From 70798bb1b68670728ed4b980cf56e375f8b9db84 Mon Sep 17 00:00:00 2001 From: Adam Black Date: Wed, 18 Aug 2021 23:36:11 -0400 Subject: [PATCH] update documentation --- .Rbuildignore | 3 + LICENSE.md | 194 +++++++++++++++++++++++++++++++++++++++ NAMESPACE | 3 +- errorReport.txt | 26 ------ extras/codeToRun.R | 10 +- man/createForeignKeys.Rd | 14 --- man/createPrimaryKeys.Rd | 14 --- man/writeDDL.Rd | 56 +++++++++-- man/writeForeignKeys.Rd | 22 ----- man/writeIndex.Rd | 18 ---- man/writePrimaryKeys.Rd | 22 ----- 11 files changed, 253 insertions(+), 129 deletions(-) create mode 100644 LICENSE.md delete mode 100644 errorReport.txt delete mode 100644 man/createForeignKeys.Rd delete mode 100644 man/createPrimaryKeys.Rd delete mode 100644 man/writeForeignKeys.Rd delete mode 100644 man/writeIndex.Rd delete mode 100644 man/writePrimaryKeys.Rd diff --git a/.Rbuildignore b/.Rbuildignore index 91114bf..23fefec 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,5 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +^LICENSE\.md$ +.github/* +ddl/* diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..b62a9b5 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,194 @@ +Apache License +============== + +_Version 2.0, January 2004_ +_<>_ + +### Terms and Conditions for use, reproduction, and distribution + +#### 1. 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We also +recommend that a file or class name and description of purpose be included on +the same “printed page” as the copyright notice for easier identification within +third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/NAMESPACE b/NAMESPACE index e843930..4946218 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,9 +4,10 @@ export(createDdl) export(createForeignKeys) export(createPrimaryKeys) export(downloadCurrentDdl) +export(executeDdl) export(listSupportedVersions) export(parseWiki) -export(writeDDL) +export(writeDdl) export(writeForeignKeys) export(writeIndex) export(writePrimaryKeys) diff --git a/errorReport.txt b/errorReport.txt deleted file mode 100644 index 85222f6..0000000 --- a/errorReport.txt +++ /dev/null @@ -1,26 +0,0 @@ -DBMS: -sql server - -Error: -com.microsoft.sqlserver.jdbc.SQLServerException: 'fpk_NOTE_person_id' is not a constraint. - -SQL: -ALTER TABLE ohdsi.dbo.NOTE DROP CONSTRAINT fpk_NOTE_person_id - -R version: -R version 3.4.2 (2017-09-28) - -Platform: -x86_64-w64-mingw32 - -Attached base packages: -- stats -- graphics -- grDevices -- utils -- datasets -- methods -- base - -Other attached packages: -- CdmDdlBase (0.1.0) \ No newline at end of file diff --git a/extras/codeToRun.R b/extras/codeToRun.R index fcc10a0..f93dcc3 100644 --- a/extras/codeToRun.R +++ b/extras/codeToRun.R @@ -7,17 +7,17 @@ cdmVersion <- "5.3" supportedVersions <- listSupportedVersions() for (cdmVersion in supportedVersions) { - for (targetdialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) { - writeDDL(targetdialect = targetdialect, + for (targetDialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) { + writeDdl(targetDialect = targetDialect, cdmVersion = cdmVersion) - writePrimaryKeys(targetdialect = targetdialect, + writePrimaryKeys(targetDialect = targetDialect, cdmVersion = cdmVersion) - writeForeignKeys(targetdialect = targetdialect, + writeForeignKeys(targetDialect = targetDialect, cdmVersion = cdmVersion) - writeIndex(targetdialect = targetdialect, + writeIndex(targetDialect = targetDialect, cdmVersion = cdmVersion) } } diff --git a/man/createForeignKeys.Rd b/man/createForeignKeys.Rd deleted file mode 100644 index e5d54c3..0000000 --- a/man/createForeignKeys.Rd +++ /dev/null @@ -1,14 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/createForeignKeys.R -\name{createForeignKeys} -\alias{createForeignKeys} -\title{Create a foreign key sql script from two csv files that detail the OMOP CDM Specifications.} -\usage{ -createForeignKeys(cdmVersion = cdmVersion) -} -\arguments{ -\item{cdmVersionNum}{The version of the CDM you are creating, e.g. 5.3.1} -} -\description{ -Create a foreign key sql script from two csv files that detail the OMOP CDM Specifications. -} diff --git a/man/createPrimaryKeys.Rd b/man/createPrimaryKeys.Rd deleted file mode 100644 index 53e5236..0000000 --- a/man/createPrimaryKeys.Rd +++ /dev/null @@ -1,14 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/createPrimaryKeys.R -\name{createPrimaryKeys} -\alias{createPrimaryKeys} -\title{Create a primary key sql script from two csv files that detail the OMOP CDM Specifications.} -\usage{ -createPrimaryKeys(cdmVersion = cdmVersion) -} -\arguments{ -\item{cdmVersionNum}{The version of the CDM you are creating, e.g. 5.3} -} -\description{ -Create a primary key sql script from two csv files that detail the OMOP CDM Specifications. -} diff --git a/man/writeDDL.Rd b/man/writeDDL.Rd index d541d50..c245499 100644 --- a/man/writeDDL.Rd +++ b/man/writeDDL.Rd @@ -1,19 +1,61 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/writeDDL.R -\name{writeDDL} -\alias{writeDDL} +% Please edit documentation in R/writeDdl.R +\name{writeDdl} +\alias{writeDdl} +\alias{writePrimaryKeys} +\alias{writeForeignKeys} +\alias{writeIndex} \title{Write DDL script} \usage{ -writeDDL(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema") +writeDdl( + targetDialect, + cdmVersion, + outputpath, + cdmDatabaseSchema = "@cdmDatabaseSchema" +) + +writePrimaryKeys( + targetDialect, + cdmVersion, + outputpath, + cdmDatabaseSchema = "@cdmDatabaseSchema" +) + +writeForeignKeys( + targetDialect, + cdmVersion, + outputpath, + cdmDatabaseSchema = "@cdmDatabaseSchema" +) + +writeIndex( + targetDialect, + cdmVersion, + outputpath, + cdmDatabaseSchema = "@cdmDatabaseSchema" +) } \arguments{ -\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"} +\item{targetDialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"} -\item{cdmVersion}{The version of the CDM for which you are creating the DDL. e.g. 5.3.1} +\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4} + +\item{outputpath}{The directory or folder where the SQL file should be saved.} \item{cdmDatabaseSchema}{The schema of the CDM instance where the DDL will be run. For example, this would be "ohdsi.dbo" when testing on sql server. Defaults to "@cdmDatabaseSchema"} } \description{ -Write DDL script +Write the DDL to a SQL file. The SQL will be rendered (parameters replaced) and translated to the target SQL +dialect. By default the @cdmDatabaseSchema parameter is kept in the SQL file and needs to be replaced before +execution. } +\section{Functions}{ +\itemize{ +\item \code{writePrimaryKeys}: writePrimaryKeys Write the SQL code that creates the primary keys to a file. + +\item \code{writeForeignKeys}: writeForeignKeys Write the SQL code that creates the foreign keys to a file. + +\item \code{writeIndex}: writeIndex Write the rendered and translated sql that creates recommended indexes to a file. +}} + diff --git a/man/writeForeignKeys.Rd b/man/writeForeignKeys.Rd deleted file mode 100644 index fe4d855..0000000 --- a/man/writeForeignKeys.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/writeForeignKeys.R -\name{writeForeignKeys} -\alias{writeForeignKeys} -\title{Write constraint script} -\usage{ -writeForeignKeys( - targetdialect, - cdmVersion, - cdmDatabaseSchema = "@cdmDatabaseSchema" -) -} -\arguments{ -\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"} - -\item{cdmVersion}{The version of the CDM that you are creating the primary keys for} - -\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"} -} -\description{ -Write constraint script -} diff --git a/man/writeIndex.Rd b/man/writeIndex.Rd deleted file mode 100644 index 5042f3c..0000000 --- a/man/writeIndex.Rd +++ /dev/null @@ -1,18 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/writeIndex.R -\name{writeIndex} -\alias{writeIndex} -\title{Write Index script} -\usage{ -writeIndex(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema") -} -\arguments{ -\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"} - -\item{cdmVersion}{The version of the CDM that you are creating the indices for. e.g. 5.3.1} - -\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"} -} -\description{ -Write Index script -} diff --git a/man/writePrimaryKeys.Rd b/man/writePrimaryKeys.Rd deleted file mode 100644 index ad1e2ff..0000000 --- a/man/writePrimaryKeys.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/writePrimaryKeys.R -\name{writePrimaryKeys} -\alias{writePrimaryKeys} -\title{Write primary key script} -\usage{ -writePrimaryKeys( - targetdialect, - cdmVersion, - cdmDatabaseSchema = "@cdmDatabaseSchema" -) -} -\arguments{ -\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"} - -\item{cdmVersion}{The version of the CDM that you are creating the primary keys for} - -\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"} -} -\description{ -Write primary key script -}