From f5a7b4d0501791d2521865e8be05a7266b9b8b34 Mon Sep 17 00:00:00 2001 From: amrit110 Date: Fri, 11 Oct 2024 10:26:47 -0400 Subject: [PATCH] deploy: ca043e2427692c9f2347605ca9e5ab8d111ab60b --- 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 | 44 +++++++++++----- tutorials/omop.ipynb | 100 +++++++++++++++++++++--------------- 9 files changed, 239 insertions(+), 199 deletions(-) diff --git a/searchindex.js b/searchindex.js index 6520925..b2887ab 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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"teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"API Reference": [[0, "api-reference"]], "Coding guidelines": [[1, "coding-guidelines"]], "Contents:": [[2, null]], "Contributing": [[3, "contributing"]], "Contributing to cycquery": [[1, "contributing-to-cycquery"]], "Example 1. Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "Example 3. Advanced - uses ConditionRegexMatch from cycquery.ops. Get all patient encounters with diagnoses (ICD-9 long title contains schizophrenia and chronic ), in the year 2015.": [[67, "Example-3.-Advanced---uses-ConditionRegexMatch-from-cycquery.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "Example 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. Running a raw SQL string.": [[67, "Example-8.-Running-a-raw-SQL-string."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate EICUQuerier": [[64, "Imports-and-instantiate-EICUQuerier"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Installing cycquery using pip": [[3, "installing-cycquery-using-pip"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Query postgresql database": [[3, "query-postgresql-database"]], "Tutorials": [[63, "tutorials"]], "Using poetry": [[3, "using-poetry"]], "Welcome to 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"cycquery.ops.ConditionInYears", "cycquery.ops.ConditionLessThan", "cycquery.ops.ConditionLike", "cycquery.ops.ConditionRegexMatch", "cycquery.ops.ConditionStartsWith", "cycquery.ops.ConditionSubstring", "cycquery.ops.Count", "cycquery.ops.Distinct", "cycquery.ops.Drop", "cycquery.ops.DropEmpty", "cycquery.ops.DropNulls", "cycquery.ops.ExtractTimestampComponent", "cycquery.ops.FillNull", "cycquery.ops.GroupByAggregate", "cycquery.ops.Join", "cycquery.ops.Keep", "cycquery.ops.Limit", "cycquery.ops.Literal", "cycquery.ops.Or", "cycquery.ops.OrderBy", "cycquery.ops.QueryOp", "cycquery.ops.RandomizeOrder", "cycquery.ops.Rename", "cycquery.ops.Reorder", "cycquery.ops.ReorderAfter", "cycquery.ops.Sequential", "cycquery.ops.Substring", "cycquery.ops.Trim", "cycquery.ops.Union", "cycquery", "Tutorials", "eICU-CRD tutorial", "GEMINI tutorial", "MIMIC-III tutorial", "MIMIC-IV tutorial", "OMOP tutorial"], "titleterms": {"": 2, "1": [64, 65, 66, 67, 68], "10": 67, "100": 64, "101": 65, "1a": 65, "1b": 65, "1c": 65, "2": [64, 66, 67, 68], "20": 66, "2009": 67, "2010": 68, "2014": 64, "2015": [64, 65, 67], "2016": 65, "2020": 68, "2021": 67, "2a": 65, "3": [64, 66, 67], "31": 65, "4": [64, 66, 67], "5": 67, "6": 67, "7": 67, "8": 67, "9": [66, 67], "And": 23, "Or": 51, "aado2": 66, "abov": 65, "addcolumn": 19, "adddeltacolumn": 20, "adddeltaconst": 21, "addnumer": 22, "admiss": [65, 67], "advanc": 67, "after": 68, "all": [64, 66, 67, 68], "api": [0, 62], "appli": 24, "approx": 67, "apr": 65, "april": 65, "base": [4, 5], "batch": 67, "between": 65, "carevu": 66, "cast": 25, "chart": 66, "chronic": 67, "code": 1, "commit": 1, "conditionafterd": 26, "conditionbefored": 27, "conditionendswith": 28, "conditionequ": 29, "conditiongreaterthan": 30, "conditionin": 31, "conditioninmonth": 32, "conditioninyear": 33, "conditionlessthan": 34, "conditionlik": 35, "conditionregexmatch": [36, 67], "conditionstartswith": 37, "conditionsubstr": 38, "contain": 67, "content": 2, "contribut": [1, 3], "count": 39, "crd": 64, "creat": 65, "cycqueri": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 67], "databas": 3, "dataset": [62, 65], "datasetqueri": 5, "develop": 3, "diagnos": [64, 66, 67, 68], "diagnosisstr": 64, "discharg": [64, 65], "discharge_date_tim": 65, "distinct": 40, "document": [2, 3], "drop": 41, "dropempti": 42, "dropnul": 43, "each": 65, "eicu": [6, 7, 64], "eicuqueri": [7, 64], "encount": [64, 65, 66, 67], "end": 68, "event": 66, "exampl": [64, 65, 66, 67, 68], "extracttimestampcompon": 44, "femal": [64, 66, 67, 68], "fillnul": 45, "filter": 67, "from": [65, 67], "gastroenter": 66, "gemini": [8, 9, 65], "geminiqueri": [9, 65], "get": [3, 64, 65, 66, 67, 68], "glucos": 64, "groupbyaggreg": 46, "guidelin": 1, "have": 66, "hemoglobin": 67, "hook": 1, "hospit": [64, 65], "how": 65, "icd": [66, 67], "iii": 66, "import": [64, 65, 66, 67, 68], "index": 67, "infecti": 67, "instal": 3, "instanti": [64, 65, 66, 67, 68], "interfac": [10, 11], "iv": 67, "join": 47, "keep": [48, 65], "keyword": 67, "lab": [64, 66, 67], "later": 67, "less": 66, "limit": [49, 64], "liter": 50, "long": [66, 67], "lymphadenopathi": 67, "mai": 65, "male": 66, "mani": 65, "march": 65, "measur": 68, "medic": 64, "mimic": [66, 67], "mimiciii": [12, 13], "mimiciiiqueri": [13, 66], "mimiciv": [14, 15], "mimicivqueri": [15, 67], "mortal": [66, 68], "most": 65, "number": 65, "occur": 67, "omop": [16, 17, 68], "omopqueri": [17, 68], "one": 65, "onli": 65, "op": [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67], "orderbi": 52, "outcom": [66, 68], "partit": 67, "patient": [64, 65, 66, 67, 68], "patient_id_hash": 65, "per": 65, "pip": 3, "place": 65, "poetri": 3, "postgresql": 3, "potassium": [64, 66], "pre": 1, "queri": 3, "queryinterfac": 11, "queryop": 53, "radiologi": 67, "randomizeord": 54, "raw": 67, "recent": 65, "record": 65, "refer": 0, "renam": 55, "reorder": 56, "reorderaft": 57, "report": 67, "return": 67, "routin": 67, "row": 64, "run": 67, "schizophrenia": [64, 67], "search": 64, "sepsi": 68, "sequenti": 58, "set": 65, "sign": 67, "sodium": 65, "sort": 65, "sql": 67, "start": 3, "string": 67, "subject_id": 67, "subset": 65, "substr": [59, 64], "tabl": 65, "take": 65, "teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file diff --git a/tutorials/eicu.html b/tutorials/eicu.html index 7a475eb..a0fdbb9 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-10-01 16:05:00,713 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-10-11 10:03:37,592 INFO cycquery.orm    - Database setup, ready to run queries!
@@ -679,7 +679,7 @@

Example 1. Get all female patients discharged in 2014 (limit to 100 rows). 
-2024-10-01 16:05:02,203 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:03:38,579 INFO cycquery.orm    - Query returned successfully!

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

Example 1. Get all female patients discharged in 2014 (limit to 100 rows). 
-2024-10-01 16:05:02,205 INFO cycquery.utils.profile - Finished executing function run_query in 0.651641 s
+2024-10-11 10:03:38,581 INFO cycquery.utils.profile - Finished executing function run_query in 0.170236 s

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

Example 2. Get all patient encounters with diagnoses ( 
-2024-10-01 16:05:03,620 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:03:39,534 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get all patient encounters with diagnoses ( 
-2024-10-01 16:05:03,622 INFO cycquery.utils.profile - Finished executing function run_query in 1.385223 s
+2024-10-11 10:03:39,536 INFO cycquery.utils.profile - Finished executing function run_query in 0.923233 s

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

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

-2024-10-01 16:05:04,041 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:03:40,069 INFO cycquery.orm    - Query returned successfully!
@@ -779,7 +779,7 @@

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

-2024-10-01 16:05:04,047 INFO cycquery.utils.profile - Finished executing function run_query in 0.382669 s
+2024-10-11 10:03:40,071 INFO cycquery.utils.profile - Finished executing function run_query in 0.486850 s
@@ -818,7 +818,7 @@

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

-2024-10-01 16:05:11,900 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:03:44,141 INFO cycquery.orm    - Query returned successfully!
@@ -826,7 +826,7 @@

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

-2024-10-01 16:05:11,902 INFO cycquery.utils.profile - Finished executing function run_query in 7.801912 s
+2024-10-11 10:03:44,143 INFO cycquery.utils.profile - Finished executing function run_query in 4.032112 s
diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb index e56ff61..c56c391 100644 --- a/tutorials/eicu.ipynb +++ b/tutorials/eicu.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:04:57.743899Z", - "iopub.status.busy": "2024-10-01T20:04:57.742789Z", - "iopub.status.idle": "2024-10-01T20:05:01.531124Z", - "shell.execute_reply": "2024-10-01T20:05:01.529088Z" + "iopub.execute_input": "2024-10-11T14:03:35.111332Z", + "iopub.status.busy": "2024-10-11T14:03:35.110110Z", + "iopub.status.idle": "2024-10-11T14:03:38.390373Z", + "shell.execute_reply": "2024-10-11T14:03:38.388596Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:00,713 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-10-11 10:03:37,592 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -124,10 +124,10 @@ "id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:01.540127Z", - "iopub.status.busy": "2024-10-01T20:05:01.538235Z", - "iopub.status.idle": "2024-10-01T20:05:02.214346Z", - "shell.execute_reply": "2024-10-01T20:05:02.212279Z" + "iopub.execute_input": "2024-10-11T14:03:38.397772Z", + "iopub.status.busy": "2024-10-11T14:03:38.396948Z", + "iopub.status.idle": "2024-10-11T14:03:38.588580Z", + "shell.execute_reply": "2024-10-11T14:03:38.586813Z" }, "tags": [] }, @@ -136,14 +136,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:02,203 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:03:38,579 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:02,205 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.651641 s\n" + "2024-10-11 10:03:38,581 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.170236 s\n" ] }, { @@ -180,10 +180,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:02.222547Z", - "iopub.status.busy": "2024-10-01T20:05:02.221864Z", - "iopub.status.idle": "2024-10-01T20:05:03.631297Z", - "shell.execute_reply": "2024-10-01T20:05:03.627986Z" + "iopub.execute_input": "2024-10-11T14:03:38.596396Z", + "iopub.status.busy": "2024-10-11T14:03:38.594869Z", + "iopub.status.idle": "2024-10-11T14:03:39.543370Z", + "shell.execute_reply": "2024-10-11T14:03:39.541602Z" }, "tags": [] }, @@ -192,14 +192,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:03,620 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:03:39,534 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:03,622 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.385223 s\n" + "2024-10-11 10:03:39,536 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.923233 s\n" ] }, { @@ -236,10 +236,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:03.639215Z", - "iopub.status.busy": "2024-10-01T20:05:03.638412Z", - "iopub.status.idle": "2024-10-01T20:05:04.070202Z", - "shell.execute_reply": "2024-10-01T20:05:04.068472Z" + "iopub.execute_input": "2024-10-11T14:03:39.551008Z", + "iopub.status.busy": "2024-10-11T14:03:39.549980Z", + "iopub.status.idle": "2024-10-11T14:03:40.079404Z", + "shell.execute_reply": "2024-10-11T14:03:40.077526Z" }, "tags": [] }, @@ -248,14 +248,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:04,041 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:03:40,069 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:04,047 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.382669 s\n" + "2024-10-11 10:03:40,071 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.486850 s\n" ] }, { @@ -298,10 +298,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:04.078243Z", - "iopub.status.busy": "2024-10-01T20:05:04.077111Z", - "iopub.status.idle": "2024-10-01T20:05:11.911457Z", - "shell.execute_reply": "2024-10-01T20:05:11.909768Z" + "iopub.execute_input": "2024-10-11T14:03:40.087395Z", + "iopub.status.busy": "2024-10-11T14:03:40.085936Z", + "iopub.status.idle": "2024-10-11T14:03:44.149996Z", + "shell.execute_reply": "2024-10-11T14:03:44.148201Z" }, "tags": [] }, @@ -310,14 +310,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:11,900 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:03:44,141 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:11,902 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 7.801912 s\n" + "2024-10-11 10:03:44,143 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.032112 s\n" ] }, { diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html index 9bcd72f..57f5d48 100644 --- a/tutorials/mimiciii.html +++ b/tutorials/mimiciii.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-10-01 16:05:28,856 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-10-11 10:04:00,312 INFO cycquery.orm    - Database setup, ready to run queries!

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

Example 1. Get all male patients with a mortality outcome. 
-2024-10-01 16:05:36,267 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:04:06,957 INFO cycquery.orm    - Query returned successfully!

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

Example 1. Get all male patients with a mortality outcome. 
-2024-10-01 16:05:36,269 INFO cycquery.utils.profile - Finished executing function run_query in 0.319342 s
+2024-10-11 10:04:06,959 INFO cycquery.utils.profile - Finished executing function run_query in 0.204972 s

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

Example 2. Get all female patient encounters with diagnoses ( 
-2024-10-01 16:05:39,635 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:04:08,672 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get all female patient encounters with diagnoses ( 
-2024-10-01 16:05:39,637 INFO cycquery.utils.profile - Finished executing function run_query in 3.320573 s
+2024-10-11 10:04:08,673 INFO cycquery.utils.profile - Finished executing function run_query in 1.662382 s

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

Example 3. Get potassium lab tests for female patients. 
-2024-10-01 16:05:39,925 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:04:08,968 INFO cycquery.orm    - Query returned successfully!

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

Example 3. Get potassium lab tests for female patients. 
-2024-10-01 16:05:39,927 INFO cycquery.utils.profile - Finished executing function run_query in 0.243667 s
+2024-10-11 10:04:08,969 INFO cycquery.utils.profile - Finished executing function run_query in 0.247393 s

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

Example 4. Get AaDO2 carevue chart events for male patients that have a 
-2024-10-01 16:22:36,593 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:17:37,144 INFO cycquery.orm    - Query returned successfully!

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

Example 4. Get AaDO2 carevue chart events for male patients that have a 
-2024-10-01 16:22:36,647 INFO cycquery.utils.profile - Finished executing function run_query in 1016.653061 s
+2024-10-11 10:17:37,193 INFO cycquery.utils.profile - Finished executing function run_query in 808.157255 s

diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb index f569b4b..9de6f37 100644 --- a/tutorials/mimiciii.ipynb +++ b/tutorials/mimiciii.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:19.669639Z", - "iopub.status.busy": "2024-10-01T20:05:19.668557Z", - "iopub.status.idle": "2024-10-01T20:05:35.932568Z", - "shell.execute_reply": "2024-10-01T20:05:35.927746Z" + "iopub.execute_input": "2024-10-11T14:03:52.359854Z", + "iopub.status.busy": "2024-10-11T14:03:52.358662Z", + "iopub.status.idle": "2024-10-11T14:04:06.737597Z", + "shell.execute_reply": "2024-10-11T14:04:06.735693Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:28,856 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-10-11 10:04:00,312 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -94,10 +94,10 @@ "id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:35.941533Z", - "iopub.status.busy": "2024-10-01T20:05:35.940082Z", - "iopub.status.idle": "2024-10-01T20:05:36.276772Z", - "shell.execute_reply": "2024-10-01T20:05:36.274981Z" + "iopub.execute_input": "2024-10-11T14:04:06.745311Z", + "iopub.status.busy": "2024-10-11T14:04:06.744461Z", + "iopub.status.idle": "2024-10-11T14:04:06.966818Z", + "shell.execute_reply": "2024-10-11T14:04:06.965099Z" }, "tags": [] }, @@ -106,14 +106,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:36,267 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:04:06,957 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:36,269 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.319342 s\n" + "2024-10-11 10:04:06,959 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.204972 s\n" ] }, { @@ -150,10 +150,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:36.284969Z", - "iopub.status.busy": "2024-10-01T20:05:36.283406Z", - "iopub.status.idle": "2024-10-01T20:05:39.644662Z", - "shell.execute_reply": "2024-10-01T20:05:39.642828Z" + "iopub.execute_input": "2024-10-11T14:04:06.974489Z", + "iopub.status.busy": "2024-10-11T14:04:06.973474Z", + "iopub.status.idle": "2024-10-11T14:04:08.681313Z", + "shell.execute_reply": "2024-10-11T14:04:08.679550Z" }, "tags": [] }, @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:39,635 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:04:08,672 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:39,637 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.320573 s\n" + "2024-10-11 10:04:08,673 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.662382 s\n" ] }, { @@ -211,10 +211,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:39.651302Z", - "iopub.status.busy": "2024-10-01T20:05:39.650261Z", - "iopub.status.idle": "2024-10-01T20:05:39.934356Z", - "shell.execute_reply": "2024-10-01T20:05:39.932646Z" + "iopub.execute_input": "2024-10-11T14:04:08.688878Z", + "iopub.status.busy": "2024-10-11T14:04:08.687529Z", + "iopub.status.idle": "2024-10-11T14:04:08.977298Z", + "shell.execute_reply": "2024-10-11T14:04:08.975468Z" }, "tags": [] }, @@ -223,14 +223,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:39,925 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:04:08,968 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:05:39,927 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.243667 s\n" + "2024-10-11 10:04:08,969 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.247393 s\n" ] }, { @@ -264,10 +264,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:05:39.941194Z", - "iopub.status.busy": "2024-10-01T20:05:39.940551Z", - "iopub.status.idle": "2024-10-01T20:22:36.680196Z", - "shell.execute_reply": "2024-10-01T20:22:36.678370Z" + "iopub.execute_input": "2024-10-11T14:04:08.984896Z", + "iopub.status.busy": "2024-10-11T14:04:08.983925Z", + "iopub.status.idle": "2024-10-11T14:17:37.202045Z", + "shell.execute_reply": "2024-10-11T14:17:37.200034Z" }, "tags": [] }, @@ -276,14 +276,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:22:36,593 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:17:37,144 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:22:36,647 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1016.653061 s\n" + "2024-10-11 10:17:37,193 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 808.157255 s\n" ] }, { diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html index a3e874f..250b0bb 100644 --- a/tutorials/mimiciv.html +++ b/tutorials/mimiciv.html @@ -615,7 +615,7 @@

Imports and instantiate 
-2024-10-01 16:23:08,887 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-10-11 10:18:01,492 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -660,7 +660,7 @@

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

-2024-10-01 16:23:12,788 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:18:06,253 INFO cycquery.orm    - Query returned successfully!
@@ -668,7 +668,7 @@

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

-2024-10-01 16:23:12,790 INFO cycquery.utils.profile - Finished executing function run_query in 1.393220 s
+2024-10-11 10:18:06,255 INFO cycquery.utils.profile - Finished executing function run_query in 2.310790 s
@@ -713,7 +713,7 @@

Example 2. Get all patient encounters with diagnoses ( 
-2024-10-01 16:23:26,347 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:18:21,279 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get all patient encounters with diagnoses ( 
-2024-10-01 16:23:26,349 INFO cycquery.utils.profile - Finished executing function run_query in 13.475876 s
+2024-10-11 10:18:21,281 INFO cycquery.utils.profile - Finished executing function run_query in 14.957633 s

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

Example 3. Advanced - uses 
-2024-10-01 16:23:30,077 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:18:25,069 INFO cycquery.orm    - Query returned successfully!

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

Example 3. Advanced - uses 
-2024-10-01 16:23:30,079 INFO cycquery.utils.profile - Finished executing function run_query in 3.661972 s
+2024-10-11 10:18:25,071 INFO cycquery.utils.profile - Finished executing function run_query in 3.714619 s

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

Example 4. Get routine vital signs for patients from year 2015. 
-2024-10-01 16:23:38,082 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:18:30,629 INFO cycquery.orm    - Query returned successfully!

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

Example 4. Get routine vital signs for patients from year 2015. 
-2024-10-01 16:23:38,083 INFO cycquery.utils.profile - Finished executing function run_query in 7.940803 s
+2024-10-11 10:18:30,631 INFO cycquery.utils.profile - Finished executing function run_query in 5.485932 s

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

Example 5. Get hemoglobin lab tests for patients from year 2009. 
-2024-10-01 16:23:42,275 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:18:36,946 INFO cycquery.orm    - Query returned successfully!

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

Example 5. Get hemoglobin lab tests for patients from year 2009. 
-2024-10-01 16:23:42,277 INFO cycquery.utils.profile - Finished executing function run_query in 4.119322 s
+2024-10-11 10:18:36,948 INFO cycquery.utils.profile - Finished executing function run_query in 6.241206 s

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

Example 6. Get radiology reports and filter on keywords 
-2024-10-01 16:25:10,112 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:20:08,323 INFO cycquery.orm    - Query returned successfully!

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

Example 6. Get radiology reports and filter on keywords 
-2024-10-01 16:25:10,114 INFO cycquery.utils.profile - Finished executing function run_query in 87.780566 s
+2024-10-11 10:20:08,325 INFO cycquery.utils.profile - Finished executing function run_query in 91.312438 s

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

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

-2024-10-01 16:25:11,273 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:20:09,656 INFO cycquery.orm    - Query returned successfully!
@@ -978,7 +978,7 @@

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

-2024-10-01 16:25:11,275 INFO cycquery.utils.profile - Finished executing function run_query in 1.080360 s
+2024-10-11 10:20:09,658 INFO cycquery.utils.profile - Finished executing function run_query in 1.229999 s
@@ -1006,7 +1006,7 @@

Example 8. Running a raw SQL string. 
-2024-10-01 16:25:11,749 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:20:10,129 INFO cycquery.orm    - Query returned successfully!

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

Example 8. Running a raw SQL string. 
-2024-10-01 16:25:11,751 INFO cycquery.utils.profile - Finished executing function run_query in 0.013766 s
+2024-10-11 10:20:10,131 INFO cycquery.utils.profile - Finished executing function run_query in 0.014086 s

diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb index 37e13e0..c0d95b2 100644 --- a/tutorials/mimiciv.ipynb +++ b/tutorials/mimiciv.ipynb @@ -35,10 +35,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:22:54.702463Z", - "iopub.status.busy": "2024-10-01T20:22:54.701082Z", - "iopub.status.idle": "2024-10-01T20:23:11.350828Z", - "shell.execute_reply": "2024-10-01T20:23:11.349190Z" + "iopub.execute_input": "2024-10-11T14:17:51.685153Z", + "iopub.status.busy": "2024-10-11T14:17:51.684514Z", + "iopub.status.idle": "2024-10-11T14:18:03.899007Z", + "shell.execute_reply": "2024-10-11T14:18:03.897038Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:08,887 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-10-11 10:18:01,492 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -105,10 +105,10 @@ "id": "cdfadaa4-6fd6-4fd7-85cf-e012aa0799e1", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:23:11.357916Z", - "iopub.status.busy": "2024-10-01T20:23:11.356877Z", - "iopub.status.idle": "2024-10-01T20:23:12.798571Z", - "shell.execute_reply": "2024-10-01T20:23:12.796723Z" + "iopub.execute_input": "2024-10-11T14:18:03.907058Z", + "iopub.status.busy": "2024-10-11T14:18:03.905425Z", + "iopub.status.idle": "2024-10-11T14:18:06.263688Z", + "shell.execute_reply": "2024-10-11T14:18:06.261604Z" } }, "outputs": [ @@ -116,14 +116,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:12,788 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:18:06,253 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:12,790 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.393220 s\n" + "2024-10-11 10:18:06,255 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.310790 s\n" ] }, { @@ -160,10 +160,10 @@ "id": "a89a9cf0", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:23:12.805853Z", - "iopub.status.busy": "2024-10-01T20:23:12.804911Z", - "iopub.status.idle": "2024-10-01T20:23:26.355994Z", - "shell.execute_reply": "2024-10-01T20:23:26.354275Z" + "iopub.execute_input": "2024-10-11T14:18:06.271128Z", + "iopub.status.busy": "2024-10-11T14:18:06.269719Z", + "iopub.status.idle": "2024-10-11T14:18:21.290085Z", + "shell.execute_reply": "2024-10-11T14:18:21.288056Z" } }, "outputs": [ @@ -171,14 +171,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:26,347 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:18:21,279 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:26,349 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 13.475876 s\n" + "2024-10-11 10:18:21,281 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 14.957633 s\n" ] }, { @@ -225,10 +225,10 @@ "id": "03936cee", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:23:26.363079Z", - "iopub.status.busy": "2024-10-01T20:23:26.361705Z", - "iopub.status.idle": "2024-10-01T20:23:30.086744Z", - "shell.execute_reply": "2024-10-01T20:23:30.085061Z" + "iopub.execute_input": "2024-10-11T14:18:21.298853Z", + "iopub.status.busy": "2024-10-11T14:18:21.297508Z", + "iopub.status.idle": "2024-10-11T14:18:25.080157Z", + "shell.execute_reply": "2024-10-11T14:18:25.078296Z" } }, "outputs": [ @@ -236,14 +236,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:30,077 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:18:25,069 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:30,079 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.661972 s\n" + "2024-10-11 10:18:25,071 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.714619 s\n" ] }, { @@ -290,10 +290,10 @@ "id": "56a72377", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:23:30.095455Z", - "iopub.status.busy": "2024-10-01T20:23:30.093356Z", - "iopub.status.idle": "2024-10-01T20:23:38.091485Z", - "shell.execute_reply": "2024-10-01T20:23:38.089713Z" + "iopub.execute_input": "2024-10-11T14:18:25.088192Z", + "iopub.status.busy": "2024-10-11T14:18:25.086821Z", + "iopub.status.idle": "2024-10-11T14:18:30.640389Z", + "shell.execute_reply": "2024-10-11T14:18:30.638481Z" } }, "outputs": [ @@ -301,14 +301,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:38,082 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:18:30,629 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:38,083 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 7.940803 s\n" + "2024-10-11 10:18:30,631 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.485932 s\n" ] }, { @@ -351,10 +351,10 @@ "id": "bce11f81", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:23:38.099045Z", - "iopub.status.busy": "2024-10-01T20:23:38.097959Z", - "iopub.status.idle": "2024-10-01T20:23:42.284684Z", - "shell.execute_reply": "2024-10-01T20:23:42.282925Z" + "iopub.execute_input": "2024-10-11T14:18:30.648126Z", + "iopub.status.busy": "2024-10-11T14:18:30.647042Z", + "iopub.status.idle": "2024-10-11T14:18:36.955682Z", + "shell.execute_reply": "2024-10-11T14:18:36.953952Z" } }, "outputs": [ @@ -362,14 +362,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:42,275 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:18:36,946 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:23:42,277 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.119322 s\n" + "2024-10-11 10:18:36,948 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 6.241206 s\n" ] }, { @@ -412,10 +412,10 @@ "id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:23:42.298161Z", - "iopub.status.busy": "2024-10-01T20:23:42.296376Z", - "iopub.status.idle": "2024-10-01T20:25:10.122048Z", - "shell.execute_reply": "2024-10-01T20:25:10.120289Z" + "iopub.execute_input": "2024-10-11T14:18:36.963684Z", + "iopub.status.busy": "2024-10-11T14:18:36.962224Z", + "iopub.status.idle": "2024-10-11T14:20:08.333276Z", + "shell.execute_reply": "2024-10-11T14:20:08.331501Z" }, "tags": [] }, @@ -424,14 +424,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:10,112 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:20:08,323 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:10,114 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 87.780566 s\n" + "2024-10-11 10:20:08,325 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 91.312438 s\n" ] }, { @@ -480,10 +480,10 @@ "id": "28683d70-376e-4d9b-883d-1a7de634e455", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:25:10.129182Z", - "iopub.status.busy": "2024-10-01T20:25:10.127822Z", - "iopub.status.idle": "2024-10-01T20:25:11.727130Z", - "shell.execute_reply": "2024-10-01T20:25:11.725133Z" + "iopub.execute_input": "2024-10-11T14:20:08.341166Z", + "iopub.status.busy": "2024-10-11T14:20:08.339709Z", + "iopub.status.idle": "2024-10-11T14:20:10.107163Z", + "shell.execute_reply": "2024-10-11T14:20:10.105260Z" } }, "outputs": [ @@ -491,14 +491,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:11,273 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:20:09,656 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:11,275 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.080360 s\n" + "2024-10-11 10:20:09,658 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.229999 s\n" ] }, { @@ -543,10 +543,10 @@ "id": "a853deec", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:25:11.735377Z", - "iopub.status.busy": "2024-10-01T20:25:11.733886Z", - "iopub.status.idle": "2024-10-01T20:25:11.758574Z", - "shell.execute_reply": "2024-10-01T20:25:11.756917Z" + "iopub.execute_input": "2024-10-11T14:20:10.115220Z", + "iopub.status.busy": "2024-10-11T14:20:10.114079Z", + "iopub.status.idle": "2024-10-11T14:20:10.138383Z", + "shell.execute_reply": "2024-10-11T14:20:10.136659Z" }, "tags": [] }, @@ -555,14 +555,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:11,749 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:20:10,129 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:11,751 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013766 s\n" + "2024-10-11 10:20:10,131 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.014086 s\n" ] }, { diff --git a/tutorials/omop.html b/tutorials/omop.html index 7be9578..32866a3 100644 --- a/tutorials/omop.html +++ b/tutorials/omop.html @@ -623,7 +623,7 @@

Imports and instantiate 
-2024-10-01 16:25:23,333 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-10-11 10:20:23,549 INFO cycquery.orm    - Database setup, ready to run queries!

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

Example 1. Get all patient visits in or after 2010. 
-2024-10-01 16:25:24,977 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:20:25,407 INFO cycquery.orm    - Query returned successfully!

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

Example 1. Get all patient visits in or after 2010. 
-2024-10-01 16:25:24,979 INFO cycquery.utils.profile - Finished executing function run_query in 0.320281 s
+2024-10-11 10:20:25,410 INFO cycquery.utils.profile - Finished executing function run_query in 0.568863 s

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

Example 2. Get measurements for all visits in or after 2020. 
-2024-10-01 16:25:25,911 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:20:26,797 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get measurements for all visits in or after 2020. 
-2024-10-01 16:25:25,913 INFO cycquery.utils.profile - Finished executing function run_query in 0.704169 s
+2024-10-11 10:20:26,799 INFO cycquery.utils.profile - Finished executing function run_query in 0.892611 s

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

Imports and instantiate 
-2024-10-01 16:25:32,849 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-10-11 10:20:34,968 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -858,7 +858,7 @@

Example 1. Get all patient visits that ended in a mortality outcome in or af 

-2024-10-01 16:25:40,800 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:20:42,992 INFO cycquery.orm    - Query returned successfully!
@@ -866,7 +866,7 @@

Example 1. Get all patient visits that ended in a mortality outcome in or af 

-2024-10-01 16:25:40,801 INFO cycquery.utils.profile - Finished executing function run_query in 1.161417 s
+2024-10-11 10:20:42,994 INFO cycquery.utils.profile - Finished executing function run_query in 1.276970 s
@@ -922,7 +922,7 @@

Example 2. Get all measurements for female patient visits with 
-2024-10-01 16:30:25,213 INFO cycquery.orm    - Query returned successfully!
+2024-10-11 10:25:23,932 INFO cycquery.orm    - Query returned successfully!

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

Example 2. Get all measurements for female patient visits with 
-2024-10-01 16:30:25,321 INFO cycquery.utils.profile - Finished executing function run_query in 284.280096 s
+2024-10-11 10:25:23,934 INFO cycquery.utils.profile - Finished executing function run_query in 280.691683 s

@@ -956,8 +956,28 @@

Example 2. Get all measurements for female patient visits with 
 measurement_concept_name
-Body weight            51
-No matching concept    49
+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 4fea666..2b3f98a 100644 --- a/tutorials/omop.ipynb +++ b/tutorials/omop.ipynb @@ -45,10 +45,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:25:18.934140Z", - "iopub.status.busy": "2024-10-01T20:25:18.933018Z", - "iopub.status.idle": "2024-10-01T20:25:24.618322Z", - "shell.execute_reply": "2024-10-01T20:25:24.616469Z" + "iopub.execute_input": "2024-10-11T14:20:17.931387Z", + "iopub.status.busy": "2024-10-11T14:20:17.930459Z", + "iopub.status.idle": "2024-10-11T14:20:24.791593Z", + "shell.execute_reply": "2024-10-11T14:20:24.789865Z" } }, "outputs": [ @@ -56,7 +56,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:23,333 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-10-11 10:20:23,549 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -151,10 +151,10 @@ "id": "3a3d9cb9-fe40-45b8-ba2f-8de52a3b7f4f", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:25:24.626815Z", - "iopub.status.busy": "2024-10-01T20:25:24.625233Z", - "iopub.status.idle": "2024-10-01T20:25:25.114924Z", - "shell.execute_reply": "2024-10-01T20:25:25.113193Z" + "iopub.execute_input": "2024-10-11T14:20:24.799559Z", + "iopub.status.busy": "2024-10-11T14:20:24.797936Z", + "iopub.status.idle": "2024-10-11T14:20:25.796608Z", + "shell.execute_reply": "2024-10-11T14:20:25.794840Z" } }, "outputs": [ @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:24,977 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:20:25,407 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:24,979 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.320281 s\n" + "2024-10-11 10:20:25,410 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.568863 s\n" ] }, { @@ -227,10 +227,10 @@ "id": "030e2491-a7cc-42f3-a1ca-618212b3524c", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:25:25.121291Z", - "iopub.status.busy": "2024-10-01T20:25:25.120718Z", - "iopub.status.idle": "2024-10-01T20:25:25.920435Z", - "shell.execute_reply": "2024-10-01T20:25:25.918658Z" + "iopub.execute_input": "2024-10-11T14:20:25.804188Z", + "iopub.status.busy": "2024-10-11T14:20:25.803187Z", + "iopub.status.idle": "2024-10-11T14:20:26.806825Z", + "shell.execute_reply": "2024-10-11T14:20:26.804948Z" } }, "outputs": [ @@ -238,14 +238,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:25,911 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:20:26,797 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:25,913 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.704169 s\n" + "2024-10-11 10:20:26,799 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.892611 s\n" ] }, { @@ -303,10 +303,10 @@ "id": "0622b3df-2864-4f32-bd98-806019f59c50", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:25:25.927591Z", - "iopub.status.busy": "2024-10-01T20:25:25.926558Z", - "iopub.status.idle": "2024-10-01T20:25:39.588625Z", - "shell.execute_reply": "2024-10-01T20:25:39.586878Z" + "iopub.execute_input": "2024-10-11T14:20:26.815828Z", + "iopub.status.busy": "2024-10-11T14:20:26.814005Z", + "iopub.status.idle": "2024-10-11T14:20:41.646355Z", + "shell.execute_reply": "2024-10-11T14:20:41.644718Z" }, "tags": [] }, @@ -315,7 +315,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:32,849 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-10-11 10:20:34,968 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -357,10 +357,10 @@ "id": "40ff2e83-75e4-4119-aa33-26f95e63ddaa", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:25:39.594828Z", - "iopub.status.busy": "2024-10-01T20:25:39.593798Z", - "iopub.status.idle": "2024-10-01T20:25:40.809394Z", - "shell.execute_reply": "2024-10-01T20:25:40.807647Z" + "iopub.execute_input": "2024-10-11T14:20:41.653888Z", + "iopub.status.busy": "2024-10-11T14:20:41.653061Z", + "iopub.status.idle": "2024-10-11T14:20:43.001614Z", + "shell.execute_reply": "2024-10-11T14:20:42.999935Z" }, "tags": [] }, @@ -369,14 +369,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:40,800 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:20:42,992 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:25:40,801 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.161417 s\n" + "2024-10-11 10:20:42,994 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.276970 s\n" ] }, { @@ -419,10 +419,10 @@ "id": "46fd771c-5da7-4bce-aec7-08a5210a069b", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:25:40.816615Z", - "iopub.status.busy": "2024-10-01T20:25:40.815140Z", - "iopub.status.idle": "2024-10-01T20:30:25.330074Z", - "shell.execute_reply": "2024-10-01T20:30:25.328478Z" + "iopub.execute_input": "2024-10-11T14:20:43.009278Z", + "iopub.status.busy": "2024-10-11T14:20:43.007852Z", + "iopub.status.idle": "2024-10-11T14:25:23.942520Z", + "shell.execute_reply": "2024-10-11T14:25:23.940757Z" }, "tags": [] }, @@ -431,14 +431,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:30:25,213 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-10-11 10:25:23,932 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-10-01 16:30:25,321 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 284.280096 s\n" + "2024-10-11 10:25:23,934 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 280.691683 s\n" ] }, { @@ -488,10 +488,10 @@ "id": "d20a2581-f613-4ab8-9feb-3e84b8835db1", "metadata": { "execution": { - "iopub.execute_input": "2024-10-01T20:30:25.369069Z", - "iopub.status.busy": "2024-10-01T20:30:25.367822Z", - "iopub.status.idle": "2024-10-01T20:30:25.850784Z", - "shell.execute_reply": "2024-10-01T20:30:25.848960Z" + "iopub.execute_input": "2024-10-11T14:25:24.001717Z", + "iopub.status.busy": "2024-10-11T14:25:24.000976Z", + "iopub.status.idle": "2024-10-11T14:25:24.765883Z", + "shell.execute_reply": "2024-10-11T14:25:24.763631Z" }, "tags": [] }, @@ -500,8 +500,28 @@ "data": { "text/plain": [ "measurement_concept_name\n", - "Body weight 51\n", - "No matching concept 49\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]" ] },