "iopub.status.busy": "2024-04-18T15:40:06.002653Z",
- "iopub.status.idle": "2024-04-18T15:40:09.019118Z",
- "shell.execute_reply": "2024-04-18T15:40:09.017503Z"
+ "iopub.execute_input": "2024-04-18T15:57:52.406704Z",
+ "iopub.status.busy": "2024-04-18T15:57:52.405459Z",
+ "iopub.status.idle": "2024-04-18T15:57:54.726296Z",
+ "shell.execute_reply": "2024-04-18T15:57:54.724676Z"
}
},
"outputs": [
@@ -171,14 +171,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:09,010 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:57:54,717 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:09,012 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.946522 s\n"
+ "2024-04-18 11:57:54,719 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.251988 s\n"
]
},
{
@@ -225,10 +225,10 @@
"id": "03936cee",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:09.026281Z",
- "iopub.status.busy": "2024-04-18T15:40:09.024974Z",
- "iopub.status.idle": "2024-04-18T15:40:13.028021Z",
- "shell.execute_reply": "2024-04-18T15:40:13.026369Z"
+ "iopub.execute_input": "2024-04-18T15:57:54.733842Z",
+ "iopub.status.busy": "2024-04-18T15:57:54.732541Z",
+ "iopub.status.idle": "2024-04-18T15:57:58.474544Z",
+ "shell.execute_reply": "2024-04-18T15:57:58.472879Z"
}
},
"outputs": [
@@ -236,14 +236,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:13,018 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:57:58,465 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:13,020 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.936798 s\n"
+ "2024-04-18 11:57:58,466 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.676533 s\n"
]
},
{
@@ -290,10 +290,10 @@
"id": "56a72377",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:13.035256Z",
- "iopub.status.busy": "2024-04-18T15:40:13.033966Z",
- "iopub.status.idle": "2024-04-18T15:40:17.688619Z",
- "shell.execute_reply": "2024-04-18T15:40:17.686931Z"
+ "iopub.execute_input": "2024-04-18T15:57:58.481241Z",
+ "iopub.status.busy": "2024-04-18T15:57:58.480543Z",
+ "iopub.status.idle": "2024-04-18T15:58:02.080174Z",
+ "shell.execute_reply": "2024-04-18T15:58:02.078501Z"
}
},
"outputs": [
@@ -301,14 +301,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:17,679 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:58:02,071 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:17,681 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.587958 s\n"
+ "2024-04-18 11:58:02,072 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.533433 s\n"
]
},
{
@@ -351,10 +351,10 @@
"id": "bce11f81",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:17.695933Z",
- "iopub.status.busy": "2024-04-18T15:40:17.694711Z",
- "iopub.status.idle": "2024-04-18T15:40:21.804585Z",
- "shell.execute_reply": "2024-04-18T15:40:21.802914Z"
+ "iopub.execute_input": "2024-04-18T15:58:02.087741Z",
+ "iopub.status.busy": "2024-04-18T15:58:02.086456Z",
+ "iopub.status.idle": "2024-04-18T15:58:06.678478Z",
+ "shell.execute_reply": "2024-04-18T15:58:06.676835Z"
}
},
"outputs": [
@@ -362,14 +362,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:21,795 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:58:06,669 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:21,797 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.043617 s\n"
+ "2024-04-18 11:58:06,671 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.522759 s\n"
]
},
{
@@ -412,10 +412,10 @@
"id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:21.811786Z",
- "iopub.status.busy": "2024-04-18T15:40:21.810462Z",
- "iopub.status.idle": "2024-04-18T15:40:33.189389Z",
- "shell.execute_reply": "2024-04-18T15:40:33.187770Z"
+ "iopub.execute_input": "2024-04-18T15:58:06.686134Z",
+ "iopub.status.busy": "2024-04-18T15:58:06.684789Z",
+ "iopub.status.idle": "2024-04-18T15:58:18.070793Z",
+ "shell.execute_reply": "2024-04-18T15:58:18.069162Z"
},
"tags": []
},
@@ -424,14 +424,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:33,180 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:58:18,062 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:33,182 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 11.322607 s\n"
+ "2024-04-18 11:58:18,063 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 11.330467 s\n"
]
},
{
@@ -480,10 +480,10 @@
"id": "28683d70-376e-4d9b-883d-1a7de634e455",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:33.198425Z",
- "iopub.status.busy": "2024-04-18T15:40:33.197400Z",
- "iopub.status.idle": "2024-04-18T15:40:34.668254Z",
- "shell.execute_reply": "2024-04-18T15:40:34.666275Z"
+ "iopub.execute_input": "2024-04-18T15:58:18.078311Z",
+ "iopub.status.busy": "2024-04-18T15:58:18.077017Z",
+ "iopub.status.idle": "2024-04-18T15:58:19.484539Z",
+ "shell.execute_reply": "2024-04-18T15:58:19.482823Z"
}
},
"outputs": [
@@ -491,14 +491,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:34,314 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:58:19,146 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:34,317 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.030955 s\n"
+ "2024-04-18 11:58:19,147 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.983342 s\n"
]
},
{
@@ -543,10 +543,10 @@
"id": "a853deec",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:34.676201Z",
- "iopub.status.busy": "2024-04-18T15:40:34.674613Z",
- "iopub.status.idle": "2024-04-18T15:40:34.699461Z",
- "shell.execute_reply": "2024-04-18T15:40:34.697717Z"
+ "iopub.execute_input": "2024-04-18T15:58:19.491580Z",
+ "iopub.status.busy": "2024-04-18T15:58:19.490552Z",
+ "iopub.status.idle": "2024-04-18T15:58:19.513388Z",
+ "shell.execute_reply": "2024-04-18T15:58:19.511711Z"
},
"tags": []
},
@@ -555,14 +555,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:34,690 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:58:19,505 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:34,692 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013542 s\n"
+ "2024-04-18 11:58:19,506 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.012544 s\n"
]
},
{
diff --git a/tutorials/omop.html b/tutorials/omop.html
index fe14592..8b104ca 100644
--- a/tutorials/omop.html
+++ b/tutorials/omop.html
@@ -623,7 +623,7 @@ Imports and instantiate
-2024-04-18 11:40:41,216 INFO cycquery.orm - Database setup, ready to run queries!
+2024-04-18 11:58:26,062 INFO cycquery.orm - Database setup, ready to run queries!
@@ -698,7 +698,7 @@ Example 1. Get all patient visits in or after 2010.
-2024-04-18 11:40:42,751 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:58:27,311 INFO cycquery.orm - Query returned successfully!
@@ -706,7 +706,7 @@ Example 1. Get all patient visits in or after 2010.
-2024-04-18 11:40:42,753 INFO cycquery.utils.profile - Finished executing function run_query in 0.343278 s
+2024-04-18 11:58:27,313 INFO cycquery.utils.profile - Finished executing function run_query in 0.079233 s
@@ -764,7 +764,7 @@ Example 2. Get measurements for all visits in or after 2020.
-2024-04-18 11:40:43,525 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:58:27,700 INFO cycquery.orm - Query returned successfully!
@@ -772,7 +772,7 @@ Example 2. Get measurements for all visits in or after 2020.
-2024-04-18 11:40:43,527 INFO cycquery.utils.profile - Finished executing function run_query in 0.585587 s
+2024-04-18 11:58:27,702 INFO cycquery.utils.profile - Finished executing function run_query in 0.133449 s
@@ -818,7 +818,7 @@ Imports and instantiate
-2024-04-18 11:40:49,583 INFO cycquery.orm - Database setup, ready to run queries!
+2024-04-18 11:58:33,556 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
-2024-04-18 11:40:56,215 INFO cycquery.orm - Query returned successfully!
+2024-04-18 11:58:40,016 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
-2024-04-18 11:40:56,217 INFO cycquery.utils.profile - Finished executing function run_query in 0.668646 s
+2024-04-18 11:58:40,018 INFO cycquery.utils.profile - Finished executing function run_query in 0.515327 s
@@ -922,7 +922,7 @@ Example 2. Get all measurements for female patient visits with
-2024-04-18 11:44:19,561 INFO cycquery.orm - Query returned successfully!
+2024-04-18 12:01:57,969 INFO cycquery.orm - Query returned successfully!
@@ -930,7 +930,7 @@ Example 2. Get all measurements for female patient visits with
-2024-04-18 11:44:19,563 INFO cycquery.utils.profile - Finished executing function run_query in 203.103100 s
+2024-04-18 12:01:57,972 INFO cycquery.utils.profile - Finished executing function run_query in 197.711404 s
@@ -956,8 +956,7 @@ Example 2. Get all measurements for female patient visits with
measurement_concept_name
-Body weight 51
-No matching concept 49
+No matching concept 100
Name: count, dtype: int64[pyarrow]
diff --git a/tutorials/omop.ipynb b/tutorials/omop.ipynb
index fd0e4f9..e30491b 100644
--- a/tutorials/omop.ipynb
+++ b/tutorials/omop.ipynb
@@ -45,10 +45,10 @@
"id": "53009e6b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:38.676848Z",
- "iopub.status.busy": "2024-04-18T15:40:38.675913Z",
- "iopub.status.idle": "2024-04-18T15:40:42.356896Z",
- "shell.execute_reply": "2024-04-18T15:40:42.355236Z"
+ "iopub.execute_input": "2024-04-18T15:58:23.506589Z",
+ "iopub.status.busy": "2024-04-18T15:58:23.505642Z",
+ "iopub.status.idle": "2024-04-18T15:58:27.183069Z",
+ "shell.execute_reply": "2024-04-18T15:58:27.181364Z"
}
},
"outputs": [
@@ -56,7 +56,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:41,216 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-04-18 11:58:26,062 \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": "2024-04-18T15:40:42.368537Z",
- "iopub.status.busy": "2024-04-18T15:40:42.367042Z",
- "iopub.status.idle": "2024-04-18T15:40:42.837841Z",
- "shell.execute_reply": "2024-04-18T15:40:42.836234Z"
+ "iopub.execute_input": "2024-04-18T15:58:27.190589Z",
+ "iopub.status.busy": "2024-04-18T15:58:27.189137Z",
+ "iopub.status.idle": "2024-04-18T15:58:27.457191Z",
+ "shell.execute_reply": "2024-04-18T15:58:27.455556Z"
}
},
"outputs": [
@@ -162,14 +162,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:42,751 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:58:27,311 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:42,753 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.343278 s\n"
+ "2024-04-18 11:58:27,313 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.079233 s\n"
]
},
{
@@ -227,10 +227,10 @@
"id": "030e2491-a7cc-42f3-a1ca-618212b3524c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:42.844948Z",
- "iopub.status.busy": "2024-04-18T15:40:42.843651Z",
- "iopub.status.idle": "2024-04-18T15:40:43.534242Z",
- "shell.execute_reply": "2024-04-18T15:40:43.532632Z"
+ "iopub.execute_input": "2024-04-18T15:58:27.464684Z",
+ "iopub.status.busy": "2024-04-18T15:58:27.463355Z",
+ "iopub.status.idle": "2024-04-18T15:58:27.709222Z",
+ "shell.execute_reply": "2024-04-18T15:58:27.707570Z"
}
},
"outputs": [
@@ -238,14 +238,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:43,525 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:58:27,700 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:43,527 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.585587 s\n"
+ "2024-04-18 11:58:27,702 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.133449 s\n"
]
},
{
@@ -303,10 +303,10 @@
"id": "0622b3df-2864-4f32-bd98-806019f59c50",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:43.541576Z",
- "iopub.status.busy": "2024-04-18T15:40:43.540295Z",
- "iopub.status.idle": "2024-04-18T15:40:55.479748Z",
- "shell.execute_reply": "2024-04-18T15:40:55.478050Z"
+ "iopub.execute_input": "2024-04-18T15:58:27.716882Z",
+ "iopub.status.busy": "2024-04-18T15:58:27.715554Z",
+ "iopub.status.idle": "2024-04-18T15:58:39.434419Z",
+ "shell.execute_reply": "2024-04-18T15:58:39.432742Z"
},
"tags": []
},
@@ -315,7 +315,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:49,583 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-04-18 11:58:33,556 \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": "2024-04-18T15:40:55.486755Z",
- "iopub.status.busy": "2024-04-18T15:40:55.485756Z",
- "iopub.status.idle": "2024-04-18T15:40:56.224438Z",
- "shell.execute_reply": "2024-04-18T15:40:56.222814Z"
+ "iopub.execute_input": "2024-04-18T15:58:39.441816Z",
+ "iopub.status.busy": "2024-04-18T15:58:39.440485Z",
+ "iopub.status.idle": "2024-04-18T15:58:40.025063Z",
+ "shell.execute_reply": "2024-04-18T15:58:40.023455Z"
},
"tags": []
},
@@ -369,14 +369,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:56,215 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 11:58:40,016 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:40:56,217 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.668646 s\n"
+ "2024-04-18 11:58:40,018 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.515327 s\n"
]
},
{
@@ -419,10 +419,10 @@
"id": "46fd771c-5da7-4bce-aec7-08a5210a069b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:40:56.231225Z",
- "iopub.status.busy": "2024-04-18T15:40:56.230251Z",
- "iopub.status.idle": "2024-04-18T15:44:19.571701Z",
- "shell.execute_reply": "2024-04-18T15:44:19.569921Z"
+ "iopub.execute_input": "2024-04-18T15:58:40.032210Z",
+ "iopub.status.busy": "2024-04-18T15:58:40.031007Z",
+ "iopub.status.idle": "2024-04-18T16:01:57.979452Z",
+ "shell.execute_reply": "2024-04-18T16:01:57.977776Z"
},
"tags": []
},
@@ -431,14 +431,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:44:19,561 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-04-18 12:01:57,969 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-04-18 11:44:19,563 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 203.103100 s\n"
+ "2024-04-18 12:01:57,972 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 197.711404 s\n"
]
},
{
@@ -488,10 +488,10 @@
"id": "d20a2581-f613-4ab8-9feb-3e84b8835db1",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-04-18T15:44:19.578967Z",
- "iopub.status.busy": "2024-04-18T15:44:19.578212Z",
- "iopub.status.idle": "2024-04-18T15:44:19.737797Z",
- "shell.execute_reply": "2024-04-18T15:44:19.736052Z"
+ "iopub.execute_input": "2024-04-18T16:01:57.986229Z",
+ "iopub.status.busy": "2024-04-18T16:01:57.985501Z",
+ "iopub.status.idle": "2024-04-18T16:01:58.186112Z",
+ "shell.execute_reply": "2024-04-18T16:01:58.184452Z"
},
"tags": []
},
@@ -500,8 +500,7 @@
"data": {
"text/plain": [
"measurement_concept_name\n",
- "Body weight 51\n",
- "No matching concept 49\n",
+ "No matching concept 100\n",
"Name: count, dtype: int64[pyarrow]"
]
},