From ca724fc5c7fa01bc9887701fe5625ca20bbcd799 Mon Sep 17 00:00:00 2001 From: Gowtham Rao Date: Fri, 27 Sep 2024 10:20:59 -0400 Subject: [PATCH] Release 3.33.0 * Create Script to Check Cohort definitions for domain change and vocabulary drift.R * Add script of VA Cipher * Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 2 to 4.1.7. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v2...v4.1.7) --- .github/workflows/R_CMD_check_Hades.yaml | 2 +- DESCRIPTION | 6 +- NEWS.md | 9 + docs/404.html | 18 +- ...ohortDefinitionSubmissionRequirements.html | 21 +- ...ortDefinitionsInOhdsiPhenotypeLibrary.html | 28 +- .../htmltools-fill-0.5.8.1/fill.css | 21 + .../reactwidget-2.0.0/react-tools.umd.cjs | 1 + ...SetDefinitionsInOhdsiPhenotypeLibrary.html | 28 +- .../htmltools-fill-0.5.8.1/fill.css | 21 + 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| 68 +- inst/sql/sql_server/935.sql | 64 +- inst/sql/sql_server/936.sql | 62 +- inst/sql/sql_server/938.sql | 74 +- inst/sql/sql_server/939.sql | 68 +- inst/sql/sql_server/940.sql | 68 +- inst/sql/sql_server/941.sql | 68 +- inst/sql/sql_server/942.sql | 62 +- inst/sql/sql_server/943.sql | 62 +- inst/sql/sql_server/944.sql | 68 +- inst/sql/sql_server/945.sql | 272 +- inst/sql/sql_server/946.sql | 62 +- inst/sql/sql_server/947.sql | 58 +- inst/sql/sql_server/948.sql | 62 +- inst/sql/sql_server/95.sql | 62 +- inst/sql/sql_server/950.sql | 80 +- inst/sql/sql_server/953.sql | 74 +- inst/sql/sql_server/954.sql | 68 +- inst/sql/sql_server/955.sql | 62 +- inst/sql/sql_server/956.sql | 68 +- inst/sql/sql_server/957.sql | 76 +- inst/sql/sql_server/963.sql | 68 +- inst/sql/sql_server/964.sql | 74 +- inst/sql/sql_server/965.sql | 106 +- inst/sql/sql_server/967.sql | 106 +- inst/sql/sql_server/976.sql | 62 +- inst/sql/sql_server/979.sql | 74 +- inst/sql/sql_server/980.sql | 74 +- inst/sql/sql_server/982.sql | 68 +- inst/sql/sql_server/986.sql | 68 +- inst/sql/sql_server/989.sql | 62 +- inst/sql/sql_server/990.sql | 62 +- inst/sql/sql_server/991.sql | 62 +- inst/sql/sql_server/992.sql | 68 +- inst/sql/sql_server/993.sql | 62 +- inst/sql/sql_server/994.sql | 68 +- inst/sql/sql_server/996.sql | 68 +- inst/sql/sql_server/997.sql | 68 +- inst/sql/sql_server/998.sql | 58 +- inst/sql/sql_server/999.sql | 68 +- 1085 files changed, 32925 insertions(+), 56167 deletions(-) create mode 100644 docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary_files/htmltools-fill-0.5.8.1/fill.css create mode 100644 docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary_files/reactwidget-2.0.0/react-tools.umd.cjs create mode 100644 docs/articles/ConceptSetDefinitionsInOhdsiPhenotypeLibrary_files/htmltools-fill-0.5.8.1/fill.css create mode 100644 docs/articles/ConceptSetDefinitionsInOhdsiPhenotypeLibrary_files/reactwidget-2.0.0/react-tools.umd.cjs delete mode 100644 extras/PhenotypeLibrary.pdf create mode 100644 extras/Script to Check Cohort definitions for domain change and vocabulary drift.R create mode 100644 extras/VP Cipher Mapping.R create mode 100644 inst/cohorts/1316.json create mode 100644 inst/cohorts/1317.json create mode 100644 inst/sql/sql_server/1316.sql create mode 100644 inst/sql/sql_server/1317.sql diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml index 5068891e..7930891d 100644 --- a/.github/workflows/R_CMD_check_Hades.yaml +++ b/.github/workflows/R_CMD_check_Hades.yaml @@ -156,7 +156,7 @@ jobs: - name: Download package tarball if: ${{ env.new_version != '' }} - uses: actions/download-artifact@v2 + uses: actions/download-artifact@v4.1.7 with: name: package_tarball diff --git a/DESCRIPTION b/DESCRIPTION index 225b1ab9..68a564db 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: PhenotypeLibrary Type: Package Title: The OHDSI Phenotype Library -Version: 3.32.0 -Date: 2024-01-06 +Version: 3.33.0 +Date: 2024-09-27 Author: Gowtham Rao [aut, cre] Maintainer: Gowtham Rao Description: A repository to store the content of the OHDSI Phenotype library. @@ -19,7 +19,7 @@ Suggests: testthat, knitr License: Apache License -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 Roxygen: list(markdown = TRUE) Encoding: UTF-8 Language: en-US diff --git a/NEWS.md b/NEWS.md index 2663ee14..f0ea40c1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,12 @@ +PhenotypeLibrary 3.33.0 +====================== +Accepted Cohorts: No cohorts were accepted in this release. + +New Cohorts: 2 were added. + + 1316: Acquired Neutropenia or unspecified leukopenia (21Pe, 365Era) + 1317: [P] Reyes syndrome + PhenotypeLibrary 3.32.0 ====================== Accepted Cohorts: No cohorts were accepted in this release. diff --git a/docs/404.html b/docs/404.html index b11cf75b..1b2ecb3e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found (404) • PhenotypeLibrary - + @@ -18,7 +18,7 @@ - +
@@ -44,7 +44,7 @@
  • @@ -111,7 +111,7 @@
    • - +
    @@ -139,16 +139,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/CohortDefinitionSubmissionRequirements.html b/docs/articles/CohortDefinitionSubmissionRequirements.html index 6ed2e66d..ebbe0f6b 100644 --- a/docs/articles/CohortDefinitionSubmissionRequirements.html +++ b/docs/articles/CohortDefinitionSubmissionRequirements.html @@ -6,20 +6,19 @@ Cohort Definition Submission Requirements • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,7 +111,7 @@
    • - +
    @@ -121,7 +120,7 @@

    Cohort Definition Submission Requirements

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/CohortDefinitionSubmissionRequirements.Rmd @@ -216,16 +215,16 @@

    2024-01-06

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary.html b/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary.html index 1f23c07e..344e6947 100644 --- a/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary.html +++ b/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary.html @@ -6,20 +6,19 @@ Cohort Definitions in OHDSI Phenotype Library • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,9 +111,10 @@
    • - - + + +
    @@ -123,7 +123,7 @@

    Cohort Definitions in OHDSI Phenotype

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/CohortDefinitionsInOhdsiPhenotypeLibrary.Rmd @@ -150,8 +150,8 @@

    2024-01-06

    window.URL.revokeObjectURL(url); }); }); -
    - +
    +
    - - + + diff --git a/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary_files/htmltools-fill-0.5.8.1/fill.css b/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary_files/htmltools-fill-0.5.8.1/fill.css new file mode 100644 index 00000000..841ea9d5 --- /dev/null +++ b/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary_files/htmltools-fill-0.5.8.1/fill.css @@ -0,0 +1,21 @@ +@layer htmltools { + .html-fill-container { + display: flex; + flex-direction: column; + /* Prevent the container from expanding vertically or horizontally beyond its + parent's constraints. */ + min-height: 0; + min-width: 0; + } + .html-fill-container > .html-fill-item { + /* Fill items can grow and shrink freely within + available vertical space in fillable container */ + flex: 1 1 auto; + min-height: 0; + min-width: 0; + } + .html-fill-container > :not(.html-fill-item) { + /* Prevent shrinking or growing of non-fill items */ + flex: 0 0 auto; + } +} diff --git a/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary_files/reactwidget-2.0.0/react-tools.umd.cjs b/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary_files/reactwidget-2.0.0/react-tools.umd.cjs new file mode 100644 index 00000000..92b8d86d --- /dev/null +++ b/docs/articles/CohortDefinitionsInOhdsiPhenotypeLibrary_files/reactwidget-2.0.0/react-tools.umd.cjs @@ -0,0 +1 @@ +(function(s,u){typeof exports=="object"&&typeof module<"u"?u(exports):typeof define=="function"&&define.amd?define(["exports"],u):(s=typeof globalThis<"u"?globalThis:s||self,u(s.reactR={}))})(this,function(s){"use strict";function u(n,t){if(typeof t=="string")return t;if(t.name[0]===t.name[0].toUpperCase()&&!n.hasOwnProperty(t.name))throw new Error("Unknown component: "+t.name);for(let i in t.attribs)g(t.attribs[i])&&(t.attribs[i]=u(n,t.attribs[i]));for(var a=n.hasOwnProperty(t.name)?n[t.name]:t.name,r=[a,t.attribs],e=0;e Concept Set Definitions in OHDSI Phenotype Library • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,9 +111,10 @@
    • - - + + +
    @@ -123,7 +123,7 @@

    Concept Set Definitions in OHDSI Phenotype

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/ConceptSetDefinitionsInOhdsiPhenotypeLibrary.Rmd @@ -132,8 +132,8 @@

    2024-01-06

    -
    - +
    +
    - - + + diff --git a/docs/articles/ConceptSetDefinitionsInOhdsiPhenotypeLibrary_files/htmltools-fill-0.5.8.1/fill.css b/docs/articles/ConceptSetDefinitionsInOhdsiPhenotypeLibrary_files/htmltools-fill-0.5.8.1/fill.css new file mode 100644 index 00000000..841ea9d5 --- /dev/null +++ b/docs/articles/ConceptSetDefinitionsInOhdsiPhenotypeLibrary_files/htmltools-fill-0.5.8.1/fill.css @@ -0,0 +1,21 @@ +@layer htmltools { + .html-fill-container { + display: flex; + flex-direction: column; + /* Prevent the container from expanding vertically or horizontally beyond its + parent's constraints. */ + min-height: 0; + min-width: 0; + } + .html-fill-container > .html-fill-item { + /* Fill items can grow and shrink freely within + available vertical space in fillable container */ + flex: 1 1 auto; + min-height: 0; + min-width: 0; + } + .html-fill-container > :not(.html-fill-item) { + /* Prevent shrinking or growing of non-fill items */ + flex: 0 0 auto; + } +} diff --git a/docs/articles/ConceptSetDefinitionsInOhdsiPhenotypeLibrary_files/reactwidget-2.0.0/react-tools.umd.cjs b/docs/articles/ConceptSetDefinitionsInOhdsiPhenotypeLibrary_files/reactwidget-2.0.0/react-tools.umd.cjs new file mode 100644 index 00000000..92b8d86d --- /dev/null +++ b/docs/articles/ConceptSetDefinitionsInOhdsiPhenotypeLibrary_files/reactwidget-2.0.0/react-tools.umd.cjs @@ -0,0 +1 @@ +(function(s,u){typeof exports=="object"&&typeof module<"u"?u(exports):typeof define=="function"&&define.amd?define(["exports"],u):(s=typeof globalThis<"u"?globalThis:s||self,u(s.reactR={}))})(this,function(s){"use strict";function u(n,t){if(typeof t=="string")return t;if(t.name[0]===t.name[0].toUpperCase()&&!n.hasOwnProperty(t.name))throw new Error("Unknown component: "+t.name);for(let i in t.attribs)g(t.attribs[i])&&(t.attribs[i]=u(n,t.attribs[i]));for(var a=n.hasOwnProperty(t.name)?n[t.name]:t.name,r=[a,t.attribs],e=0;e Guidance on writing clinical description for Condition Phenotypes • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,7 +111,7 @@
    • - +
    @@ -122,7 +121,7 @@

    Guidance on writing clinical description for

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/GuidanceOnClinicalDescriptionForConditionPhenotypes.Rmd @@ -466,9 +465,7 @@
    Sub-prompts
    +
    @@ -481,16 +478,16 @@
    Sub-prompts

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/GuidanceOnCohortDefinitionSetRObject.html b/docs/articles/GuidanceOnCohortDefinitionSetRObject.html index ac80c5e4..146573bc 100644 --- a/docs/articles/GuidanceOnCohortDefinitionSetRObject.html +++ b/docs/articles/GuidanceOnCohortDefinitionSetRObject.html @@ -6,20 +6,19 @@ Guidance on Cohort Definition Set R Object • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,7 +111,7 @@
    • - +
    @@ -121,7 +120,7 @@

    Guidance on Cohort Definition Set R Object

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/GuidanceOnCohortDefinitionSetRObject.Rmd @@ -170,9 +169,7 @@

    Downloading Cohorts from ATLAS - -

    +
    @@ -185,16 +182,16 @@

    Downloading Cohorts from ATLAS

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/GuidanceOnLiteratureReview.html b/docs/articles/GuidanceOnLiteratureReview.html index f876a0df..8226822f 100644 --- a/docs/articles/GuidanceOnLiteratureReview.html +++ b/docs/articles/GuidanceOnLiteratureReview.html @@ -6,20 +6,19 @@ Guidance on literature review • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,7 +111,7 @@
    • - +
    @@ -121,7 +120,7 @@

    Guidance on literature review

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/GuidanceOnLiteratureReview.Rmd @@ -295,9 +294,7 @@

    Develop a Search Strategy - -

    +
    @@ -310,16 +307,16 @@

    Develop a Search Strategy

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/GuidanceOnPerformingPeerReview.html b/docs/articles/GuidanceOnPerformingPeerReview.html index ae981c7f..f30817fa 100644 --- a/docs/articles/GuidanceOnPerformingPeerReview.html +++ b/docs/articles/GuidanceOnPerformingPeerReview.html @@ -6,20 +6,19 @@ Guidance on performing peer review • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,7 +111,7 @@
    • - +
    @@ -121,7 +120,7 @@

    Guidance on performing peer review

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/GuidanceOnPerformingPeerReview.Rmd @@ -215,9 +214,7 @@

    Level 4 - -

    +
    @@ -230,16 +227,16 @@

    Level 4

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/GuidanceOnWritingAnEvaluationReport.html b/docs/articles/GuidanceOnWritingAnEvaluationReport.html index a5140880..02352dc2 100644 --- a/docs/articles/GuidanceOnWritingAnEvaluationReport.html +++ b/docs/articles/GuidanceOnWritingAnEvaluationReport.html @@ -6,20 +6,19 @@ Guidance on writing an evaluation report • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,7 +111,7 @@
    • - +
    @@ -121,7 +120,7 @@

    Guidance on writing an evaluation report

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/GuidanceOnWritingAnEvaluationReport.Rmd @@ -153,16 +152,16 @@

    2024-01-06

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/GuidanceOnWritingCohortDefinitionLogicDescription.html b/docs/articles/GuidanceOnWritingCohortDefinitionLogicDescription.html index a3ce078b..11ab0fe4 100644 --- a/docs/articles/GuidanceOnWritingCohortDefinitionLogicDescription.html +++ b/docs/articles/GuidanceOnWritingCohortDefinitionLogicDescription.html @@ -6,20 +6,19 @@ Guidance on writing Cohort Definition Logic Description • PhenotypeLibrary - + - - +
    @@ -45,7 +44,7 @@
  • @@ -112,7 +111,7 @@
    • - +
    @@ -122,7 +121,7 @@

    Guidance on writing Cohort Definition Logic

    Gowtham A. Rao

    -

    2024-01-06

    +

    2024-09-27

    Source: vignettes/GuidanceOnWritingCohortDefinitionLogicDescription.Rmd @@ -196,9 +195,7 @@
    +
    @@ -211,16 +208,16 @@