From d25769f576be536453cca7501decb0c812c965db Mon Sep 17 00:00:00 2001 From: Maxim Moinat Date: Fri, 8 Apr 2022 17:16:56 +0200 Subject: [PATCH 1/4] fixes #333 --- docs/RabbitInAHat.html | 2 +- docs/RabbitInAHat.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/RabbitInAHat.html b/docs/RabbitInAHat.html index 188affaa..19a66572 100644 --- a/docs/RabbitInAHat.html +++ b/docs/RabbitInAHat.html @@ -418,7 +418,7 @@

Selecting Desired CDM Version

Loading in a Custom CDM

-

There are times when users might need to load in a customized version of the CDM, for instance if they are sandboxing new features. To load in a custom CDM schema, first you must create a CSV file that uses the same format as the existing CDMv5 schema file.

+

There are times when users might need to load in a customized version of the CDM, for instance if they are sandboxing new features. To load in a custom CDM schema, first you must create a CSV file that uses the same format as given for the CDM versions.

Once you have created the CSV file, load it into RiaH as shown below:

diff --git a/docs/RabbitInAHat.md b/docs/RabbitInAHat.md index 0f15da3e..5ed7925e 100644 --- a/docs/RabbitInAHat.md +++ b/docs/RabbitInAHat.md @@ -51,7 +51,7 @@ However, `person.associated_provider_id` exists only in CDMv4 (it was renamed to ## Loading in a Custom CDM There are times when users might need to load in a customized version of the CDM, for instance if they are sandboxing new features. -To load in a custom CDM schema, first you must create a CSV file that uses the same format as [the existing CDMv5 schema file](https://github.com/OHDSI/WhiteRabbit/blob/master/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.csv). +To load in a custom CDM schema, first you must create a CSV file that uses the same format as [given for the CDM versions](https://github.com/OHDSI/WhiteRabbit/blob/master/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel). Once you have created the CSV file, load it into RiaH as shown below: From 936a2c11c1d598116b1b85b8cdc58448965d229b Mon Sep 17 00:00:00 2001 From: Daijiro Wachi Date: Fri, 13 May 2022 15:41:51 +0900 Subject: [PATCH 2/4] docs: fixes overlapped header --- docs/style.css | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/style.css b/docs/style.css index 7959f5a7..44edb2ed 100644 --- a/docs/style.css +++ b/docs/style.css @@ -1,3 +1,6 @@ +body { + margin-top: 60px; +} .rmdimportant { padding: 1em 1em 1em 4em; margin-bottom: 10px; From f26a94f8ea741dc25f0a419e009191831c09375c Mon Sep 17 00:00:00 2001 From: Maxim Moinat Date: Mon, 8 Aug 2022 17:05:29 +0200 Subject: [PATCH 3/4] Update documentation to align wording with application --- docs/WhiteRabbit.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/WhiteRabbit.md b/docs/WhiteRabbit.md index 57118b8c..a5b2bcf8 100644 --- a/docs/WhiteRabbit.md +++ b/docs/WhiteRabbit.md @@ -7,7 +7,7 @@ pagetitle: "White Rabbit" ## Scope and purpose WhiteRabbit is a software tool to help prepare for ETLs (Extraction, Transformation, Loading) of longitudinal health care databases into the [Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)](https://github.com/OHDSI/CommonDataModel). -The source data can be in delimited text files, SAS files, or in a database (MySQL, SQL Server, Oracle, PostgreSQL, Microsoft Access, Amazon RedShift, PDW, Teradata, Google BigQuery, Azure SQL Database). +The source data can be in delimited text files, SAS files, or in a database (MySQL, SQL Server, Oracle, PostgreSQL, Microsoft Access, Amazon RedShift, PDW, Teradata, Google BigQuery, Azure). Note that for support of the OHDSI analytical tooling, the OMOP CDM will need to be in one of a limited set of database platforms (SQL Server, Oracle, PostgreSQL, Amazon RedShift, Google BigQuery, Impala). WhiteRabbit’s main function is to perform a scan of the source data, providing detailed information on the tables, fields, and values that appear in a field. @@ -67,7 +67,7 @@ Use the “Pick Folder” button to navigate in your local environment where you Here you can specify the location of the source data. The following source types are supported: - delimited text files, SAS files, MySQL, SQL Server, Oracle, PostgreSQL, Microsoft Access, Amazon RedShift, PDW, Teradata, Google BigQuery, Azure SQL Database. + delimited text files, SAS files, MySQL, SQL Server, Oracle, PostgreSQL, Microsoft Access, Amazon RedShift, PDW, Teradata, Google BigQuery, Azure. Below are connection instructions for each data type of data source. Once you have entered the necessary information, the “Test connection” button can ensure a connection can be made. @@ -137,7 +137,7 @@ Authentication via service account credentials: * _**Password:**_ OAuth private key path (full path to the private key JSON file) * _**Database name:**_ data set name within ProjectID named in Server location field -#### Azure SQL Database +#### Azure * _**Server location:**_ server address string including database name (e.g. `.database.windows.net:1433;database=`) * _**User name:**_ name of the user used to log into the server From 5a05dc870c4e61af2924e2564d7f841dfe51adc7 Mon Sep 17 00:00:00 2001 From: Max Thonagel <12283268+thoniTUB@users.noreply.github.com> Date: Fri, 10 Feb 2023 17:25:41 +0100 Subject: [PATCH 4/4] enforce english locale when writing unique fraction --- .../main/java/org/ohdsi/whiteRabbit/scan/SourceDataScan.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/scan/SourceDataScan.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/scan/SourceDataScan.java index 3bfe9637..af099b8c 100644 --- a/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/scan/SourceDataScan.java +++ b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/scan/SourceDataScan.java @@ -254,7 +254,7 @@ private void createFieldOverviewSheet() { fieldInfo.nProcessed, fieldInfo.getFractionEmpty(), fieldInfo.hasValuesTrimmed() ? String.format("<= %d", uniqueCount) : uniqueCount, - fieldInfo.hasValuesTrimmed() ? String.format("<= %.3f", fractionUnique) : fractionUnique + fieldInfo.hasValuesTrimmed() ? String.format(Locale.ENGLISH, "<= %.3f", fractionUnique) : fractionUnique )); if (calculateNumericStats) { values.addAll(Arrays.asList(