From debe07afea72c548d3117b9177be2dcd2a83daae Mon Sep 17 00:00:00 2001 From: amrit110 Date: Wed, 20 Nov 2024 06:33:52 -0500 Subject: [PATCH] deploy: 728abb1fcacafa78666f6746f55b304babf4d4a5 --- 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 | 43 ++++------------ tutorials/omop.ipynb | 99 ++++++++++++++---------------------- 9 files changed, 197 insertions(+), 239 deletions(-) diff --git a/searchindex.js b/searchindex.js index 9b41952..7030317 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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"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.Literal", "cycquery.ops.Or", "cycquery.ops.OrderBy", "cycquery.ops.QueryOp", "cycquery.ops.RandomizeOrder", "cycquery.ops.Rename", "cycquery.ops.Reorder", "cycquery.ops.ReorderAfter", "cycquery.ops.Sequential", "cycquery.ops.Substring", "cycquery.ops.Trim", "cycquery.ops.Union", "cycquery", "Tutorials", "eICU-CRD tutorial", "GEMINI tutorial", "MIMIC-III tutorial", "MIMIC-IV tutorial", "OMOP tutorial"], "titleterms": {"": 2, "1": [64, 65, 66, 67, 68], "10": 67, "100": 64, "101": 65, "1a": 65, "1b": 65, "1c": 65, "2": [64, 66, 67, 68], "20": 66, "2009": 67, "2010": 68, "2014": 64, "2015": [64, 65, 67], "2016": 65, "2020": 68, "2021": 67, "2a": 65, "3": [64, 66, 67], "31": 65, "4": [64, 66, 67], "5": 67, "6": 67, "7": 67, "8": 67, "9": [66, 67], "And": 23, "Or": 51, "aado2": 66, "abov": 65, "addcolumn": 19, "adddeltacolumn": 20, "adddeltaconst": 21, "addnumer": 22, "admiss": [65, 67], "advanc": 67, "after": 68, "all": [64, 66, 67, 68], "api": [0, 62], "appli": 24, "approx": 67, "apr": 65, "april": 65, "base": [4, 5], "batch": 67, "between": 65, "carevu": 66, "cast": 25, "chart": 66, "chronic": 67, "code": 1, "commit": 1, "conditionafterd": 26, "conditionbefored": 27, "conditionendswith": 28, "conditionequ": 29, "conditiongreaterthan": 30, "conditionin": 31, "conditioninmonth": 32, "conditioninyear": 33, "conditionlessthan": 34, "conditionlik": 35, "conditionregexmatch": [36, 67], "conditionstartswith": 37, "conditionsubstr": 38, "contain": 67, "content": 2, "contribut": [1, 3], "count": 39, "crd": 64, "creat": 65, "cycqueri": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 67], "databas": 3, "dataset": [62, 65], "datasetqueri": 5, "develop": 3, "diagnos": [64, 66, 67, 68], "diagnosisstr": 64, "discharg": [64, 65], "discharge_date_tim": 65, "distinct": 40, "document": [2, 3], "drop": 41, "dropempti": 42, "dropnul": 43, "each": 65, "eicu": [6, 7, 64], "eicuqueri": [7, 64], "encount": [64, 65, 66, 67], "end": 68, "event": 66, "exampl": [64, 65, 66, 67, 68], "extracttimestampcompon": 44, "femal": [64, 66, 67, 68], "fillnul": 45, "filter": 67, "from": [65, 67], "gastroenter": 66, "gemini": [8, 9, 65], "geminiqueri": [9, 65], "get": [3, 64, 65, 66, 67, 68], "glucos": 64, "groupbyaggreg": 46, "guidelin": 1, "have": 66, "hemoglobin": 67, "hook": 1, "hospit": [64, 65], "how": 65, "icd": [66, 67], "iii": 66, "import": [64, 65, 66, 67, 68], "index": 67, "infecti": 67, "instal": 3, "instanti": [64, 65, 66, 67, 68], "interfac": [10, 11], "iv": 67, "join": 47, "keep": [48, 65], "keyword": 67, "lab": [64, 66, 67], "later": 67, "less": 66, "limit": [49, 64], "liter": 50, "long": [66, 67], "lymphadenopathi": 67, "mai": 65, "male": 66, "mani": 65, "march": 65, "measur": 68, "medic": 64, "mimic": [66, 67], "mimiciii": [12, 13], "mimiciiiqueri": [13, 66], "mimiciv": [14, 15], "mimicivqueri": [15, 67], "mortal": [66, 68], "most": 65, "number": 65, "occur": 67, "omop": [16, 17, 68], "omopqueri": [17, 68], "one": 65, "onli": 65, "op": [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67], "orderbi": 52, "outcom": [66, 68], "partit": 67, "patient": [64, 65, 66, 67, 68], "patient_id_hash": 65, "per": 65, "pip": 3, "place": 65, "poetri": 3, "postgresql": 3, "potassium": [64, 66], "pre": 1, "queri": 3, "queryinterfac": 11, "queryop": 53, "radiologi": 67, "randomizeord": 54, "raw": 67, "recent": 65, "record": 65, "refer": 0, "renam": 55, "reorder": 56, "reorderaft": 57, "report": 67, "return": 67, "routin": 67, "row": 64, "run": 67, "schizophrenia": [64, 67], "search": 64, "sepsi": 68, "sequenti": 58, "set": 65, "sign": 67, "sodium": 65, "sort": 65, "sql": 67, "start": 3, "string": 67, "subject_id": 67, "subset": 65, "substr": [59, 64], "tabl": 65, "take": 65, "teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file diff --git a/tutorials/eicu.html b/tutorials/eicu.html index 89f0d34..19e6f77 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-11-20 00:34:49,450 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-11-20 05:43:00,894 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). 
-2024-11-20 00:34:50,408 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 05:43:01,944 INFO cycquery.orm    - Query returned successfully!

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

Example 1. Get all female patients discharged in 2014 (limit to 100 rows). 
-2024-11-20 00:34:50,410 INFO cycquery.utils.profile - Finished executing function run_query in 0.203213 s
+2024-11-20 05:43:01,946 INFO cycquery.utils.profile - Finished executing function run_query in 0.285067 s

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

Example 2. Get all patient encounters with diagnoses ( 
-2024-11-20 00:34:52,697 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 05:43:06,716 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get all patient encounters with diagnoses ( 
-2024-11-20 00:34:52,699 INFO cycquery.utils.profile - Finished executing function run_query in 2.256952 s
+2024-11-20 05:43:06,718 INFO cycquery.utils.profile - Finished executing function run_query in 4.741402 s

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

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

-2024-11-20 00:34:53,885 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 05:43:07,270 INFO cycquery.orm    - Query returned successfully!
@@ -779,7 +779,7 @@

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

-2024-11-20 00:34:53,887 INFO cycquery.utils.profile - Finished executing function run_query in 1.146802 s
+2024-11-20 05:43:07,272 INFO cycquery.utils.profile - Finished executing function run_query in 0.506820 s
@@ -818,7 +818,7 @@

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

-2024-11-20 00:34:55,228 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 05:43:09,861 INFO cycquery.orm    - Query returned successfully!
@@ -826,7 +826,7 @@

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

-2024-11-20 00:34:55,230 INFO cycquery.utils.profile - Finished executing function run_query in 1.303408 s
+2024-11-20 05:43:09,863 INFO cycquery.utils.profile - Finished executing function run_query in 2.551167 s
diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb index c6c8f7b..5d1ef6c 100644 --- a/tutorials/eicu.ipynb +++ b/tutorials/eicu.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T05:34:47.408959Z", - "iopub.status.busy": "2024-11-20T05:34:47.407985Z", - "iopub.status.idle": "2024-11-20T05:34:50.186107Z", - "shell.execute_reply": "2024-11-20T05:34:50.184172Z" + "iopub.execute_input": "2024-11-20T10:42:58.841327Z", + "iopub.status.busy": "2024-11-20T10:42:58.840218Z", + "iopub.status.idle": "2024-11-20T10:43:01.637862Z", + "shell.execute_reply": "2024-11-20T10:43:01.635883Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:49,450 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-11-20 05:43:00,894 \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": "2024-11-20T05:34:50.194038Z", - "iopub.status.busy": "2024-11-20T05:34:50.192776Z", - "iopub.status.idle": "2024-11-20T05:34:50.418150Z", - "shell.execute_reply": "2024-11-20T05:34:50.416241Z" + "iopub.execute_input": "2024-11-20T10:43:01.646726Z", + "iopub.status.busy": "2024-11-20T10:43:01.645226Z", + "iopub.status.idle": "2024-11-20T10:43:01.953244Z", + "shell.execute_reply": "2024-11-20T10:43:01.951531Z" }, "tags": [] }, @@ -136,14 +136,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:50,408 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 05:43:01,944 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:50,410 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.203213 s\n" + "2024-11-20 05:43:01,946 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.285067 s\n" ] }, { @@ -180,10 +180,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T05:34:50.425440Z", - "iopub.status.busy": "2024-11-20T05:34:50.424534Z", - "iopub.status.idle": "2024-11-20T05:34:52.706118Z", - "shell.execute_reply": "2024-11-20T05:34:52.704480Z" + "iopub.execute_input": "2024-11-20T10:43:01.960848Z", + "iopub.status.busy": "2024-11-20T10:43:01.959623Z", + "iopub.status.idle": "2024-11-20T10:43:06.726419Z", + "shell.execute_reply": "2024-11-20T10:43:06.724613Z" }, "tags": [] }, @@ -192,14 +192,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:52,697 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 05:43:06,716 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:52,699 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.256952 s\n" + "2024-11-20 05:43:06,718 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.741402 s\n" ] }, { @@ -236,10 +236,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T05:34:52.713618Z", - "iopub.status.busy": "2024-11-20T05:34:52.712403Z", - "iopub.status.idle": "2024-11-20T05:34:53.894862Z", - "shell.execute_reply": "2024-11-20T05:34:53.892958Z" + "iopub.execute_input": "2024-11-20T10:43:06.734799Z", + "iopub.status.busy": "2024-11-20T10:43:06.733077Z", + "iopub.status.idle": "2024-11-20T10:43:07.279272Z", + "shell.execute_reply": "2024-11-20T10:43:07.277533Z" }, "tags": [] }, @@ -248,14 +248,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:53,885 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 05:43:07,270 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:53,887 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.146802 s\n" + "2024-11-20 05:43:07,272 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.506820 s\n" ] }, { @@ -298,10 +298,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T05:34:53.903171Z", - "iopub.status.busy": "2024-11-20T05:34:53.901436Z", - "iopub.status.idle": "2024-11-20T05:34:55.238566Z", - "shell.execute_reply": "2024-11-20T05:34:55.236622Z" + "iopub.execute_input": "2024-11-20T10:43:07.287633Z", + "iopub.status.busy": "2024-11-20T10:43:07.285996Z", + "iopub.status.idle": "2024-11-20T10:43:09.871035Z", + "shell.execute_reply": "2024-11-20T10:43:09.869071Z" }, "tags": [] }, @@ -310,14 +310,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:55,228 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 05:43:09,861 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:34:55,230 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.303408 s\n" + "2024-11-20 05:43:09,863 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.551167 s\n" ] }, { diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html index ab685c2..e977286 100644 --- a/tutorials/mimiciii.html +++ b/tutorials/mimiciii.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-11-20 00:35:08,458 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-11-20 05:43:22,707 INFO cycquery.orm    - Database setup, ready to run queries!

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

Example 1. Get all male patients with a mortality outcome. 
-2024-11-20 00:35:14,769 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 05:43:29,122 INFO cycquery.orm    - Query returned successfully!

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

Example 1. Get all male patients with a mortality outcome. 
-2024-11-20 00:35:14,770 INFO cycquery.utils.profile - Finished executing function run_query in 0.242612 s
+2024-11-20 05:43:29,124 INFO cycquery.utils.profile - Finished executing function run_query in 0.371992 s

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

Example 2. Get all female patient encounters with diagnoses ( 
-2024-11-20 00:35:21,001 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 05:43:39,240 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get all female patient encounters with diagnoses ( 
-2024-11-20 00:35:21,003 INFO cycquery.utils.profile - Finished executing function run_query in 6.181985 s
+2024-11-20 05:43:39,242 INFO cycquery.utils.profile - Finished executing function run_query in 10.067851 s

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

Example 3. Get potassium lab tests for female patients. 
-2024-11-20 00:35:21,365 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 05:43:39,628 INFO cycquery.orm    - Query returned successfully!

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

Example 3. Get potassium lab tests for female patients. 
-2024-11-20 00:35:21,367 INFO cycquery.utils.profile - Finished executing function run_query in 0.315991 s
+2024-11-20 05:43:39,630 INFO cycquery.utils.profile - Finished executing function run_query in 0.337543 s

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

Example 4. Get AaDO2 carevue chart events for male patients that have a 
-2024-11-20 01:16:35,253 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:17:57,933 INFO cycquery.orm    - Query returned successfully!

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

Example 4. Get AaDO2 carevue chart events for male patients that have a 
-2024-11-20 01:16:35,255 INFO cycquery.utils.profile - Finished executing function run_query in 2473.821842 s
+2024-11-20 06:17:57,937 INFO cycquery.utils.profile - Finished executing function run_query in 2058.240027 s

diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb index 0fc02ba..db645a2 100644 --- a/tutorials/mimiciii.ipynb +++ b/tutorials/mimiciii.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T05:35:01.092631Z", - "iopub.status.busy": "2024-11-20T05:35:01.091507Z", - "iopub.status.idle": "2024-11-20T05:35:14.511795Z", - "shell.execute_reply": "2024-11-20T05:35:14.510018Z" + "iopub.execute_input": "2024-11-20T10:43:15.333983Z", + "iopub.status.busy": "2024-11-20T10:43:15.332499Z", + "iopub.status.idle": "2024-11-20T10:43:28.736292Z", + "shell.execute_reply": "2024-11-20T10:43:28.734475Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:35:08,458 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-11-20 05:43:22,707 \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": "2024-11-20T05:35:14.519943Z", - "iopub.status.busy": "2024-11-20T05:35:14.518392Z", - "iopub.status.idle": "2024-11-20T05:35:14.777990Z", - "shell.execute_reply": "2024-11-20T05:35:14.776335Z" + "iopub.execute_input": "2024-11-20T10:43:28.744197Z", + "iopub.status.busy": "2024-11-20T10:43:28.742637Z", + "iopub.status.idle": "2024-11-20T10:43:29.131509Z", + "shell.execute_reply": "2024-11-20T10:43:29.129753Z" }, "tags": [] }, @@ -106,14 +106,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:35:14,769 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 05:43:29,122 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:35:14,770 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.242612 s\n" + "2024-11-20 05:43:29,124 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.371992 s\n" ] }, { @@ -150,10 +150,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T05:35:14.785536Z", - "iopub.status.busy": "2024-11-20T05:35:14.784189Z", - "iopub.status.idle": "2024-11-20T05:35:21.010431Z", - "shell.execute_reply": "2024-11-20T05:35:21.008766Z" + "iopub.execute_input": "2024-11-20T10:43:29.138695Z", + "iopub.status.busy": "2024-11-20T10:43:29.137741Z", + "iopub.status.idle": "2024-11-20T10:43:39.250034Z", + "shell.execute_reply": "2024-11-20T10:43:39.248308Z" }, "tags": [] }, @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:35:21,001 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 05:43:39,240 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:35:21,003 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 6.181985 s\n" + "2024-11-20 05:43:39,242 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 10.067851 s\n" ] }, { @@ -211,10 +211,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T05:35:21.017927Z", - "iopub.status.busy": "2024-11-20T05:35:21.016604Z", - "iopub.status.idle": "2024-11-20T05:35:21.374683Z", - "shell.execute_reply": "2024-11-20T05:35:21.372997Z" + "iopub.execute_input": "2024-11-20T10:43:39.257626Z", + "iopub.status.busy": "2024-11-20T10:43:39.256404Z", + "iopub.status.idle": "2024-11-20T10:43:39.637343Z", + "shell.execute_reply": "2024-11-20T10:43:39.635642Z" }, "tags": [] }, @@ -223,14 +223,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:35:21,365 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 05:43:39,628 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 00:35:21,367 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.315991 s\n" + "2024-11-20 05:43:39,630 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.337543 s\n" ] }, { @@ -264,10 +264,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T05:35:21.381952Z", - "iopub.status.busy": "2024-11-20T05:35:21.380913Z", - "iopub.status.idle": "2024-11-20T06:16:35.263988Z", - "shell.execute_reply": "2024-11-20T06:16:35.262075Z" + "iopub.execute_input": "2024-11-20T10:43:39.645008Z", + "iopub.status.busy": "2024-11-20T10:43:39.643616Z", + "iopub.status.idle": "2024-11-20T11:17:57.947113Z", + "shell.execute_reply": "2024-11-20T11:17:57.944777Z" }, "tags": [] }, @@ -276,14 +276,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:16:35,253 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:17:57,933 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:16:35,255 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2473.821842 s\n" + "2024-11-20 06:17:57,937 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2058.240027 s\n" ] }, { diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html index 1d568cb..1abdf58 100644 --- a/tutorials/mimiciv.html +++ b/tutorials/mimiciv.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-11-20 01:16:49,605 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-11-20 06:18:11,891 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 

-2024-11-20 01:16:53,048 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:18:14,622 INFO cycquery.orm    - Query returned successfully!
@@ -668,7 +668,7 @@

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

-2024-11-20 01:16:53,050 INFO cycquery.utils.profile - Finished executing function run_query in 1.081479 s
+2024-11-20 06:18:14,624 INFO cycquery.utils.profile - Finished executing function run_query in 0.391459 s
@@ -713,7 +713,7 @@

Example 2. Get all patient encounters with diagnoses ( 
-2024-11-20 01:16:58,952 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:18:17,663 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get all patient encounters with diagnoses ( 
-2024-11-20 01:16:58,954 INFO cycquery.utils.profile - Finished executing function run_query in 5.828614 s
+2024-11-20 06:18:17,665 INFO cycquery.utils.profile - Finished executing function run_query in 2.965096 s

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

Example 3. Advanced - uses 
-2024-11-20 01:17:02,744 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:18:21,483 INFO cycquery.orm    - Query returned successfully!

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

Example 3. Advanced - uses 
-2024-11-20 01:17:02,746 INFO cycquery.utils.profile - Finished executing function run_query in 3.728091 s
+2024-11-20 06:18:21,485 INFO cycquery.utils.profile - Finished executing function run_query in 3.748332 s

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

Example 4. Get routine vital signs for patients from year 2015. 
-2024-11-20 01:17:29,794 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:18:25,954 INFO cycquery.orm    - Query returned successfully!

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

Example 4. Get routine vital signs for patients from year 2015. 
-2024-11-20 01:17:29,796 INFO cycquery.utils.profile - Finished executing function run_query in 26.976392 s
+2024-11-20 06:18:25,956 INFO cycquery.utils.profile - Finished executing function run_query in 4.399047 s

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

Example 5. Get hemoglobin lab tests for patients from year 2009. 
-2024-11-20 01:17:46,403 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:18:33,541 INFO cycquery.orm    - Query returned successfully!

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

Example 5. Get hemoglobin lab tests for patients from year 2009. 
-2024-11-20 01:17:46,404 INFO cycquery.utils.profile - Finished executing function run_query in 16.535176 s
+2024-11-20 06:18:33,543 INFO cycquery.utils.profile - Finished executing function run_query in 7.514830 s

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

Example 6. Get radiology reports and filter on keywords 
-2024-11-20 01:29:13,436 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:23:27,194 INFO cycquery.orm    - Query returned successfully!

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

Example 6. Get radiology reports and filter on keywords 
-2024-11-20 01:29:13,437 INFO cycquery.utils.profile - Finished executing function run_query in 686.971302 s
+2024-11-20 06:23:27,195 INFO cycquery.utils.profile - Finished executing function run_query in 293.589607 s

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

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

-2024-11-20 01:29:15,620 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:23:28,413 INFO cycquery.orm    - Query returned successfully!
@@ -978,7 +978,7 @@

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

-2024-11-20 01:29:15,622 INFO cycquery.utils.profile - Finished executing function run_query in 2.079561 s
+2024-11-20 06:23:28,415 INFO cycquery.utils.profile - Finished executing function run_query in 1.116994 s
@@ -1006,7 +1006,7 @@

Example 8. Running a raw SQL string. 
-2024-11-20 01:29:15,969 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:23:28,769 INFO cycquery.orm    - Query returned successfully!

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

Example 8. Running a raw SQL string. 
-2024-11-20 01:29:15,970 INFO cycquery.utils.profile - Finished executing function run_query in 0.013794 s
+2024-11-20 06:23:28,771 INFO cycquery.utils.profile - Finished executing function run_query in 0.013242 s

diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb index f795466..1f27ba5 100644 --- a/tutorials/mimiciv.ipynb +++ b/tutorials/mimiciv.ipynb @@ -35,10 +35,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:16:39.780559Z", - "iopub.status.busy": "2024-11-20T06:16:39.779488Z", - "iopub.status.idle": "2024-11-20T06:16:51.921944Z", - "shell.execute_reply": "2024-11-20T06:16:51.919960Z" + "iopub.execute_input": "2024-11-20T11:18:01.975921Z", + "iopub.status.busy": "2024-11-20T11:18:01.974892Z", + "iopub.status.idle": "2024-11-20T11:18:14.188080Z", + "shell.execute_reply": "2024-11-20T11:18:14.186384Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:16:49,605 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-11-20 06:18:11,891 \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": "2024-11-20T06:16:51.930673Z", - "iopub.status.busy": "2024-11-20T06:16:51.929294Z", - "iopub.status.idle": "2024-11-20T06:16:53.057370Z", - "shell.execute_reply": "2024-11-20T06:16:53.055697Z" + "iopub.execute_input": "2024-11-20T11:18:14.196325Z", + "iopub.status.busy": "2024-11-20T11:18:14.194698Z", + "iopub.status.idle": "2024-11-20T11:18:14.631838Z", + "shell.execute_reply": "2024-11-20T11:18:14.630173Z" } }, "outputs": [ @@ -116,14 +116,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:16:53,048 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:18:14,622 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:16:53,050 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.081479 s\n" + "2024-11-20 06:18:14,624 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.391459 s\n" ] }, { @@ -160,10 +160,10 @@ "id": "a89a9cf0", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:16:53.064897Z", - "iopub.status.busy": "2024-11-20T06:16:53.063497Z", - "iopub.status.idle": "2024-11-20T06:16:58.961704Z", - "shell.execute_reply": "2024-11-20T06:16:58.960047Z" + "iopub.execute_input": "2024-11-20T11:18:14.639614Z", + "iopub.status.busy": "2024-11-20T11:18:14.638214Z", + "iopub.status.idle": "2024-11-20T11:18:17.673115Z", + "shell.execute_reply": "2024-11-20T11:18:17.671438Z" } }, "outputs": [ @@ -171,14 +171,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:16:58,952 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:18:17,663 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:16:58,954 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.828614 s\n" + "2024-11-20 06:18:17,665 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.965096 s\n" ] }, { @@ -225,10 +225,10 @@ "id": "03936cee", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:16:58.969198Z", - "iopub.status.busy": "2024-11-20T06:16:58.967883Z", - "iopub.status.idle": "2024-11-20T06:17:02.753799Z", - "shell.execute_reply": "2024-11-20T06:17:02.752103Z" + "iopub.execute_input": "2024-11-20T11:18:17.679942Z", + "iopub.status.busy": "2024-11-20T11:18:17.679332Z", + "iopub.status.idle": "2024-11-20T11:18:21.493311Z", + "shell.execute_reply": "2024-11-20T11:18:21.491597Z" } }, "outputs": [ @@ -236,14 +236,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:17:02,744 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:18:21,483 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:17:02,746 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.728091 s\n" + "2024-11-20 06:18:21,485 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.748332 s\n" ] }, { @@ -290,10 +290,10 @@ "id": "56a72377", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:17:02.761313Z", - "iopub.status.busy": "2024-11-20T06:17:02.759935Z", - "iopub.status.idle": "2024-11-20T06:17:29.803980Z", - "shell.execute_reply": "2024-11-20T06:17:29.802281Z" + "iopub.execute_input": "2024-11-20T11:18:21.500898Z", + "iopub.status.busy": "2024-11-20T11:18:21.499488Z", + "iopub.status.idle": "2024-11-20T11:18:25.964549Z", + "shell.execute_reply": "2024-11-20T11:18:25.962455Z" } }, "outputs": [ @@ -301,14 +301,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:17:29,794 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:18:25,954 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:17:29,796 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 26.976392 s\n" + "2024-11-20 06:18:25,956 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.399047 s\n" ] }, { @@ -351,10 +351,10 @@ "id": "bce11f81", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:17:29.811063Z", - "iopub.status.busy": "2024-11-20T06:17:29.810242Z", - "iopub.status.idle": "2024-11-20T06:17:46.412104Z", - "shell.execute_reply": "2024-11-20T06:17:46.410451Z" + "iopub.execute_input": "2024-11-20T11:18:25.972129Z", + "iopub.status.busy": "2024-11-20T11:18:25.970816Z", + "iopub.status.idle": "2024-11-20T11:18:33.550908Z", + "shell.execute_reply": "2024-11-20T11:18:33.549203Z" } }, "outputs": [ @@ -362,14 +362,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:17:46,403 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:18:33,541 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:17:46,404 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 16.535176 s\n" + "2024-11-20 06:18:33,543 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 7.514830 s\n" ] }, { @@ -412,10 +412,10 @@ "id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:17:46.419627Z", - "iopub.status.busy": "2024-11-20T06:17:46.418382Z", - "iopub.status.idle": "2024-11-20T06:29:13.445449Z", - "shell.execute_reply": "2024-11-20T06:29:13.443752Z" + "iopub.execute_input": "2024-11-20T11:18:33.557959Z", + "iopub.status.busy": "2024-11-20T11:18:33.557068Z", + "iopub.status.idle": "2024-11-20T11:23:27.203306Z", + "shell.execute_reply": "2024-11-20T11:23:27.201621Z" }, "tags": [] }, @@ -424,14 +424,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:13,436 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:23:27,194 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:13,437 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 686.971302 s\n" + "2024-11-20 06:23:27,195 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 293.589607 s\n" ] }, { @@ -480,10 +480,10 @@ "id": "28683d70-376e-4d9b-883d-1a7de634e455", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:29:13.452345Z", - "iopub.status.busy": "2024-11-20T06:29:13.451739Z", - "iopub.status.idle": "2024-11-20T06:29:15.946200Z", - "shell.execute_reply": "2024-11-20T06:29:15.944242Z" + "iopub.execute_input": "2024-11-20T11:23:27.210511Z", + "iopub.status.busy": "2024-11-20T11:23:27.209286Z", + "iopub.status.idle": "2024-11-20T11:23:28.747339Z", + "shell.execute_reply": "2024-11-20T11:23:28.745497Z" } }, "outputs": [ @@ -491,14 +491,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:15,620 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:23:28,413 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:15,622 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.079561 s\n" + "2024-11-20 06:23:28,415 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.116994 s\n" ] }, { @@ -543,10 +543,10 @@ "id": "a853deec", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:29:15.954288Z", - "iopub.status.busy": "2024-11-20T06:29:15.952825Z", - "iopub.status.idle": "2024-11-20T06:29:15.977306Z", - "shell.execute_reply": "2024-11-20T06:29:15.975692Z" + "iopub.execute_input": "2024-11-20T11:23:28.755548Z", + "iopub.status.busy": "2024-11-20T11:23:28.753864Z", + "iopub.status.idle": "2024-11-20T11:23:28.778072Z", + "shell.execute_reply": "2024-11-20T11:23:28.776366Z" }, "tags": [] }, @@ -555,14 +555,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:15,969 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:23:28,769 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:15,970 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013794 s\n" + "2024-11-20 06:23:28,771 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013242 s\n" ] }, { diff --git a/tutorials/omop.html b/tutorials/omop.html index 7a67cce..2e8b1e1 100644 --- a/tutorials/omop.html +++ b/tutorials/omop.html @@ -623,7 +623,7 @@

Imports and instantiate 
-2024-11-20 01:29:23,963 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-11-20 06:23:35,535 INFO cycquery.orm    - Database setup, ready to run queries!

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

Example 1. Get all patient visits in or after 2010. 
-2024-11-20 01:29:34,355 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:23:37,787 INFO cycquery.orm    - Query returned successfully!

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

Example 1. Get all patient visits in or after 2010. 
-2024-11-20 01:29:34,357 INFO cycquery.utils.profile - Finished executing function run_query in 9.074612 s
+2024-11-20 06:23:37,789 INFO cycquery.utils.profile - Finished executing function run_query in 0.985569 s

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

Example 2. Get measurements for all visits in or after 2020. 
-2024-11-20 01:29:48,668 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:23:40,249 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get measurements for all visits in or after 2020. 
-2024-11-20 01:29:48,670 INFO cycquery.utils.profile - Finished executing function run_query in 13.814946 s
+2024-11-20 06:23:40,251 INFO cycquery.utils.profile - Finished executing function run_query in 1.885854 s

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

Imports and instantiate 
-2024-11-20 01:30:04,610 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-11-20 06:23:48,129 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 

-2024-11-20 01:30:13,492 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:23:55,566 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 

-2024-11-20 01:30:13,494 INFO cycquery.utils.profile - Finished executing function run_query in 2.426398 s
+2024-11-20 06:23:55,568 INFO cycquery.utils.profile - Finished executing function run_query in 1.264936 s
@@ -922,7 +922,7 @@

Example 2. Get all measurements for female patient visits with 
-2024-11-20 01:51:06,179 INFO cycquery.orm    - Query returned successfully!
+2024-11-20 06:32:59,003 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get all measurements for female patient visits with 
-2024-11-20 01:51:06,181 INFO cycquery.utils.profile - Finished executing function run_query in 1252.407178 s
+2024-11-20 06:32:59,005 INFO cycquery.utils.profile - Finished executing function run_query in 543.173872 s

@@ -956,28 +956,7 @@

Example 2. Get all measurements for female patient visits with 
 measurement_concept_name
-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
+No matching concept    100
 Name: count, dtype: int64[pyarrow]

diff --git a/tutorials/omop.ipynb b/tutorials/omop.ipynb index bde0105..0c5a398 100644 --- a/tutorials/omop.ipynb +++ b/tutorials/omop.ipynb @@ -45,10 +45,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:29:21.198144Z", - "iopub.status.busy": "2024-11-20T06:29:21.197128Z", - "iopub.status.idle": "2024-11-20T06:29:25.230191Z", - "shell.execute_reply": "2024-11-20T06:29:25.228443Z" + "iopub.execute_input": "2024-11-20T11:23:32.840042Z", + "iopub.status.busy": "2024-11-20T11:23:32.838938Z", + "iopub.status.idle": "2024-11-20T11:23:36.752500Z", + "shell.execute_reply": "2024-11-20T11:23:36.750750Z" } }, "outputs": [ @@ -56,7 +56,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:23,963 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-11-20 06:23:35,535 \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": "2024-11-20T06:29:25.238214Z", - "iopub.status.busy": "2024-11-20T06:29:25.236863Z", - "iopub.status.idle": "2024-11-20T06:29:34.741931Z", - "shell.execute_reply": "2024-11-20T06:29:34.739998Z" + "iopub.execute_input": "2024-11-20T11:23:36.760673Z", + "iopub.status.busy": "2024-11-20T11:23:36.759061Z", + "iopub.status.idle": "2024-11-20T11:23:38.253828Z", + "shell.execute_reply": "2024-11-20T11:23:38.251901Z" } }, "outputs": [ @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:34,355 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:23:37,787 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:34,357 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 9.074612 s\n" + "2024-11-20 06:23:37,789 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.985569 s\n" ] }, { @@ -227,10 +227,10 @@ "id": "030e2491-a7cc-42f3-a1ca-618212b3524c", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:29:34.749622Z", - "iopub.status.busy": "2024-11-20T06:29:34.748184Z", - "iopub.status.idle": "2024-11-20T06:29:48.677655Z", - "shell.execute_reply": "2024-11-20T06:29:48.675806Z" + "iopub.execute_input": "2024-11-20T11:23:38.262285Z", + "iopub.status.busy": "2024-11-20T11:23:38.260399Z", + "iopub.status.idle": "2024-11-20T11:23:40.258973Z", + "shell.execute_reply": "2024-11-20T11:23:40.257117Z" } }, "outputs": [ @@ -238,14 +238,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:48,668 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:23:40,249 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:29:48,670 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 13.814946 s\n" + "2024-11-20 06:23:40,251 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.885854 s\n" ] }, { @@ -303,10 +303,10 @@ "id": "0622b3df-2864-4f32-bd98-806019f59c50", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:29:48.685590Z", - "iopub.status.busy": "2024-11-20T06:29:48.684467Z", - "iopub.status.idle": "2024-11-20T06:30:10.988859Z", - "shell.execute_reply": "2024-11-20T06:30:10.987074Z" + "iopub.execute_input": "2024-11-20T11:23:40.266890Z", + "iopub.status.busy": "2024-11-20T11:23:40.265710Z", + "iopub.status.idle": "2024-11-20T11:23:54.230825Z", + "shell.execute_reply": "2024-11-20T11:23:54.228962Z" }, "tags": [] }, @@ -315,7 +315,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:30:04,610 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-11-20 06:23:48,129 \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": "2024-11-20T06:30:10.996879Z", - "iopub.status.busy": "2024-11-20T06:30:10.995242Z", - "iopub.status.idle": "2024-11-20T06:30:13.502221Z", - "shell.execute_reply": "2024-11-20T06:30:13.500269Z" + "iopub.execute_input": "2024-11-20T11:23:54.238359Z", + "iopub.status.busy": "2024-11-20T11:23:54.237248Z", + "iopub.status.idle": "2024-11-20T11:23:55.576432Z", + "shell.execute_reply": "2024-11-20T11:23:55.574533Z" }, "tags": [] }, @@ -369,14 +369,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:30:13,492 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:23:55,566 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:30:13,494 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.426398 s\n" + "2024-11-20 06:23:55,568 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.264936 s\n" ] }, { @@ -419,10 +419,10 @@ "id": "46fd771c-5da7-4bce-aec7-08a5210a069b", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:30:13.513723Z", - "iopub.status.busy": "2024-11-20T06:30:13.511104Z", - "iopub.status.idle": "2024-11-20T06:51:06.189191Z", - "shell.execute_reply": "2024-11-20T06:51:06.187456Z" + "iopub.execute_input": "2024-11-20T11:23:55.583835Z", + "iopub.status.busy": "2024-11-20T11:23:55.582722Z", + "iopub.status.idle": "2024-11-20T11:32:59.013474Z", + "shell.execute_reply": "2024-11-20T11:32:59.011677Z" }, "tags": [] }, @@ -431,14 +431,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:51:06,179 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-11-20 06:32:59,003 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-11-20 01:51:06,181 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1252.407178 s\n" + "2024-11-20 06:32:59,005 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 543.173872 s\n" ] }, { @@ -488,10 +488,10 @@ "id": "d20a2581-f613-4ab8-9feb-3e84b8835db1", "metadata": { "execution": { - "iopub.execute_input": "2024-11-20T06:51:06.196661Z", - "iopub.status.busy": "2024-11-20T06:51:06.195288Z", - "iopub.status.idle": "2024-11-20T06:51:06.213014Z", - "shell.execute_reply": "2024-11-20T06:51:06.211151Z" + "iopub.execute_input": "2024-11-20T11:32:59.020714Z", + "iopub.status.busy": "2024-11-20T11:32:59.019810Z", + "iopub.status.idle": "2024-11-20T11:32:59.036360Z", + "shell.execute_reply": "2024-11-20T11:32:59.034647Z" }, "tags": [] }, @@ -500,28 +500,7 @@ "data": { "text/plain": [ "measurement_concept_name\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", + "No matching concept 100\n", "Name: count, dtype: int64[pyarrow]" ] },