diff --git a/_modules/cycquery/mimiciv.html b/_modules/cycquery/mimiciv.html index 6f572ba..bbb22a5 100644 --- a/_modules/cycquery/mimiciv.html +++ b/_modules/cycquery/mimiciv.html @@ -258,20 +258,13 @@

Source code for cycquery.mimiciv

         return QueryInterface(self.db, table)
-
-[docs] - def diagnoses( +
+[docs] + def diagnoses_icd( self, ) -> QueryInterface: """Query MIMIC diagnosis data. - Parameters - ---------- - join - Join arguments. - ops - Additional operations to apply to the query. - Returns ------- cycquery.interface.QueryInterface @@ -290,6 +283,31 @@

Source code for cycquery.mimiciv

         return QueryInterface(self.db, table)
+
+[docs] + def procedures_icd( + self, + ) -> QueryInterface: + """Query MIMIC procedures data. + + Returns + ------- + cycquery.interface.QueryInterface + Constructed query, wrapped in an interface object. + + """ + table = self.get_table("mimiciv_hosp", "procedures_icd") + + # Join with procedures dimension table. + table = qo.Join( + join_table=self.get_table("mimiciv_hosp", "d_icd_procedures"), + on=["icd_code", "icd_version"], + on_to_type=["str", "int"], + )(table) + + return QueryInterface(self.db, table)
+ +
[docs] def labevents( diff --git a/_sources/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst.txt b/_sources/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst.txt index 78813c1..1f04b4b 100644 --- a/_sources/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst.txt +++ b/_sources/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst.txt @@ -17,7 +17,7 @@ cycquery.mimiciv.MIMICIVQuerier :nosignatures: ~MIMICIVQuerier.chartevents - ~MIMICIVQuerier.diagnoses + ~MIMICIVQuerier.diagnoses_icd ~MIMICIVQuerier.get_table ~MIMICIVQuerier.labevents ~MIMICIVQuerier.list_columns @@ -25,6 +25,7 @@ cycquery.mimiciv.MIMICIVQuerier ~MIMICIVQuerier.list_schemas ~MIMICIVQuerier.list_tables ~MIMICIVQuerier.patients + ~MIMICIVQuerier.procedures_icd diff --git a/_sources/tutorials/mimiciv.ipynb.txt b/_sources/tutorials/mimiciv.ipynb.txt index 049614a..a05874c 100644 --- a/_sources/tutorials/mimiciv.ipynb.txt +++ b/_sources/tutorials/mimiciv.ipynb.txt @@ -107,7 +107,7 @@ " qo.ConditionInYears(\"admittime\", \"2015\"),\n", ")\n", "patient_admissions = patient_admissions.ops(ops)\n", - "diagnoses = querier.diagnoses()\n", + "diagnoses = querier.diagnoses_icd()\n", "diagnoses_ops = qo.Sequential(\n", " qo.ConditionEquals(\"icd_version\", 10),\n", " qo.ConditionSubstring(\"long_title\", \"schizophrenia\"),\n", @@ -143,7 +143,7 @@ " qo.ConditionInYears(\"admittime\", \"2015\"),\n", ")\n", "patient_admissions = patient_admissions.ops(ops)\n", - "diagnoses = querier.diagnoses()\n", + "diagnoses = querier.diagnoses_icd()\n", "diagnoses_ops = qo.Sequential(\n", " qo.ConditionEquals(\"icd_version\", 9),\n", " qo.ConditionRegexMatch(\"long_title\", r\"(?=.*schizophrenia)(?=.*chronic)\"),\n", diff --git a/api.html b/api.html index 1ff4418..ac2affc 100644 --- a/api.html +++ b/api.html @@ -538,7 +538,7 @@

API Referencecycquery.mimiciv.MIMICIVQuerier diff --git a/genindex.html b/genindex.html index 8e8cee6..1ce872b 100644 --- a/genindex.html +++ b/genindex.html @@ -437,12 +437,12 @@

D

    +
  • diagnoses_icd() (MIMICIVQuerier method) +
  • Distinct (class in cycquery.ops)
  • Drop (class in cycquery.ops) @@ -670,11 +670,13 @@

    P

    - + diff --git a/objects.inv b/objects.inv index c3bc963..082e8d5 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html b/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html index a9bd921..2f42c40 100644 --- a/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html +++ b/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html @@ -200,7 +200,7 @@

    cycquery.mimiciv.MIMICIVQuerier

    chartevents

    Query ICU chart events from the ICU module.

    -

    diagnoses

    +

    diagnoses_icd

    Query MIMIC diagnosis data.

    get_table

    @@ -224,6 +224,9 @@

    cycquery.mimiciv.MIMICIVQuerier

    patients

    Query MIMIC patient data.

    +

    procedures_icd

    +

    Query MIMIC procedures data.

    +
    @@ -241,21 +244,15 @@

    cycquery.mimiciv.MIMICIVQuerier -
    -diagnoses()[source]
    +
    +diagnoses_icd()[source]

    Query MIMIC diagnosis data.

    -
    Parameters:
    -
      -

    • join – Join arguments.

      • -

    • ops – Additional operations to apply to the query.

      • -
    -
    -
    Returns:
    -

    Constructed query, wrapped in an interface object.

    +
    Returns:
    +

    Constructed query, wrapped in an interface object.

    -
    Return type:
    -

    cycquery.interface.QueryInterface

    +
    Return type:
    +

    cycquery.interface.QueryInterface

    @@ -381,6 +378,20 @@

    cycquery.mimiciv.MIMICIVQuerier +
    +procedures_icd()[source]
    +

    Query MIMIC procedures data.

    +
    +
    Returns:
    +

    Constructed query, wrapped in an interface object.

    +
    +
    Return type:
    +

    cycquery.interface.QueryInterface

    +
    +
    +
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"vital": 67, "sign": 67, "5": 67, "hemoglobin": 67, "2009": 67, "6": 67, "radiologi": 67, "report": 67, "filter": 67, "keyword": 67, "lymphadenopathi": 67, "infecti": 67, "occur": 67, "togeth": 67, "7": 67, "return": 67, "batch": 67, "partit": 67, "index": 67, "subject_id": 67, "8": 67, "run": 67, "raw": 67, "sql": 67, "string": 67, "visit": 68, "after": 68, "2010": 68, "measur": 68, "2020": 68, "end": 68, "sepsi": 68}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx.ext.intersphinx": 1, "nbsphinx": 4, "sphinx": 60}, "alltitles": {"API Reference": [[0, "api-reference"]], "Contributing to cyclops-query": [[1, "contributing-to-cyclops-query"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Coding guidelines": [[1, "coding-guidelines"]], "Welcome to cyclops-query\u2019s documentation!": [[2, "welcome-to-cyclops-query-s-documentation"]], "Contents:": [[2, null]], "cyclops-query": [[3, "cyclops-query"]], "\ud83d\udc23 Getting Started": [[3, "getting-started"]], "Installing cyclops-query using pip": [[3, "installing-cyclops-query-using-pip"]], "Query postgresql database": [[3, "query-postgresql-database"]], "\ud83e\uddd1\ud83c\udfff\u200d\ud83d\udcbb Developing": [[3, "developing"]], "Using poetry": [[3, "using-poetry"]], "Contributing": [[3, "contributing"]], "\ud83d\udcda Documentation": [[3, "documentation"]], "\ud83c\udf93 Citation": [[3, "citation"]], "cycquery.base": [[4, "module-cycquery.base"]], "cycquery.base.DatasetQuerier": [[5, "cycquery-base-datasetquerier"]], "cycquery.eicu": [[6, "module-cycquery.eicu"]], "cycquery.eicu.EICUQuerier": [[7, "cycquery-eicu-eicuquerier"]], "cycquery.gemini": [[8, "module-cycquery.gemini"]], "cycquery.gemini.GEMINIQuerier": [[9, "cycquery-gemini-geminiquerier"]], "cycquery.interface": [[10, "module-cycquery.interface"]], "cycquery.interface.QueryInterface": [[11, "cycquery-interface-queryinterface"]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, "cycquery-mimiciii-mimiciiiquerier"]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, "cycquery-mimiciv-mimicivquerier"]], "cycquery.omop": [[16, "module-cycquery.omop"]], "cycquery.omop.OMOPQuerier": [[17, "cycquery-omop-omopquerier"]], "cycquery.ops": [[18, "module-cycquery.ops"]], "cycquery.ops.AddColumn": [[19, "cycquery-ops-addcolumn"]], "cycquery.ops.AddDeltaColumn": [[20, "cycquery-ops-adddeltacolumn"]], "cycquery.ops.AddDeltaConstant": [[21, "cycquery-ops-adddeltaconstant"]], "cycquery.ops.AddNumeric": [[22, "cycquery-ops-addnumeric"]], "cycquery.ops.And": [[23, "cycquery-ops-and"]], "cycquery.ops.Apply": [[24, "cycquery-ops-apply"]], "cycquery.ops.Cast": [[25, "cycquery-ops-cast"]], "cycquery.ops.ConditionAfterDate": [[26, "cycquery-ops-conditionafterdate"]], "cycquery.ops.ConditionBeforeDate": [[27, "cycquery-ops-conditionbeforedate"]], "cycquery.ops.ConditionEndsWith": [[28, "cycquery-ops-conditionendswith"]], "cycquery.ops.ConditionEquals": [[29, "cycquery-ops-conditionequals"]], "cycquery.ops.ConditionGreaterThan": [[30, "cycquery-ops-conditiongreaterthan"]], "cycquery.ops.ConditionIn": [[31, "cycquery-ops-conditionin"]], "cycquery.ops.ConditionInMonths": [[32, "cycquery-ops-conditioninmonths"]], "cycquery.ops.ConditionInYears": [[33, "cycquery-ops-conditioninyears"]], "cycquery.ops.ConditionLessThan": [[34, "cycquery-ops-conditionlessthan"]], "cycquery.ops.ConditionLike": [[35, "cycquery-ops-conditionlike"]], "cycquery.ops.ConditionRegexMatch": [[36, "cycquery-ops-conditionregexmatch"]], "cycquery.ops.ConditionStartsWith": [[37, "cycquery-ops-conditionstartswith"]], "cycquery.ops.ConditionSubstring": [[38, "cycquery-ops-conditionsubstring"]], "cycquery.ops.Count": [[39, "cycquery-ops-count"]], "cycquery.ops.Distinct": [[40, "cycquery-ops-distinct"]], "cycquery.ops.Drop": [[41, "cycquery-ops-drop"]], "cycquery.ops.DropEmpty": [[42, "cycquery-ops-dropempty"]], "cycquery.ops.DropNulls": [[43, "cycquery-ops-dropnulls"]], "cycquery.ops.ExtractTimestampComponent": [[44, "cycquery-ops-extracttimestampcomponent"]], "cycquery.ops.FillNull": [[45, "cycquery-ops-fillnull"]], "cycquery.ops.GroupByAggregate": [[46, "cycquery-ops-groupbyaggregate"]], "cycquery.ops.Join": [[47, "cycquery-ops-join"]], "cycquery.ops.Keep": [[48, "cycquery-ops-keep"]], "cycquery.ops.Limit": [[49, "cycquery-ops-limit"]], "cycquery.ops.Literal": [[50, "cycquery-ops-literal"]], "cycquery.ops.Or": [[51, "cycquery-ops-or"]], "cycquery.ops.OrderBy": [[52, "cycquery-ops-orderby"]], "cycquery.ops.QueryOp": [[53, "cycquery-ops-queryop"]], "cycquery.ops.RandomizeOrder": [[54, "cycquery-ops-randomizeorder"]], "cycquery.ops.Rename": [[55, "cycquery-ops-rename"]], "cycquery.ops.Reorder": [[56, "cycquery-ops-reorder"]], "cycquery.ops.ReorderAfter": [[57, "cycquery-ops-reorderafter"]], "cycquery.ops.Sequential": [[58, "cycquery-ops-sequential"]], "cycquery.ops.Substring": [[59, "cycquery-ops-substring"]], "cycquery.ops.Trim": [[60, "cycquery-ops-trim"]], "cycquery.ops.Union": [[61, "cycquery-ops-union"]], "cycquery": [[62, "module-cycquery"]], "dataset APIs": [[62, "dataset-apis"]], "Tutorials": [[63, "tutorials"]], "eICU-CRD tutorial": [[64, "eICU-CRD-tutorial"]], "Imports and instantiate EICUQuerier": [[64, "Imports-and-instantiate-EICUQuerier"]], "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 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 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 glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "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 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?"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "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 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "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."]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "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 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 3. Advanced - uses ConditionRegexMatch from cyclops.query.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-cyclops.query.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "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."]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "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 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."]]}, "indexentries": {"cycquery.base": [[4, "module-cycquery.base"]], "module": [[4, "module-cycquery.base"], [6, "module-cycquery.eicu"], [8, "module-cycquery.gemini"], [10, "module-cycquery.interface"], [12, "module-cycquery.mimiciii"], [14, "module-cycquery.mimiciv"], [16, "module-cycquery.omop"], [18, "module-cycquery.ops"], [62, "module-cycquery"]], "datasetquerier (class in cycquery.base)": [[5, "cycquery.base.DatasetQuerier"]], "db (datasetquerier attribute)": [[5, "cycquery.base.DatasetQuerier.db"]], "get_table() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.get_table"]], "list_columns() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_columns"]], "list_custom_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_custom_tables"]], "list_schemas() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_schemas"]], "list_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_tables"]], "cycquery.eicu": [[6, "module-cycquery.eicu"]], "eicuquerier (class in cycquery.eicu)": [[7, "cycquery.eicu.EICUQuerier"]], "get_table() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.get_table"]], "list_columns() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_columns"]], "list_custom_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_custom_tables"]], "list_schemas() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_schemas"]], "list_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_tables"]], "cycquery.gemini": [[8, "module-cycquery.gemini"]], "geminiquerier (class in cycquery.gemini)": [[9, "cycquery.gemini.GEMINIQuerier"]], "care_units() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.care_units"]], "diagnoses() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.diagnoses"]], "get_table() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.get_table"]], "imaging() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.imaging"]], "ip_admin() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.ip_admin"]], "list_columns() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_columns"]], "list_custom_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_custom_tables"]], "list_schemas() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_schemas"]], "list_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_tables"]], "room_transfer() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.room_transfer"]], "cycquery.interface": [[10, "module-cycquery.interface"]], "queryinterface (class in cycquery.interface)": [[11, "cycquery.interface.QueryInterface"]], "__init__() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.__init__"]], "clear_data() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.clear_data"]], "data (queryinterface property)": [[11, "cycquery.interface.QueryInterface.data"]], "join() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.join"]], "ops() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.ops"]], "run() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.run"]], "save() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.save"]], "union() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union"]], "union_all() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union_all"]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii"]], "mimiciiiquerier (class in cycquery.mimiciii)": [[13, "cycquery.mimiciii.MIMICIIIQuerier"]], "chartevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.chartevents"]], "diagnoses() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.diagnoses"]], "get_table() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.get_table"]], "labevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.labevents"]], "list_columns() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_columns"]], "list_custom_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_custom_tables"]], "list_schemas() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_schemas"]], "list_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_tables"]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv"]], "mimicivquerier (class in cycquery.mimiciv)": [[15, "cycquery.mimiciv.MIMICIVQuerier"]], "chartevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.chartevents"]], "diagnoses() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.diagnoses"]], "get_table() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.get_table"]], "labevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.labevents"]], "list_columns() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_columns"]], "list_custom_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_custom_tables"]], "list_schemas() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_schemas"]], "list_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_tables"]], "patients() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.patients"]], "cycquery.omop": [[16, "module-cycquery.omop"]], "omopquerier (class in cycquery.omop)": [[17, "cycquery.omop.OMOPQuerier"]], "get_table() (omopquerier method)": [[17, 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"alltitles": {"API Reference": [[0, "api-reference"]], "Contributing to cyclops-query": [[1, "contributing-to-cyclops-query"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Coding guidelines": [[1, "coding-guidelines"]], "Welcome to cyclops-query\u2019s documentation!": [[2, "welcome-to-cyclops-query-s-documentation"]], "Contents:": [[2, null]], "cyclops-query": [[3, "cyclops-query"]], "\ud83d\udc23 Getting Started": [[3, "getting-started"]], "Installing cyclops-query using pip": [[3, "installing-cyclops-query-using-pip"]], "Query postgresql database": [[3, "query-postgresql-database"]], "\ud83e\uddd1\ud83c\udfff\u200d\ud83d\udcbb Developing": [[3, "developing"]], "Using poetry": [[3, "using-poetry"]], "Contributing": [[3, "contributing"]], "\ud83d\udcda Documentation": [[3, "documentation"]], "\ud83c\udf93 Citation": [[3, "citation"]], "cycquery.base": [[4, "module-cycquery.base"]], "cycquery.base.DatasetQuerier": [[5, "cycquery-base-datasetquerier"]], "cycquery.eicu": [[6, 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"cycquery-ops-conditionregexmatch"]], "cycquery.ops.ConditionStartsWith": [[37, "cycquery-ops-conditionstartswith"]], "cycquery.ops.ConditionSubstring": [[38, "cycquery-ops-conditionsubstring"]], "cycquery.ops.Count": [[39, "cycquery-ops-count"]], "cycquery.ops.Distinct": [[40, "cycquery-ops-distinct"]], "cycquery.ops.Drop": [[41, "cycquery-ops-drop"]], "cycquery.ops.DropEmpty": [[42, "cycquery-ops-dropempty"]], "cycquery.ops.DropNulls": [[43, "cycquery-ops-dropnulls"]], "cycquery.ops.ExtractTimestampComponent": [[44, "cycquery-ops-extracttimestampcomponent"]], "cycquery.ops.FillNull": [[45, "cycquery-ops-fillnull"]], "cycquery.ops.GroupByAggregate": [[46, "cycquery-ops-groupbyaggregate"]], "cycquery.ops.Join": [[47, "cycquery-ops-join"]], "cycquery.ops.Keep": [[48, "cycquery-ops-keep"]], "cycquery.ops.Limit": [[49, "cycquery-ops-limit"]], "cycquery.ops.Literal": [[50, "cycquery-ops-literal"]], "cycquery.ops.Or": [[51, "cycquery-ops-or"]], "cycquery.ops.OrderBy": [[52, 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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 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 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 glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "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 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?"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "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 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "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."]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "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 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 3. Advanced - uses ConditionRegexMatch from cyclops.query.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-cyclops.query.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "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."]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "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 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."]]}, "indexentries": {"cycquery.base": [[4, "module-cycquery.base"]], "module": [[4, "module-cycquery.base"], [6, "module-cycquery.eicu"], [8, "module-cycquery.gemini"], [10, "module-cycquery.interface"], [12, "module-cycquery.mimiciii"], [14, "module-cycquery.mimiciv"], [16, "module-cycquery.omop"], [18, "module-cycquery.ops"], [62, "module-cycquery"]], "datasetquerier (class in cycquery.base)": [[5, "cycquery.base.DatasetQuerier"]], "db (datasetquerier attribute)": [[5, "cycquery.base.DatasetQuerier.db"]], "get_table() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.get_table"]], "list_columns() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_columns"]], "list_custom_tables() (datasetquerier method)": [[5, 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"__call__() (conditionregexmatch method)": [[36, "cycquery.ops.ConditionRegexMatch.__call__"]], "conditionstartswith (class in cycquery.ops)": [[37, "cycquery.ops.ConditionStartsWith"]], "__call__() (conditionstartswith method)": [[37, "cycquery.ops.ConditionStartsWith.__call__"]], "conditionsubstring (class in cycquery.ops)": [[38, "cycquery.ops.ConditionSubstring"]], "__call__() (conditionsubstring method)": [[38, "cycquery.ops.ConditionSubstring.__call__"]], "count (class in cycquery.ops)": [[39, "cycquery.ops.Count"]], "__call__() (count method)": [[39, "cycquery.ops.Count.__call__"]], "distinct (class in cycquery.ops)": [[40, "cycquery.ops.Distinct"]], "__call__() (distinct method)": [[40, "cycquery.ops.Distinct.__call__"]], "drop (class in cycquery.ops)": [[41, "cycquery.ops.Drop"]], "__call__() (drop method)": [[41, "cycquery.ops.Drop.__call__"]], "dropempty (class in cycquery.ops)": [[42, "cycquery.ops.DropEmpty"]], "__call__() (dropempty method)": [[42, 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[[49, "cycquery.ops.Limit"]], "__call__() (limit method)": [[49, "cycquery.ops.Limit.__call__"]], "literal (class in cycquery.ops)": [[50, "cycquery.ops.Literal"]], "__call__() (literal method)": [[50, "cycquery.ops.Literal.__call__"]], "or (class in cycquery.ops)": [[51, "cycquery.ops.Or"]], "__call__() (or method)": [[51, "cycquery.ops.Or.__call__"]], "orderby (class in cycquery.ops)": [[52, "cycquery.ops.OrderBy"]], "__call__() (orderby method)": [[52, "cycquery.ops.OrderBy.__call__"]], "queryop (class in cycquery.ops)": [[53, "cycquery.ops.QueryOp"]], "__call__() (queryop method)": [[53, "cycquery.ops.QueryOp.__call__"]], "randomizeorder (class in cycquery.ops)": [[54, "cycquery.ops.RandomizeOrder"]], "__call__() (randomizeorder method)": [[54, "cycquery.ops.RandomizeOrder.__call__"]], "rename (class in cycquery.ops)": [[55, "cycquery.ops.Rename"]], "__call__() (rename method)": [[55, "cycquery.ops.Rename.__call__"]], "reorder (class in cycquery.ops)": [[56, 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"trim (class in cycquery.ops)": [[60, "cycquery.ops.Trim"]], "__call__() (trim method)": [[60, "cycquery.ops.Trim.__call__"]], "union (class in cycquery.ops)": [[61, "cycquery.ops.Union"]], "__call__() (union method)": [[61, "cycquery.ops.Union.__call__"]], "cycquery": [[62, "module-cycquery"]]}}) \ No newline at end of file diff --git a/tutorials/eicu.html b/tutorials/eicu.html index cfca35c..5925054 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -478,7 +478,7 @@

    Imports and instantiate 
    -2023-11-23 23:02:46,526 INFO cycquery.orm    - Database setup, ready to run queries!
+2023-11-30 10:57:47,714 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -542,8 +542,8 @@

Example 1. Get all female patients discharged in 2014 (limit to 100 rows). 
-2023-11-23 23:02:47,372 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:02:47,373 INFO cycquery.utils.profile - Finished executing function run_query in 0.049122 s
+2023-11-30 10:57:48,545 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:57:48,547 INFO cycquery.utils.profile - Finished executing function run_query in 0.051502 s

@@ -578,8 +578,8 @@

Example 2. Get all patient encounters with diagnoses ( 
-2023-11-23 23:02:47,470 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:02:47,471 INFO cycquery.utils.profile - Finished executing function run_query in 0.076606 s
+2023-11-30 10:57:48,647 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:57:48,648 INFO cycquery.utils.profile - Finished executing function run_query in 0.080850 s

@@ -620,8 +620,8 @@

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

-2023-11-23 23:02:47,536 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:02:47,537 INFO cycquery.utils.profile - Finished executing function run_query in 0.042015 s
+2023-11-30 10:57:48,725 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:57:48,726 INFO cycquery.utils.profile - Finished executing function run_query in 0.043461 s
@@ -660,8 +660,8 @@

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

-2023-11-23 23:02:47,732 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:02:47,734 INFO cycquery.utils.profile - Finished executing function run_query in 0.172433 s
+2023-11-30 10:57:48,925 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:57:48,926 INFO cycquery.utils.profile - Finished executing function run_query in 0.176353 s
diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb index a8eeb4c..aefdb8a 100644 --- a/tutorials/eicu.ipynb +++ b/tutorials/eicu.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:02:45.255676Z", - "iopub.status.busy": "2023-11-24T04:02:45.254871Z", - "iopub.status.idle": "2023-11-24T04:02:47.310521Z", - "shell.execute_reply": "2023-11-24T04:02:47.308493Z" + "iopub.execute_input": "2023-11-30T15:57:46.342748Z", + "iopub.status.busy": "2023-11-30T15:57:46.342220Z", + "iopub.status.idle": "2023-11-30T15:57:48.479913Z", + "shell.execute_reply": "2023-11-30T15:57:48.478338Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:46,526 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2023-11-30 10:57:47,714 \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": "2023-11-24T04:02:47.318608Z", - "iopub.status.busy": "2023-11-24T04:02:47.318001Z", - "iopub.status.idle": "2023-11-24T04:02:47.380018Z", - "shell.execute_reply": "2023-11-24T04:02:47.378439Z" + "iopub.execute_input": "2023-11-30T15:57:48.486858Z", + "iopub.status.busy": "2023-11-30T15:57:48.486147Z", + "iopub.status.idle": "2023-11-30T15:57:48.553084Z", + "shell.execute_reply": "2023-11-30T15:57:48.551735Z" }, "tags": [] }, @@ -136,14 +136,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:47,372 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:57:48,545 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:47,373 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.049122 s\n" + "2023-11-30 10:57:48,547 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.051502 s\n" ] }, { @@ -180,10 +180,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:02:47.388281Z", - "iopub.status.busy": "2023-11-24T04:02:47.387707Z", - "iopub.status.idle": "2023-11-24T04:02:47.477725Z", - "shell.execute_reply": "2023-11-24T04:02:47.476146Z" + "iopub.execute_input": "2023-11-30T15:57:48.558894Z", + "iopub.status.busy": "2023-11-30T15:57:48.558499Z", + "iopub.status.idle": "2023-11-30T15:57:48.654669Z", + "shell.execute_reply": "2023-11-30T15:57:48.653155Z" }, "tags": [] }, @@ -192,14 +192,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:47,470 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:57:48,647 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:47,471 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.076606 s\n" + "2023-11-30 10:57:48,648 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.080850 s\n" ] }, { @@ -236,10 +236,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:02:47.484192Z", - "iopub.status.busy": "2023-11-24T04:02:47.483783Z", - "iopub.status.idle": "2023-11-24T04:02:47.543610Z", - "shell.execute_reply": "2023-11-24T04:02:47.542126Z" + "iopub.execute_input": "2023-11-30T15:57:48.660954Z", + "iopub.status.busy": "2023-11-30T15:57:48.660433Z", + "iopub.status.idle": "2023-11-30T15:57:48.731893Z", + "shell.execute_reply": "2023-11-30T15:57:48.730734Z" }, "tags": [] }, @@ -248,14 +248,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:47,536 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:57:48,725 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:47,537 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.042015 s\n" + "2023-11-30 10:57:48,726 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.043461 s\n" ] }, { @@ -298,10 +298,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:02:47.552203Z", - "iopub.status.busy": "2023-11-24T04:02:47.551770Z", - "iopub.status.idle": "2023-11-24T04:02:47.739998Z", - "shell.execute_reply": "2023-11-24T04:02:47.738444Z" + "iopub.execute_input": "2023-11-30T15:57:48.738010Z", + "iopub.status.busy": "2023-11-30T15:57:48.737469Z", + "iopub.status.idle": "2023-11-30T15:57:48.932894Z", + "shell.execute_reply": "2023-11-30T15:57:48.931308Z" }, "tags": [] }, @@ -310,14 +310,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:47,732 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:57:48,925 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:47,734 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.172433 s\n" + "2023-11-30 10:57:48,926 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.176353 s\n" ] }, { diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html index 9575f4d..6e6d0ec 100644 --- a/tutorials/mimiciii.html +++ b/tutorials/mimiciii.html @@ -478,7 +478,7 @@

Imports and instantiate 
-2023-11-23 23:02:55,952 INFO cycquery.orm    - Database setup, ready to run queries!
+2023-11-30 10:57:58,196 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -512,8 +512,8 @@

Example 1. Get all male patients with a mortality outcome. 
-2023-11-23 23:03:02,968 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:03:02,970 INFO cycquery.utils.profile - Finished executing function run_query in 0.041348 s
+2023-11-30 10:58:05,033 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:58:05,035 INFO cycquery.utils.profile - Finished executing function run_query in 0.045610 s

@@ -553,8 +553,8 @@

Example 2. Get all female patient encounters with diagnoses ( 
-2023-11-23 23:03:03,110 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:03:03,112 INFO cycquery.utils.profile - Finished executing function run_query in 0.106162 s
+2023-11-30 10:58:05,174 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:58:05,176 INFO cycquery.utils.profile - Finished executing function run_query in 0.101629 s

@@ -586,8 +586,8 @@

Example 3. Get potassium lab tests for female patients. 
-2023-11-23 23:03:03,184 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:03:03,186 INFO cycquery.utils.profile - Finished executing function run_query in 0.038073 s
+2023-11-30 10:58:05,252 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:58:05,253 INFO cycquery.utils.profile - Finished executing function run_query in 0.042548 s

@@ -624,8 +624,8 @@

Example 4. Get AaDO2 carevue chart events for male patients that have a 
-2023-11-23 23:04:12,719 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:04:12,720 INFO cycquery.utils.profile - Finished executing function run_query in 69.493639 s
+2023-11-30 10:59:15,015 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:59:15,016 INFO cycquery.utils.profile - Finished executing function run_query in 69.718738 s

diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb index a261fcd..ffe4564 100644 --- a/tutorials/mimiciii.ipynb +++ b/tutorials/mimiciii.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:02:50.429360Z", - "iopub.status.busy": "2023-11-24T04:02:50.428712Z", - "iopub.status.idle": "2023-11-24T04:03:02.914891Z", - "shell.execute_reply": "2023-11-24T04:03:02.913605Z" + "iopub.execute_input": "2023-11-30T15:57:51.568610Z", + "iopub.status.busy": "2023-11-30T15:57:51.568074Z", + "iopub.status.idle": "2023-11-30T15:58:04.975391Z", + "shell.execute_reply": "2023-11-30T15:58:04.974041Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:02:55,952 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2023-11-30 10:57:58,196 \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": "2023-11-24T04:03:02.921508Z", - "iopub.status.busy": "2023-11-24T04:03:02.920744Z", - "iopub.status.idle": "2023-11-24T04:03:02.976704Z", - "shell.execute_reply": "2023-11-24T04:03:02.975139Z" + "iopub.execute_input": "2023-11-30T15:58:04.982507Z", + "iopub.status.busy": "2023-11-30T15:58:04.981812Z", + "iopub.status.idle": "2023-11-30T15:58:05.041549Z", + "shell.execute_reply": "2023-11-30T15:58:05.039639Z" }, "tags": [] }, @@ -106,14 +106,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:03:02,968 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:58:05,033 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:03:02,970 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.041348 s\n" + "2023-11-30 10:58:05,035 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.045610 s\n" ] }, { @@ -150,10 +150,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:03:02.983876Z", - "iopub.status.busy": "2023-11-24T04:03:02.982958Z", - "iopub.status.idle": "2023-11-24T04:03:03.118529Z", - "shell.execute_reply": "2023-11-24T04:03:03.117027Z" + "iopub.execute_input": "2023-11-30T15:58:05.048923Z", + "iopub.status.busy": "2023-11-30T15:58:05.047886Z", + "iopub.status.idle": "2023-11-30T15:58:05.182011Z", + "shell.execute_reply": "2023-11-30T15:58:05.180530Z" }, "tags": [] }, @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:03:03,110 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:58:05,174 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:03:03,112 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.106162 s\n" + "2023-11-30 10:58:05,176 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.101629 s\n" ] }, { @@ -211,10 +211,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:03:03.125314Z", - "iopub.status.busy": "2023-11-24T04:03:03.124556Z", - "iopub.status.idle": "2023-11-24T04:03:03.191228Z", - "shell.execute_reply": "2023-11-24T04:03:03.189913Z" + "iopub.execute_input": "2023-11-30T15:58:05.188701Z", + "iopub.status.busy": "2023-11-30T15:58:05.187826Z", + "iopub.status.idle": "2023-11-30T15:58:05.258898Z", + "shell.execute_reply": "2023-11-30T15:58:05.257595Z" }, "tags": [] }, @@ -223,14 +223,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:03:03,184 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:58:05,252 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:03:03,186 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.038073 s\n" + "2023-11-30 10:58:05,253 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.042548 s\n" ] }, { @@ -264,10 +264,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:03:03.198534Z", - "iopub.status.busy": "2023-11-24T04:03:03.197950Z", - "iopub.status.idle": "2023-11-24T04:04:12.723747Z", - "shell.execute_reply": "2023-11-24T04:04:12.722861Z" + "iopub.execute_input": "2023-11-30T15:58:05.265596Z", + "iopub.status.busy": "2023-11-30T15:58:05.265103Z", + "iopub.status.idle": "2023-11-30T15:59:15.021503Z", + "shell.execute_reply": "2023-11-30T15:59:15.020498Z" }, "tags": [] }, @@ -276,14 +276,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:12,719 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:59:15,015 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:12,720 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 69.493639 s\n" + "2023-11-30 10:59:15,016 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 69.718738 s\n" ] }, { diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html index 3f5b665..36c0e00 100644 --- a/tutorials/mimiciv.html +++ b/tutorials/mimiciv.html @@ -482,7 +482,7 @@

Imports and instantiate 
-2023-11-23 23:04:17,458 INFO cycquery.orm    - Database setup, ready to run queries!
+2023-11-30 10:59:20,600 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -527,8 +527,8 @@

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

-2023-11-23 23:04:20,446 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:04:20,447 INFO cycquery.utils.profile - Finished executing function run_query in 0.216739 s
+2023-11-30 10:59:23,636 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:59:23,637 INFO cycquery.utils.profile - Finished executing function run_query in 0.249856 s
@@ -554,7 +554,7 @@

Example 2. Get all patient encounters with diagnoses (qo.ConditionInYears("admittime", "2015"), ) patient_admissions = patient_admissions.ops(ops) -diagnoses = querier.diagnoses() +diagnoses = querier.diagnoses_icd() diagnoses_ops = qo.Sequential( qo.ConditionEquals("icd_version", 10), qo.ConditionSubstring("long_title", "schizophrenia"), @@ -573,8 +573,8 @@

Example 2. Get all patient encounters with diagnoses ( 
-2023-11-23 23:04:21,311 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:04:21,312 INFO cycquery.utils.profile - Finished executing function run_query in 0.818591 s
+2023-11-30 10:59:24,576 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:59:24,577 INFO cycquery.utils.profile - Finished executing function run_query in 0.897111 s

@@ -600,7 +600,7 @@

Example 3. Advanced - uses qo.ConditionInYears("admittime", "2015"), ) patient_admissions = patient_admissions.ops(ops) -diagnoses = querier.diagnoses() +diagnoses = querier.diagnoses_icd() diagnoses_ops = qo.Sequential( qo.ConditionEquals("icd_version", 9), qo.ConditionRegexMatch("long_title", r"(?=.*schizophrenia)(?=.*chronic)"), @@ -619,8 +619,8 @@

Example 3. Advanced - uses 
-2023-11-23 23:04:22,881 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:04:22,882 INFO cycquery.utils.profile - Finished executing function run_query in 1.521143 s
+2023-11-30 10:59:26,143 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 10:59:26,145 INFO cycquery.utils.profile - Finished executing function run_query in 1.535798 s

@@ -661,8 +661,8 @@

Example 4. Get routine vital signs for patients from year 2015. 
-2023-11-23 23:05:42,951 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:05:42,952 INFO cycquery.utils.profile - Finished executing function run_query in 80.028161 s
+2023-11-30 11:00:49,191 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:00:49,192 INFO cycquery.utils.profile - Finished executing function run_query in 83.003143 s

@@ -703,8 +703,8 @@

Example 5. Get hemoglobin lab tests for patients from year 2009. 
-2023-11-23 23:06:48,258 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:06:48,260 INFO cycquery.utils.profile - Finished executing function run_query in 65.272793 s
+2023-11-30 11:01:53,787 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:01:53,789 INFO cycquery.utils.profile - Finished executing function run_query in 64.557161 s

@@ -751,8 +751,8 @@

Example 6. Get radiology reports and filter on keywords 
-2023-11-23 23:06:56,241 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:06:56,243 INFO cycquery.utils.profile - Finished executing function run_query in 7.956646 s
+2023-11-30 11:02:01,566 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:02:01,567 INFO cycquery.utils.profile - Finished executing function run_query in 7.741606 s

@@ -795,8 +795,8 @@

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

-2023-11-23 23:06:56,680 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:06:56,681 INFO cycquery.utils.profile - Finished executing function run_query in 0.390611 s
+2023-11-30 11:02:01,942 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:02:01,943 INFO cycquery.utils.profile - Finished executing function run_query in 0.329142 s
@@ -824,8 +824,8 @@

Example 8. Running a raw SQL string. 
-2023-11-23 23:06:56,844 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:06:56,845 INFO cycquery.utils.profile - Finished executing function run_query in 0.007669 s
+2023-11-30 11:02:02,060 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:02:02,061 INFO cycquery.utils.profile - Finished executing function run_query in 0.005366 s

diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb index cdbff91..71d9cf4 100644 --- a/tutorials/mimiciv.ipynb +++ b/tutorials/mimiciv.ipynb @@ -35,10 +35,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:04:14.734820Z", - "iopub.status.busy": "2023-11-24T04:04:14.734320Z", - "iopub.status.idle": "2023-11-24T04:04:20.200782Z", - "shell.execute_reply": "2023-11-24T04:04:20.198875Z" + "iopub.execute_input": "2023-11-30T15:59:16.931428Z", + "iopub.status.busy": "2023-11-30T15:59:16.930463Z", + "iopub.status.idle": "2023-11-30T15:59:23.357266Z", + "shell.execute_reply": "2023-11-30T15:59:23.355674Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:17,458 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2023-11-30 10:59:20,600 \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": "2023-11-24T04:04:20.207840Z", - "iopub.status.busy": "2023-11-24T04:04:20.207192Z", - "iopub.status.idle": "2023-11-24T04:04:20.455190Z", - "shell.execute_reply": "2023-11-24T04:04:20.453584Z" + "iopub.execute_input": "2023-11-30T15:59:23.364393Z", + "iopub.status.busy": "2023-11-30T15:59:23.363658Z", + "iopub.status.idle": "2023-11-30T15:59:23.643057Z", + "shell.execute_reply": "2023-11-30T15:59:23.641874Z" } }, "outputs": [ @@ -116,14 +116,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:20,446 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:59:23,636 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:20,447 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.216739 s\n" + "2023-11-30 10:59:23,637 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.249856 s\n" ] }, { @@ -160,10 +160,10 @@ "id": "a89a9cf0", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:04:20.461369Z", - "iopub.status.busy": "2023-11-24T04:04:20.460851Z", - "iopub.status.idle": "2023-11-24T04:04:21.319512Z", - "shell.execute_reply": "2023-11-24T04:04:21.317923Z" + "iopub.execute_input": "2023-11-30T15:59:23.648872Z", + "iopub.status.busy": "2023-11-30T15:59:23.648460Z", + "iopub.status.idle": "2023-11-30T15:59:24.581339Z", + "shell.execute_reply": "2023-11-30T15:59:24.580752Z" } }, "outputs": [ @@ -171,14 +171,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:21,311 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:59:24,576 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:21,312 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.818591 s\n" + "2023-11-30 10:59:24,577 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.897111 s\n" ] }, { @@ -198,7 +198,7 @@ " qo.ConditionInYears(\"admittime\", \"2015\"),\n", ")\n", "patient_admissions = patient_admissions.ops(ops)\n", - "diagnoses = querier.diagnoses()\n", + "diagnoses = querier.diagnoses_icd()\n", "diagnoses_ops = qo.Sequential(\n", " qo.ConditionEquals(\"icd_version\", 10),\n", " qo.ConditionSubstring(\"long_title\", \"schizophrenia\"),\n", @@ -225,10 +225,10 @@ "id": "03936cee", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:04:21.326430Z", - "iopub.status.busy": "2023-11-24T04:04:21.325951Z", - "iopub.status.idle": "2023-11-24T04:04:22.888030Z", - "shell.execute_reply": "2023-11-24T04:04:22.886790Z" + "iopub.execute_input": "2023-11-30T15:59:24.588735Z", + "iopub.status.busy": "2023-11-30T15:59:24.588371Z", + "iopub.status.idle": "2023-11-30T15:59:26.151157Z", + "shell.execute_reply": "2023-11-30T15:59:26.149921Z" } }, "outputs": [ @@ -236,14 +236,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:22,881 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 10:59:26,143 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:04:22,882 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.521143 s\n" + "2023-11-30 10:59:26,145 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.535798 s\n" ] }, { @@ -263,7 +263,7 @@ " qo.ConditionInYears(\"admittime\", \"2015\"),\n", ")\n", "patient_admissions = patient_admissions.ops(ops)\n", - "diagnoses = querier.diagnoses()\n", + "diagnoses = querier.diagnoses_icd()\n", "diagnoses_ops = qo.Sequential(\n", " qo.ConditionEquals(\"icd_version\", 9),\n", " qo.ConditionRegexMatch(\"long_title\", r\"(?=.*schizophrenia)(?=.*chronic)\"),\n", @@ -290,10 +290,10 @@ "id": "56a72377", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:04:22.893888Z", - "iopub.status.busy": "2023-11-24T04:04:22.893317Z", - "iopub.status.idle": "2023-11-24T04:05:42.956139Z", - "shell.execute_reply": "2023-11-24T04:05:42.955234Z" + "iopub.execute_input": "2023-11-30T15:59:26.157067Z", + "iopub.status.busy": "2023-11-30T15:59:26.156565Z", + "iopub.status.idle": "2023-11-30T16:00:49.198640Z", + "shell.execute_reply": "2023-11-30T16:00:49.197506Z" } }, "outputs": [ @@ -301,14 +301,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:05:42,951 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:00:49,191 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:05:42,952 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 80.028161 s\n" + "2023-11-30 11:00:49,192 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 83.003143 s\n" ] }, { @@ -351,10 +351,10 @@ "id": "bce11f81", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:05:42.963801Z", - "iopub.status.busy": "2023-11-24T04:05:42.963353Z", - "iopub.status.idle": "2023-11-24T04:06:48.263447Z", - "shell.execute_reply": "2023-11-24T04:06:48.262830Z" + "iopub.execute_input": "2023-11-30T16:00:49.204197Z", + "iopub.status.busy": "2023-11-30T16:00:49.203712Z", + "iopub.status.idle": "2023-11-30T16:01:53.795247Z", + "shell.execute_reply": "2023-11-30T16:01:53.793829Z" } }, "outputs": [ @@ -362,14 +362,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:06:48,258 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:01:53,787 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:06:48,260 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 65.272793 s\n" + "2023-11-30 11:01:53,789 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 64.557161 s\n" ] }, { @@ -412,10 +412,10 @@ "id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:06:48.271741Z", - "iopub.status.busy": "2023-11-24T04:06:48.271383Z", - "iopub.status.idle": "2023-11-24T04:06:56.248669Z", - "shell.execute_reply": "2023-11-24T04:06:56.247485Z" + "iopub.execute_input": "2023-11-30T16:01:53.801318Z", + "iopub.status.busy": "2023-11-30T16:01:53.800935Z", + "iopub.status.idle": "2023-11-30T16:02:01.570566Z", + "shell.execute_reply": "2023-11-30T16:02:01.569809Z" }, "tags": [] }, @@ -424,14 +424,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:06:56,241 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:02:01,566 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:06:56,243 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 7.956646 s\n" + "2023-11-30 11:02:01,567 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 7.741606 s\n" ] }, { @@ -480,10 +480,10 @@ "id": "28683d70-376e-4d9b-883d-1a7de634e455", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:06:56.253007Z", - "iopub.status.busy": "2023-11-24T04:06:56.252615Z", - "iopub.status.idle": "2023-11-24T04:06:56.830881Z", - "shell.execute_reply": "2023-11-24T04:06:56.830026Z" + "iopub.execute_input": "2023-11-30T16:02:01.578159Z", + "iopub.status.busy": "2023-11-30T16:02:01.577706Z", + "iopub.status.idle": "2023-11-30T16:02:02.051458Z", + "shell.execute_reply": "2023-11-30T16:02:02.050813Z" } }, "outputs": [ @@ -491,14 +491,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:06:56,680 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:02:01,942 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:06:56,681 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.390611 s\n" + "2023-11-30 11:02:01,943 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.329142 s\n" ] }, { @@ -543,10 +543,10 @@ "id": "a853deec", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:06:56.836422Z", - "iopub.status.busy": "2023-11-24T04:06:56.835981Z", - "iopub.status.idle": "2023-11-24T04:06:56.849061Z", - "shell.execute_reply": "2023-11-24T04:06:56.848138Z" + "iopub.execute_input": "2023-11-30T16:02:02.054940Z", + "iopub.status.busy": "2023-11-30T16:02:02.054599Z", + "iopub.status.idle": "2023-11-30T16:02:02.064070Z", + "shell.execute_reply": "2023-11-30T16:02:02.063463Z" }, "tags": [] }, @@ -555,14 +555,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:06:56,844 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:02:02,060 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:06:56,845 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.007669 s\n" + "2023-11-30 11:02:02,061 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.005366 s\n" ] }, { diff --git a/tutorials/omop.html b/tutorials/omop.html index 168962e..7d64338 100644 --- a/tutorials/omop.html +++ b/tutorials/omop.html @@ -487,7 +487,7 @@

Imports and instantiate 
-2023-11-23 23:07:00,764 INFO cycquery.orm    - Database setup, ready to run queries!
+2023-11-30 11:02:06,293 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -561,8 +561,8 @@

Example 1. Get all patient visits in or after 2010. 
-2023-11-23 23:07:02,295 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:07:02,297 INFO cycquery.utils.profile - Finished executing function run_query in 0.084236 s
+2023-11-30 11:02:07,807 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:02:07,808 INFO cycquery.utils.profile - Finished executing function run_query in 0.059113 s

@@ -620,8 +620,8 @@

Example 2. Get measurements for all visits in or after 2020. 
-2023-11-23 23:07:02,418 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:07:02,420 INFO cycquery.utils.profile - Finished executing function run_query in 0.065712 s
+2023-11-30 11:02:07,911 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:02:07,912 INFO cycquery.utils.profile - Finished executing function run_query in 0.055536 s

@@ -667,7 +667,7 @@

Imports and instantiate 
-2023-11-23 23:07:07,790 INFO cycquery.orm    - Database setup, ready to run queries!
+2023-11-30 11:02:12,075 INFO cycquery.orm    - Database setup, ready to run queries!

@@ -707,8 +707,8 @@

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

-2023-11-23 23:07:15,655 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:07:15,656 INFO cycquery.utils.profile - Finished executing function run_query in 0.957588 s
+2023-11-30 11:02:15,888 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:02:15,889 INFO cycquery.utils.profile - Finished executing function run_query in 0.916568 s
@@ -764,8 +764,8 @@

Example 2. Get all measurements for female patient visits with 
-2023-11-23 23:07:31,650 INFO cycquery.orm    - Query returned successfully!
-2023-11-23 23:07:31,651 INFO cycquery.utils.profile - Finished executing function run_query in 15.916609 s
+2023-11-30 11:02:31,871 INFO cycquery.orm    - Query returned successfully!
+2023-11-30 11:02:31,872 INFO cycquery.utils.profile - Finished executing function run_query in 15.907537 s

diff --git a/tutorials/omop.ipynb b/tutorials/omop.ipynb index d6575a3..f80c80a 100644 --- a/tutorials/omop.ipynb +++ b/tutorials/omop.ipynb @@ -45,10 +45,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:06:58.890103Z", - "iopub.status.busy": "2023-11-24T04:06:58.889613Z", - "iopub.status.idle": "2023-11-24T04:07:02.179908Z", - "shell.execute_reply": "2023-11-24T04:07:02.178011Z" + "iopub.execute_input": "2023-11-30T16:02:04.345541Z", + "iopub.status.busy": "2023-11-30T16:02:04.345017Z", + "iopub.status.idle": "2023-11-30T16:02:07.724343Z", + "shell.execute_reply": "2023-11-30T16:02:07.722495Z" } }, "outputs": [ @@ -56,7 +56,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:00,764 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2023-11-30 11:02:06,293 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -150,10 +150,10 @@ "id": "3a3d9cb9-fe40-45b8-ba2f-8de52a3b7f4f", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:07:02.188427Z", - "iopub.status.busy": "2023-11-24T04:07:02.187640Z", - "iopub.status.idle": "2023-11-24T04:07:02.312941Z", - "shell.execute_reply": "2023-11-24T04:07:02.311791Z" + "iopub.execute_input": "2023-11-30T16:02:07.732042Z", + "iopub.status.busy": "2023-11-30T16:02:07.731505Z", + "iopub.status.idle": "2023-11-30T16:02:07.823688Z", + "shell.execute_reply": "2023-11-30T16:02:07.822274Z" } }, "outputs": [ @@ -161,14 +161,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:02,295 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:02:07,807 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:02,297 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.084236 s\n" + "2023-11-30 11:02:07,808 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.059113 s\n" ] }, { @@ -226,10 +226,10 @@ "id": "030e2491-a7cc-42f3-a1ca-618212b3524c", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:07:02.319185Z", - "iopub.status.busy": "2023-11-24T04:07:02.318795Z", - "iopub.status.idle": "2023-11-24T04:07:02.425731Z", - "shell.execute_reply": "2023-11-24T04:07:02.424696Z" + "iopub.execute_input": "2023-11-30T16:02:07.829185Z", + "iopub.status.busy": "2023-11-30T16:02:07.828892Z", + "iopub.status.idle": "2023-11-30T16:02:07.918077Z", + "shell.execute_reply": "2023-11-30T16:02:07.916772Z" } }, "outputs": [ @@ -237,14 +237,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:02,418 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:02:07,911 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:02,420 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.065712 s\n" + "2023-11-30 11:02:07,912 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.055536 s\n" ] }, { @@ -302,10 +302,10 @@ "id": "0622b3df-2864-4f32-bd98-806019f59c50", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:07:02.434034Z", - "iopub.status.busy": "2023-11-24T04:07:02.433635Z", - "iopub.status.idle": "2023-11-24T04:07:14.659501Z", - "shell.execute_reply": "2023-11-24T04:07:14.657516Z" + "iopub.execute_input": "2023-11-30T16:02:07.923941Z", + "iopub.status.busy": "2023-11-30T16:02:07.923622Z", + "iopub.status.idle": "2023-11-30T16:02:14.948647Z", + "shell.execute_reply": "2023-11-30T16:02:14.948007Z" }, "tags": [] }, @@ -314,7 +314,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:07,790 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2023-11-30 11:02:12,075 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -356,10 +356,10 @@ "id": "40ff2e83-75e4-4119-aa33-26f95e63ddaa", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:07:14.666454Z", - "iopub.status.busy": "2023-11-24T04:07:14.665887Z", - "iopub.status.idle": "2023-11-24T04:07:15.660398Z", - "shell.execute_reply": "2023-11-24T04:07:15.659543Z" + "iopub.execute_input": "2023-11-30T16:02:14.953835Z", + "iopub.status.busy": "2023-11-30T16:02:14.953478Z", + "iopub.status.idle": "2023-11-30T16:02:15.893160Z", + "shell.execute_reply": "2023-11-30T16:02:15.892562Z" }, "tags": [] }, @@ -368,14 +368,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:15,655 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:02:15,888 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:15,656 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.957588 s\n" + "2023-11-30 11:02:15,889 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.916568 s\n" ] }, { @@ -418,10 +418,10 @@ "id": "46fd771c-5da7-4bce-aec7-08a5210a069b", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:07:15.673466Z", - "iopub.status.busy": "2023-11-24T04:07:15.673206Z", - "iopub.status.idle": "2023-11-24T04:07:31.655069Z", - "shell.execute_reply": "2023-11-24T04:07:31.654398Z" + "iopub.execute_input": "2023-11-30T16:02:15.900210Z", + "iopub.status.busy": "2023-11-30T16:02:15.900020Z", + "iopub.status.idle": "2023-11-30T16:02:31.877351Z", + "shell.execute_reply": "2023-11-30T16:02:31.876484Z" }, "tags": [] }, @@ -430,14 +430,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:31,650 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2023-11-30 11:02:31,871 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2023-11-23 23:07:31,651 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 15.916609 s\n" + "2023-11-30 11:02:31,872 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 15.907537 s\n" ] }, { @@ -487,10 +487,10 @@ "id": "d20a2581-f613-4ab8-9feb-3e84b8835db1", "metadata": { "execution": { - "iopub.execute_input": "2023-11-24T04:07:31.662169Z", - "iopub.status.busy": "2023-11-24T04:07:31.661861Z", - "iopub.status.idle": "2023-11-24T04:07:31.671330Z", - "shell.execute_reply": "2023-11-24T04:07:31.670203Z" + "iopub.execute_input": "2023-11-30T16:02:31.887270Z", + "iopub.status.busy": "2023-11-30T16:02:31.886974Z", + "iopub.status.idle": "2023-11-30T16:02:31.895792Z", + "shell.execute_reply": "2023-11-30T16:02:31.894686Z" }, "tags": [] },