From fd377f99e8d2fc475e3a8143e8a417f3eef4a3b1 Mon Sep 17 00:00:00 2001 From: amrit110 Date: Tue, 17 Sep 2024 10:28:14 -0400 Subject: [PATCH] deploy: 8e47cda4b08167ac505022504075999b48951b49 --- searchindex.js | 2 +- tutorials/eicu.html | 18 +++---- tutorials/eicu.ipynb | 58 ++++++++++----------- tutorials/mimiciii.html | 18 +++---- tutorials/mimiciii.ipynb | 58 ++++++++++----------- tutorials/mimiciv.html | 34 ++++++------- tutorials/mimiciv.ipynb | 106 +++++++++++++++++++-------------------- tutorials/omop.html | 45 ++++++++++++----- tutorials/omop.ipynb | 101 ++++++++++++++++++++++--------------- 9 files changed, 239 insertions(+), 201 deletions(-) diff --git a/searchindex.js b/searchindex.js index 1a42e5a..35e9ae9 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. 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"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 +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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[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 3e1cfc9..fc5fad9 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-09-17 07:41:11,900 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-09-17 10:03:04,281 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). 
-2024-09-17 07:41:12,856 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:03:05,201 INFO cycquery.orm    - Query returned successfully!

@@ -687,7 +687,7 @@

Example 1. Get all female patients discharged in 2014 (limit to 100 rows). 
-2024-09-17 07:41:12,858 INFO cycquery.utils.profile - Finished executing function run_query in 0.183889 s
+2024-09-17 10:03:05,203 INFO cycquery.utils.profile - Finished executing function run_query in 0.156461 s

@@ -722,7 +722,7 @@

Example 2. Get all patient encounters with diagnoses ( 
-2024-09-17 07:41:15,369 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:03:07,833 INFO cycquery.orm    - Query returned successfully!

@@ -730,7 +730,7 @@

Example 2. Get all patient encounters with diagnoses ( 
-2024-09-17 07:41:15,371 INFO cycquery.utils.profile - Finished executing function run_query in 2.483853 s
+2024-09-17 10:03:07,835 INFO cycquery.utils.profile - Finished executing function run_query in 2.601747 s

@@ -771,7 +771,7 @@

Example 3. Get potassium lab tests for patients discharged in the year 2014, 

-2024-09-17 07:41:15,821 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:03:08,098 INFO cycquery.orm    - Query returned successfully!
@@ -779,7 +779,7 @@

Example 3. Get potassium lab tests for patients discharged in the year 2014, 

-2024-09-17 07:41:15,823 INFO cycquery.utils.profile - Finished executing function run_query in 0.407262 s
+2024-09-17 10:03:08,099 INFO cycquery.utils.profile - Finished executing function run_query in 0.220583 s
@@ -818,7 +818,7 @@

Example 4. Get glucose medications (substring search) for female patients di 

-2024-09-17 07:41:21,962 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:03:09,401 INFO cycquery.orm    - Query returned successfully!
@@ -826,7 +826,7 @@

Example 4. Get glucose medications (substring search) for female patients di 

-2024-09-17 07:41:21,964 INFO cycquery.utils.profile - Finished executing function run_query in 6.101793 s
+2024-09-17 10:03:09,403 INFO cycquery.utils.profile - Finished executing function run_query in 1.265080 s
diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb index 1d3b36f..5447d53 100644 --- a/tutorials/eicu.ipynb +++ b/tutorials/eicu.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:41:09.842152Z", - "iopub.status.busy": "2024-09-17T11:41:09.840879Z", - "iopub.status.idle": "2024-09-17T11:41:12.653328Z", - "shell.execute_reply": "2024-09-17T11:41:12.651500Z" + "iopub.execute_input": "2024-09-17T14:03:02.283750Z", + "iopub.status.busy": "2024-09-17T14:03:02.282786Z", + "iopub.status.idle": "2024-09-17T14:03:05.025269Z", + "shell.execute_reply": "2024-09-17T14:03:05.023548Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:11,900 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-09-17 10:03:04,281 \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": "2024-09-17T11:41:12.661164Z", - "iopub.status.busy": "2024-09-17T11:41:12.659623Z", - "iopub.status.idle": "2024-09-17T11:41:12.865180Z", - "shell.execute_reply": "2024-09-17T11:41:12.863532Z" + "iopub.execute_input": "2024-09-17T14:03:05.033431Z", + "iopub.status.busy": "2024-09-17T14:03:05.031939Z", + "iopub.status.idle": "2024-09-17T14:03:05.210453Z", + "shell.execute_reply": "2024-09-17T14:03:05.208794Z" }, "tags": [] }, @@ -136,14 +136,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:12,856 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:03:05,201 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:12,858 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.183889 s\n" + "2024-09-17 10:03:05,203 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.156461 s\n" ] }, { @@ -180,10 +180,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:41:12.872462Z", - "iopub.status.busy": "2024-09-17T11:41:12.871370Z", - "iopub.status.idle": "2024-09-17T11:41:15.379456Z", - "shell.execute_reply": "2024-09-17T11:41:15.377666Z" + "iopub.execute_input": "2024-09-17T14:03:05.218060Z", + "iopub.status.busy": "2024-09-17T14:03:05.216811Z", + "iopub.status.idle": "2024-09-17T14:03:07.842113Z", + "shell.execute_reply": "2024-09-17T14:03:07.840483Z" }, "tags": [] }, @@ -192,14 +192,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:15,369 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:03:07,833 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:15,371 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.483853 s\n" + "2024-09-17 10:03:07,835 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.601747 s\n" ] }, { @@ -236,10 +236,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:41:15.386815Z", - "iopub.status.busy": "2024-09-17T11:41:15.385758Z", - "iopub.status.idle": "2024-09-17T11:41:15.830851Z", - "shell.execute_reply": "2024-09-17T11:41:15.829168Z" + "iopub.execute_input": "2024-09-17T14:03:07.849876Z", + "iopub.status.busy": "2024-09-17T14:03:07.848529Z", + "iopub.status.idle": "2024-09-17T14:03:08.107187Z", + "shell.execute_reply": "2024-09-17T14:03:08.105505Z" }, "tags": [] }, @@ -248,14 +248,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:15,821 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:03:08,098 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:15,823 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.407262 s\n" + "2024-09-17 10:03:08,099 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.220583 s\n" ] }, { @@ -298,10 +298,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:41:15.838158Z", - "iopub.status.busy": "2024-09-17T11:41:15.837113Z", - "iopub.status.idle": "2024-09-17T11:41:21.971187Z", - "shell.execute_reply": "2024-09-17T11:41:21.969559Z" + "iopub.execute_input": "2024-09-17T14:03:08.114384Z", + "iopub.status.busy": "2024-09-17T14:03:08.113374Z", + "iopub.status.idle": "2024-09-17T14:03:09.411649Z", + "shell.execute_reply": "2024-09-17T14:03:09.409692Z" }, "tags": [] }, @@ -310,14 +310,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:21,962 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:03:09,401 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:21,964 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 6.101793 s\n" + "2024-09-17 10:03:09,403 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.265080 s\n" ] }, { diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html index d0e0730..0c9299f 100644 --- a/tutorials/mimiciii.html +++ b/tutorials/mimiciii.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-09-17 07:41:35,289 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-09-17 10:03:22,195 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -649,7 +649,7 @@

Example 1. Get all male patients with a mortality outcome. 
-2024-09-17 07:41:41,641 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:03:28,482 INFO cycquery.orm    - Query returned successfully!

@@ -657,7 +657,7 @@

Example 1. Get all male patients with a mortality outcome. 
-2024-09-17 07:41:41,642 INFO cycquery.utils.profile - Finished executing function run_query in 0.180899 s
+2024-09-17 10:03:28,484 INFO cycquery.utils.profile - Finished executing function run_query in 0.229596 s

@@ -697,7 +697,7 @@

Example 2. Get all female patient encounters with diagnoses ( 
-2024-09-17 07:41:44,927 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:03:32,088 INFO cycquery.orm    - Query returned successfully!

@@ -705,7 +705,7 @@

Example 2. Get all female patient encounters with diagnoses ( 
-2024-09-17 07:41:44,929 INFO cycquery.utils.profile - Finished executing function run_query in 3.234838 s
+2024-09-17 10:03:32,090 INFO cycquery.utils.profile - Finished executing function run_query in 3.552542 s

@@ -737,7 +737,7 @@

Example 3. Get potassium lab tests for female patients. 
-2024-09-17 07:41:45,306 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:03:32,382 INFO cycquery.orm    - Query returned successfully!

@@ -745,7 +745,7 @@

Example 3. Get potassium lab tests for female patients. 
-2024-09-17 07:41:45,308 INFO cycquery.utils.profile - Finished executing function run_query in 0.330425 s
+2024-09-17 10:03:32,383 INFO cycquery.utils.profile - Finished executing function run_query in 0.247521 s

@@ -782,7 +782,7 @@

Example 4. Get AaDO2 carevue chart events for male patients that have a 
-2024-09-17 07:57:34,936 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:19:27,631 INFO cycquery.orm    - Query returned successfully!

@@ -790,7 +790,7 @@

Example 4. Get AaDO2 carevue chart events for male patients that have a 
-2024-09-17 07:57:34,938 INFO cycquery.utils.profile - Finished executing function run_query in 949.564382 s
+2024-09-17 10:19:27,633 INFO cycquery.utils.profile - Finished executing function run_query in 955.184133 s

diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb index 6e9cfd8..a7d7a2d 100644 --- a/tutorials/mimiciii.ipynb +++ b/tutorials/mimiciii.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:41:27.746254Z", - "iopub.status.busy": "2024-09-17T11:41:27.745208Z", - "iopub.status.idle": "2024-09-17T11:41:41.445852Z", - "shell.execute_reply": "2024-09-17T11:41:41.444040Z" + "iopub.execute_input": "2024-09-17T14:03:14.855205Z", + "iopub.status.busy": "2024-09-17T14:03:14.854331Z", + "iopub.status.idle": "2024-09-17T14:03:28.238189Z", + "shell.execute_reply": "2024-09-17T14:03:28.236347Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:35,289 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-09-17 10:03:22,195 \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": "2024-09-17T11:41:41.453783Z", - "iopub.status.busy": "2024-09-17T11:41:41.452140Z", - "iopub.status.idle": "2024-09-17T11:41:41.649897Z", - "shell.execute_reply": "2024-09-17T11:41:41.648246Z" + "iopub.execute_input": "2024-09-17T14:03:28.246725Z", + "iopub.status.busy": "2024-09-17T14:03:28.245008Z", + "iopub.status.idle": "2024-09-17T14:03:28.492091Z", + "shell.execute_reply": "2024-09-17T14:03:28.490283Z" }, "tags": [] }, @@ -106,14 +106,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:41,641 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:03:28,482 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:41,642 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.180899 s\n" + "2024-09-17 10:03:28,484 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.229596 s\n" ] }, { @@ -150,10 +150,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:41:41.657111Z", - "iopub.status.busy": "2024-09-17T11:41:41.656213Z", - "iopub.status.idle": "2024-09-17T11:41:44.936237Z", - "shell.execute_reply": "2024-09-17T11:41:44.934493Z" + "iopub.execute_input": "2024-09-17T14:03:28.499890Z", + "iopub.status.busy": "2024-09-17T14:03:28.498502Z", + "iopub.status.idle": "2024-09-17T14:03:32.097580Z", + "shell.execute_reply": "2024-09-17T14:03:32.095851Z" }, "tags": [] }, @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:44,927 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:03:32,088 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:44,929 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.234838 s\n" + "2024-09-17 10:03:32,090 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.552542 s\n" ] }, { @@ -211,10 +211,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:41:44.944127Z", - "iopub.status.busy": "2024-09-17T11:41:44.942645Z", - "iopub.status.idle": "2024-09-17T11:41:45.315757Z", - "shell.execute_reply": "2024-09-17T11:41:45.313951Z" + "iopub.execute_input": "2024-09-17T14:03:32.104908Z", + "iopub.status.busy": "2024-09-17T14:03:32.103701Z", + "iopub.status.idle": "2024-09-17T14:03:32.391136Z", + "shell.execute_reply": "2024-09-17T14:03:32.389456Z" }, "tags": [] }, @@ -223,14 +223,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:45,306 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:03:32,382 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:41:45,308 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.330425 s\n" + "2024-09-17 10:03:32,383 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.247521 s\n" ] }, { @@ -264,10 +264,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:41:45.323295Z", - "iopub.status.busy": "2024-09-17T11:41:45.322199Z", - "iopub.status.idle": "2024-09-17T11:57:34.946511Z", - "shell.execute_reply": "2024-09-17T11:57:34.944339Z" + "iopub.execute_input": "2024-09-17T14:03:32.398472Z", + "iopub.status.busy": "2024-09-17T14:03:32.397398Z", + "iopub.status.idle": "2024-09-17T14:19:27.640657Z", + "shell.execute_reply": "2024-09-17T14:19:27.638881Z" }, "tags": [] }, @@ -276,14 +276,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:57:34,936 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:19:27,631 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:57:34,938 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 949.564382 s\n" + "2024-09-17 10:19:27,633 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 955.184133 s\n" ] }, { diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html index 54400ac..b77cb7c 100644 --- a/tutorials/mimiciv.html +++ b/tutorials/mimiciv.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-09-17 07:57:47,514 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-09-17 10:19:45,079 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 

-2024-09-17 07:57:50,574 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:19:49,461 INFO cycquery.orm    - Query returned successfully!
@@ -668,7 +668,7 @@

Example 1. Get all patient admissions from 2021 or later (approx year of adm 

-2024-09-17 07:57:50,577 INFO cycquery.utils.profile - Finished executing function run_query in 0.672677 s
+2024-09-17 10:19:49,462 INFO cycquery.utils.profile - Finished executing function run_query in 1.986367 s
@@ -713,7 +713,7 @@

Example 2. Get all patient encounters with diagnoses ( 
-2024-09-17 07:58:06,130 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:19:58,610 INFO cycquery.orm    - Query returned successfully!

@@ -721,7 +721,7 @@

Example 2. Get all patient encounters with diagnoses ( 
-2024-09-17 07:58:06,132 INFO cycquery.utils.profile - Finished executing function run_query in 15.477935 s
+2024-09-17 10:19:58,612 INFO cycquery.utils.profile - Finished executing function run_query in 9.072297 s

@@ -766,7 +766,7 @@

Example 3. Advanced - uses 
-2024-09-17 07:58:09,912 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:20:02,401 INFO cycquery.orm    - Query returned successfully!

@@ -774,7 +774,7 @@

Example 3. Advanced - uses 
-2024-09-17 07:58:09,914 INFO cycquery.utils.profile - Finished executing function run_query in 3.710405 s
+2024-09-17 10:20:02,403 INFO cycquery.utils.profile - Finished executing function run_query in 3.719482 s

@@ -815,7 +815,7 @@

Example 4. Get routine vital signs for patients from year 2015. 
-2024-09-17 07:58:14,094 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:20:07,692 INFO cycquery.orm    - Query returned successfully!

@@ -823,7 +823,7 @@

Example 4. Get routine vital signs for patients from year 2015. 
-2024-09-17 07:58:14,095 INFO cycquery.utils.profile - Finished executing function run_query in 4.107843 s
+2024-09-17 10:20:07,694 INFO cycquery.utils.profile - Finished executing function run_query in 5.219430 s

@@ -864,7 +864,7 @@

Example 5. Get hemoglobin lab tests for patients from year 2009. 
-2024-09-17 07:58:19,169 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:20:13,117 INFO cycquery.orm    - Query returned successfully!

@@ -872,7 +872,7 @@

Example 5. Get hemoglobin lab tests for patients from year 2009. 
-2024-09-17 07:58:19,170 INFO cycquery.utils.profile - Finished executing function run_query in 5.003948 s
+2024-09-17 10:20:13,119 INFO cycquery.utils.profile - Finished executing function run_query in 5.352773 s

@@ -919,7 +919,7 @@

Example 6. Get radiology reports and filter on keywords 
-2024-09-17 08:00:41,243 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:22:23,689 INFO cycquery.orm    - Query returned successfully!

@@ -927,7 +927,7 @@

Example 6. Get radiology reports and filter on keywords 
-2024-09-17 08:00:41,245 INFO cycquery.utils.profile - Finished executing function run_query in 142.013149 s
+2024-09-17 10:22:23,691 INFO cycquery.utils.profile - Finished executing function run_query in 130.509553 s

@@ -970,7 +970,7 @@

Example 7. Get all female patient encounters from year 2015, and return batc 

-2024-09-17 08:00:42,508 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:22:24,839 INFO cycquery.orm    - Query returned successfully!
@@ -978,7 +978,7 @@

Example 7. Get all female patient encounters from year 2015, and return batc 

-2024-09-17 08:00:42,510 INFO cycquery.utils.profile - Finished executing function run_query in 1.160325 s
+2024-09-17 10:22:24,841 INFO cycquery.utils.profile - Finished executing function run_query in 1.047307 s
@@ -1006,7 +1006,7 @@

Example 8. Running a raw SQL string. 
-2024-09-17 08:00:42,843 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:22:25,425 INFO cycquery.orm    - Query returned successfully!

@@ -1014,7 +1014,7 @@

Example 8. Running a raw SQL string. 
-2024-09-17 08:00:42,845 INFO cycquery.utils.profile - Finished executing function run_query in 0.013243 s
+2024-09-17 10:22:25,427 INFO cycquery.utils.profile - Finished executing function run_query in 0.013066 s

diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb index f4eace8..d37e63c 100644 --- a/tutorials/mimiciv.ipynb +++ b/tutorials/mimiciv.ipynb @@ -35,10 +35,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:57:40.792524Z", - "iopub.status.busy": "2024-09-17T11:57:40.791174Z", - "iopub.status.idle": "2024-09-17T11:57:49.859254Z", - "shell.execute_reply": "2024-09-17T11:57:49.857378Z" + "iopub.execute_input": "2024-09-17T14:19:36.401434Z", + "iopub.status.busy": "2024-09-17T14:19:36.400053Z", + "iopub.status.idle": "2024-09-17T14:19:47.431004Z", + "shell.execute_reply": "2024-09-17T14:19:47.429254Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:57:47,514 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-09-17 10:19:45,079 \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": "2024-09-17T11:57:49.867400Z", - "iopub.status.busy": "2024-09-17T11:57:49.865999Z", - "iopub.status.idle": "2024-09-17T11:57:50.585393Z", - "shell.execute_reply": "2024-09-17T11:57:50.583355Z" + "iopub.execute_input": "2024-09-17T14:19:47.438751Z", + "iopub.status.busy": "2024-09-17T14:19:47.437162Z", + "iopub.status.idle": "2024-09-17T14:19:49.469880Z", + "shell.execute_reply": "2024-09-17T14:19:49.468209Z" } }, "outputs": [ @@ -116,14 +116,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:57:50,574 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:19:49,461 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:57:50,577 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.672677 s\n" + "2024-09-17 10:19:49,462 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.986367 s\n" ] }, { @@ -160,10 +160,10 @@ "id": "a89a9cf0", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:57:50.593280Z", - "iopub.status.busy": "2024-09-17T11:57:50.591878Z", - "iopub.status.idle": "2024-09-17T11:58:06.139655Z", - "shell.execute_reply": "2024-09-17T11:58:06.137902Z" + "iopub.execute_input": "2024-09-17T14:19:49.476666Z", + "iopub.status.busy": "2024-09-17T14:19:49.476033Z", + "iopub.status.idle": "2024-09-17T14:19:58.619611Z", + "shell.execute_reply": "2024-09-17T14:19:58.617970Z" } }, "outputs": [ @@ -171,14 +171,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:58:06,130 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:19:58,610 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:58:06,132 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 15.477935 s\n" + "2024-09-17 10:19:58,612 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 9.072297 s\n" ] }, { @@ -225,10 +225,10 @@ "id": "03936cee", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:58:06.147113Z", - "iopub.status.busy": "2024-09-17T11:58:06.146048Z", - "iopub.status.idle": "2024-09-17T11:58:09.922410Z", - "shell.execute_reply": "2024-09-17T11:58:09.920686Z" + "iopub.execute_input": "2024-09-17T14:19:58.627174Z", + "iopub.status.busy": "2024-09-17T14:19:58.625763Z", + "iopub.status.idle": "2024-09-17T14:20:02.410587Z", + "shell.execute_reply": "2024-09-17T14:20:02.408924Z" } }, "outputs": [ @@ -236,14 +236,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:58:09,912 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:20:02,401 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:58:09,914 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.710405 s\n" + "2024-09-17 10:20:02,403 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.719482 s\n" ] }, { @@ -290,10 +290,10 @@ "id": "56a72377", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:58:09.930492Z", - "iopub.status.busy": "2024-09-17T11:58:09.928742Z", - "iopub.status.idle": "2024-09-17T11:58:14.103225Z", - "shell.execute_reply": "2024-09-17T11:58:14.101562Z" + "iopub.execute_input": "2024-09-17T14:20:02.417805Z", + "iopub.status.busy": "2024-09-17T14:20:02.416743Z", + "iopub.status.idle": "2024-09-17T14:20:07.701688Z", + "shell.execute_reply": "2024-09-17T14:20:07.700052Z" } }, "outputs": [ @@ -301,14 +301,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:58:14,094 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:20:07,692 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:58:14,095 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.107843 s\n" + "2024-09-17 10:20:07,694 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.219430 s\n" ] }, { @@ -351,10 +351,10 @@ "id": "bce11f81", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:58:14.110228Z", - "iopub.status.busy": "2024-09-17T11:58:14.109204Z", - "iopub.status.idle": "2024-09-17T11:58:19.177813Z", - "shell.execute_reply": "2024-09-17T11:58:19.176459Z" + "iopub.execute_input": "2024-09-17T14:20:07.708799Z", + "iopub.status.busy": "2024-09-17T14:20:07.707719Z", + "iopub.status.idle": "2024-09-17T14:20:13.126408Z", + "shell.execute_reply": "2024-09-17T14:20:13.124688Z" } }, "outputs": [ @@ -362,14 +362,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:58:19,169 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:20:13,117 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 07:58:19,170 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.003948 s\n" + "2024-09-17 10:20:13,119 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.352773 s\n" ] }, { @@ -412,10 +412,10 @@ "id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T11:58:19.185262Z", - "iopub.status.busy": "2024-09-17T11:58:19.183893Z", - "iopub.status.idle": "2024-09-17T12:00:41.253346Z", - "shell.execute_reply": "2024-09-17T12:00:41.251442Z" + "iopub.execute_input": "2024-09-17T14:20:13.133401Z", + "iopub.status.busy": "2024-09-17T14:20:13.132517Z", + "iopub.status.idle": "2024-09-17T14:22:23.698456Z", + "shell.execute_reply": "2024-09-17T14:22:23.696776Z" }, "tags": [] }, @@ -424,14 +424,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:41,243 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:22:23,689 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:41,245 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 142.013149 s\n" + "2024-09-17 10:22:23,691 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 130.509553 s\n" ] }, { @@ -480,10 +480,10 @@ "id": "28683d70-376e-4d9b-883d-1a7de634e455", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T12:00:41.260648Z", - "iopub.status.busy": "2024-09-17T12:00:41.259680Z", - "iopub.status.idle": "2024-09-17T12:00:42.821880Z", - "shell.execute_reply": "2024-09-17T12:00:42.820131Z" + "iopub.execute_input": "2024-09-17T14:22:23.705677Z", + "iopub.status.busy": "2024-09-17T14:22:23.704761Z", + "iopub.status.idle": "2024-09-17T14:22:25.403816Z", + "shell.execute_reply": "2024-09-17T14:22:25.402075Z" } }, "outputs": [ @@ -491,14 +491,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:42,508 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:22:24,839 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:42,510 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.160325 s\n" + "2024-09-17 10:22:24,841 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.047307 s\n" ] }, { @@ -543,10 +543,10 @@ "id": "a853deec", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T12:00:42.829810Z", - "iopub.status.busy": "2024-09-17T12:00:42.828560Z", - "iopub.status.idle": "2024-09-17T12:00:42.852791Z", - "shell.execute_reply": "2024-09-17T12:00:42.851087Z" + "iopub.execute_input": "2024-09-17T14:22:25.411741Z", + "iopub.status.busy": "2024-09-17T14:22:25.410443Z", + "iopub.status.idle": "2024-09-17T14:22:25.433909Z", + "shell.execute_reply": "2024-09-17T14:22:25.432306Z" }, "tags": [] }, @@ -555,14 +555,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:42,843 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:22:25,425 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:42,845 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013243 s\n" + "2024-09-17 10:22:25,427 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013066 s\n" ] }, { diff --git a/tutorials/omop.html b/tutorials/omop.html index 6bcf83d..173725e 100644 --- a/tutorials/omop.html +++ b/tutorials/omop.html @@ -623,7 +623,7 @@

Imports and instantiate 
-2024-09-17 08:00:51,426 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-09-17 10:22:32,043 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -698,7 +698,7 @@

Example 1. Get all patient visits in or after 2010. 
-2024-09-17 08:00:53,170 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:22:33,719 INFO cycquery.orm    - Query returned successfully!

@@ -706,7 +706,7 @@

Example 1. Get all patient visits in or after 2010. 
-2024-09-17 08:00:53,171 INFO cycquery.utils.profile - Finished executing function run_query in 0.490825 s
+2024-09-17 10:22:33,721 INFO cycquery.utils.profile - Finished executing function run_query in 0.452071 s

@@ -764,7 +764,7 @@

Example 2. Get measurements for all visits in or after 2020. 
-2024-09-17 08:00:54,661 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:22:35,248 INFO cycquery.orm    - Query returned successfully!

@@ -772,7 +772,7 @@

Example 2. Get measurements for all visits in or after 2020. 
-2024-09-17 08:00:54,663 INFO cycquery.utils.profile - Finished executing function run_query in 1.271455 s
+2024-09-17 10:22:35,249 INFO cycquery.utils.profile - Finished executing function run_query in 1.150477 s

@@ -818,7 +818,7 @@

Imports and instantiate 
-2024-09-17 08:01:02,271 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-09-17 10:22:42,209 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 

-2024-09-17 08:01:09,672 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:22:49,434 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 

-2024-09-17 08:01:09,674 INFO cycquery.utils.profile - Finished executing function run_query in 1.271381 s
+2024-09-17 10:22:49,436 INFO cycquery.utils.profile - Finished executing function run_query in 1.027628 s
@@ -922,7 +922,7 @@

Example 2. Get all measurements for female patient visits with 
-2024-09-17 08:06:04,776 INFO cycquery.orm    - Query returned successfully!
+2024-09-17 10:27:12,820 INFO cycquery.orm    - Query returned successfully!

@@ -930,7 +930,7 @@

Example 2. Get all measurements for female patient visits with 
-2024-09-17 08:06:04,779 INFO cycquery.utils.profile - Finished executing function run_query in 294.857821 s
+2024-09-17 10:27:12,822 INFO cycquery.utils.profile - Finished executing function run_query in 263.137625 s

@@ -956,9 +956,28 @@

Example 2. Get all measurements for female patient visits with 
 measurement_concept_name
-Body weight            51
-No matching concept    48
-Urine output            1
+Respiratory rate                                                         52
+No matching concept                                                      21
+Glasgow coma score motor                                                  8
+Imipenem [Susceptibility] by Disk diffusion (KB)                          1
+Trimethoprim+Sulfamethoxazole [Susceptibility] by Disk diffusion (KB)     1
+Nitrofurantoin [Susceptibility] by Disk diffusion (KB)                    1
+Ciprofloxacin [Susceptibility] by Disk diffusion (KB)                     1
+cefTRIAXone [Susceptibility] by Disk diffusion (KB)                       1
+cefTAZidime [Susceptibility] by Disk diffusion (KB)                       1
+levoFLOXacin [Susceptibility] by Disk diffusion (KB)                      1
+Tobramycin [Susceptibility] by Disk diffusion (KB)                        1
+Gentamicin [Susceptibility] by Disk diffusion (KB)                        1
+Cefepime [Susceptibility] by Disk diffusion (KB)                          1
+Piperacillin+Tazobactam [Susceptibility] by Disk diffusion (KB)           1
+Ampicillin [Susceptibility] by Disk diffusion (KB)                        1
+Meropenem [Susceptibility] by Disk diffusion (KB)                         1
+Cefuroxime Parenteral [Susceptibility] by Disk diffusion (KB)             1
+ceFAZolin [Susceptibility] by Disk diffusion (KB)                         1
+Ampicillin+Sulbactam [Susceptibility] by Disk diffusion (KB)              1
+Piperacillin [Susceptibility] by Disk diffusion (KB)                      1
+Bacteria identified in Blood product unit.autologous by Culture           1
+Bacteria identified in Urine by Culture                                   1
 Name: count, dtype: int64[pyarrow]

diff --git a/tutorials/omop.ipynb b/tutorials/omop.ipynb index b8e3235..a66e180 100644 --- a/tutorials/omop.ipynb +++ b/tutorials/omop.ipynb @@ -45,10 +45,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T12:00:47.238513Z", - "iopub.status.busy": "2024-09-17T12:00:47.237082Z", - "iopub.status.idle": "2024-09-17T12:00:52.632208Z", - "shell.execute_reply": "2024-09-17T12:00:52.630412Z" + "iopub.execute_input": "2024-09-17T14:22:29.405706Z", + "iopub.status.busy": "2024-09-17T14:22:29.404703Z", + "iopub.status.idle": "2024-09-17T14:22:33.219913Z", + "shell.execute_reply": "2024-09-17T14:22:33.218081Z" } }, "outputs": [ @@ -56,7 +56,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:51,426 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-09-17 10:22:32,043 \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": "2024-09-17T12:00:52.639669Z", - "iopub.status.busy": "2024-09-17T12:00:52.638404Z", - "iopub.status.idle": "2024-09-17T12:00:53.286524Z", - "shell.execute_reply": "2024-09-17T12:00:53.284902Z" + "iopub.execute_input": "2024-09-17T14:22:33.227328Z", + "iopub.status.busy": "2024-09-17T14:22:33.226043Z", + "iopub.status.idle": "2024-09-17T14:22:33.992678Z", + "shell.execute_reply": "2024-09-17T14:22:33.990998Z" } }, "outputs": [ @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:53,170 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:22:33,719 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:53,171 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.490825 s\n" + "2024-09-17 10:22:33,721 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.452071 s\n" ] }, { @@ -227,10 +227,10 @@ "id": "030e2491-a7cc-42f3-a1ca-618212b3524c", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T12:00:53.293686Z", - "iopub.status.busy": "2024-09-17T12:00:53.292647Z", - "iopub.status.idle": "2024-09-17T12:00:54.670949Z", - "shell.execute_reply": "2024-09-17T12:00:54.669215Z" + "iopub.execute_input": "2024-09-17T14:22:33.999318Z", + "iopub.status.busy": "2024-09-17T14:22:33.998433Z", + "iopub.status.idle": "2024-09-17T14:22:35.257270Z", + "shell.execute_reply": "2024-09-17T14:22:35.255516Z" } }, "outputs": [ @@ -238,14 +238,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:54,661 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:22:35,248 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:00:54,663 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.271455 s\n" + "2024-09-17 10:22:35,249 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.150477 s\n" ] }, { @@ -303,10 +303,10 @@ "id": "0622b3df-2864-4f32-bd98-806019f59c50", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T12:00:54.678256Z", - "iopub.status.busy": "2024-09-17T12:00:54.677187Z", - "iopub.status.idle": "2024-09-17T12:01:08.333104Z", - "shell.execute_reply": "2024-09-17T12:01:08.331284Z" + "iopub.execute_input": "2024-09-17T14:22:35.264742Z", + "iopub.status.busy": "2024-09-17T14:22:35.263668Z", + "iopub.status.idle": "2024-09-17T14:22:48.338171Z", + "shell.execute_reply": "2024-09-17T14:22:48.336490Z" }, "tags": [] }, @@ -315,7 +315,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:01:02,271 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-09-17 10:22:42,209 \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": "2024-09-17T12:01:08.340845Z", - "iopub.status.busy": "2024-09-17T12:01:08.339468Z", - "iopub.status.idle": "2024-09-17T12:01:09.680984Z", - "shell.execute_reply": "2024-09-17T12:01:09.679140Z" + "iopub.execute_input": "2024-09-17T14:22:48.344923Z", + "iopub.status.busy": "2024-09-17T14:22:48.344320Z", + "iopub.status.idle": "2024-09-17T14:22:49.443113Z", + "shell.execute_reply": "2024-09-17T14:22:49.441464Z" }, "tags": [] }, @@ -369,14 +369,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:01:09,672 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:22:49,434 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:01:09,674 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.271381 s\n" + "2024-09-17 10:22:49,436 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.027628 s\n" ] }, { @@ -419,10 +419,10 @@ "id": "46fd771c-5da7-4bce-aec7-08a5210a069b", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T12:01:09.687874Z", - "iopub.status.busy": "2024-09-17T12:01:09.687207Z", - "iopub.status.idle": "2024-09-17T12:06:04.787369Z", - "shell.execute_reply": "2024-09-17T12:06:04.785397Z" + "iopub.execute_input": "2024-09-17T14:22:49.450585Z", + "iopub.status.busy": "2024-09-17T14:22:49.449296Z", + "iopub.status.idle": "2024-09-17T14:27:12.829453Z", + "shell.execute_reply": "2024-09-17T14:27:12.827718Z" }, "tags": [] }, @@ -431,14 +431,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:06:04,776 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-09-17 10:27:12,820 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-09-17 08:06:04,779 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 294.857821 s\n" + "2024-09-17 10:27:12,822 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 263.137625 s\n" ] }, { @@ -488,10 +488,10 @@ "id": "d20a2581-f613-4ab8-9feb-3e84b8835db1", "metadata": { "execution": { - "iopub.execute_input": "2024-09-17T12:06:04.795908Z", - "iopub.status.busy": "2024-09-17T12:06:04.794029Z", - "iopub.status.idle": "2024-09-17T12:06:04.813097Z", - "shell.execute_reply": "2024-09-17T12:06:04.811215Z" + "iopub.execute_input": "2024-09-17T14:27:12.836813Z", + "iopub.status.busy": "2024-09-17T14:27:12.835425Z", + "iopub.status.idle": "2024-09-17T14:27:12.920682Z", + "shell.execute_reply": "2024-09-17T14:27:12.919012Z" }, "tags": [] }, @@ -500,9 +500,28 @@ "data": { "text/plain": [ "measurement_concept_name\n", - "Body weight 51\n", - "No matching concept 48\n", - "Urine output 1\n", + "Respiratory rate 52\n", + "No matching concept 21\n", + "Glasgow coma score motor 8\n", + "Imipenem [Susceptibility] by Disk diffusion (KB) 1\n", + "Trimethoprim+Sulfamethoxazole [Susceptibility] by Disk diffusion (KB) 1\n", + "Nitrofurantoin [Susceptibility] by Disk diffusion (KB) 1\n", + "Ciprofloxacin [Susceptibility] by Disk diffusion (KB) 1\n", + "cefTRIAXone [Susceptibility] by Disk diffusion (KB) 1\n", + "cefTAZidime [Susceptibility] by Disk diffusion (KB) 1\n", + "levoFLOXacin [Susceptibility] by Disk diffusion (KB) 1\n", + "Tobramycin [Susceptibility] by Disk diffusion (KB) 1\n", + "Gentamicin [Susceptibility] by Disk diffusion (KB) 1\n", + "Cefepime [Susceptibility] by Disk diffusion (KB) 1\n", + "Piperacillin+Tazobactam [Susceptibility] by Disk diffusion (KB) 1\n", + "Ampicillin [Susceptibility] by Disk diffusion (KB) 1\n", + "Meropenem [Susceptibility] by Disk diffusion (KB) 1\n", + "Cefuroxime Parenteral [Susceptibility] by Disk diffusion (KB) 1\n", + "ceFAZolin [Susceptibility] by Disk diffusion (KB) 1\n", + "Ampicillin+Sulbactam [Susceptibility] by Disk diffusion (KB) 1\n", + "Piperacillin [Susceptibility] by Disk diffusion (KB) 1\n", + "Bacteria identified in Blood product unit.autologous by Culture 1\n", + "Bacteria identified in Urine by Culture 1\n", "Name: count, dtype: int64[pyarrow]" ] },