From 408e183adc931f27d6a77e188951bc617887a71b Mon Sep 17 00:00:00 2001 From: Maxim Moinat Date: Mon, 29 Nov 2021 14:38:31 +0100 Subject: [PATCH 1/7] bump snapshot version --- pom.xml | 2 +- rabbit-core/pom.xml | 2 +- rabbitinahat/pom.xml | 2 +- whiterabbit/pom.xml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index a5fc333c..a7b4e19d 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.ohdsi leporidae pom - 0.10.6 + 0.11.0-SNAPSHOT rabbitinahat whiterabbit diff --git a/rabbit-core/pom.xml b/rabbit-core/pom.xml index 882e7ef2..db7bd2d9 100644 --- a/rabbit-core/pom.xml +++ b/rabbit-core/pom.xml @@ -5,7 +5,7 @@ leporidae org.ohdsi - 0.10.6 + 0.11.0-SNAPSHOT 4.0.0 diff --git a/rabbitinahat/pom.xml b/rabbitinahat/pom.xml index 9b1dfcaf..b79ce2e5 100644 --- a/rabbitinahat/pom.xml +++ b/rabbitinahat/pom.xml @@ -5,7 +5,7 @@ leporidae org.ohdsi - 0.10.6 + 0.11.0-SNAPSHOT 4.0.0 diff --git a/whiterabbit/pom.xml b/whiterabbit/pom.xml index f44e5db1..ccbc331d 100644 --- a/whiterabbit/pom.xml +++ b/whiterabbit/pom.xml @@ -5,7 +5,7 @@ leporidae org.ohdsi - 0.10.6 + 0.11.0-SNAPSHOT 4.0.0 From 76963151df716bc1e3445cb4afb6df04f42e79e3 Mon Sep 17 00:00:00 2001 From: kesadae11 Date: Mon, 3 Jan 2022 11:18:13 +0100 Subject: [PATCH 2/7] Fix column names in CDMV6.0 Fix based on the documentation https://ohdsi.github.io/CommonDataModel/cdm60.html#VISIT_OCCURRENCE --- .../resources/org/ohdsi/rabbitInAHat/dataModel/CDMV6.0.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV6.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV6.0.csv index 49513460..682d1ebd 100644 --- a/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV6.0.csv +++ b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV6.0.csv @@ -35,8 +35,8 @@ provider_id,No,INTEGER,A foreign key to the provider in the provider table who w care_site_id,No,INTEGER,A foreign key to the care site in the care site table that was visited.,visit_occurrence,cdm visit_source_value,No,VARCHAR(50),The source code for the visit as it appears in the source data.,visit_occurrence,cdm visit_source_concept_id,Yes,INTEGER,A foreign key to a Concept that refers to the code used in the source.,visit_occurrence,cdm -admitting_source_concept_id,Yes,INTEGER,A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.,visit_occurrence,cdm -admitting_source_value,No,VARCHAR(50),The source code for the admitting source as it appears in the source data.,visit_occurrence,cdm +admitted_from_concept_id,Yes,INTEGER,Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example. ,visit_occurrence,cdm +admitted_from_source_value,No,VARCHAR(50),The source code for the admitting source as it appears in the source data.,visit_occurrence,cdm discharge_to_concept_id,Yes,INTEGER,A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the discharge disposition for a visit.,visit_occurrence,cdm discharge_to_source_value,No,VARCHAR(50),The source code for the discharge disposition as it appears in the source data.,visit_occurrence,cdm preceding_visit_occurrence_id,No,INTEGER,A foreign key to the VISIT_OCCURRENCE table of the visit immediately preceding this visit,visit_occurrence,cdm From cff9be2f1e6fa378312a8366c621b614ce954df8 Mon Sep 17 00:00:00 2001 From: Maxim Moinat Date: Wed, 26 Jan 2022 14:06:24 +0100 Subject: [PATCH 3/7] fix where fake data generator takes wrong connection details --- .../org/ohdsi/whiteRabbit/WhiteRabbitMain.java | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java index 8c4b084c..c0b006e1 100644 --- a/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java +++ b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java @@ -947,21 +947,21 @@ private DbSettings getTargetDbSettings() { dbSettings.dbType = DbType.MYSQL; else if (targetType.getSelectedItem().toString().equals("Oracle")) dbSettings.dbType = DbType.ORACLE; - else if (sourceType.getSelectedItem().toString().equals("PostgreSQL")) + else if (targetType.getSelectedItem().toString().equals("PostgreSQL")) dbSettings.dbType = DbType.POSTGRESQL; - else if (sourceType.getSelectedItem().toString().equals("SQL Server")) { + else if (targetType.getSelectedItem().toString().equals("SQL Server")) { dbSettings.dbType = DbType.MSSQL; - if (sourceUserField.getText().length() != 0) { // Not using windows authentication - String[] parts = sourceUserField.getText().split("/"); + if (targetUserField.getText().length() != 0) { // Not using windows authentication + String[] parts = targetUserField.getText().split("/"); if (parts.length == 2) { dbSettings.user = parts[1]; dbSettings.domain = parts[0]; } } - } else if (sourceType.getSelectedItem().toString().equals("PDW")) { + } else if (targetType.getSelectedItem().toString().equals("PDW")) { dbSettings.dbType = DbType.PDW; - if (sourceUserField.getText().length() != 0) { // Not using windows authentication - String[] parts = sourceUserField.getText().split("/"); + if (targetUserField.getText().length() != 0) { // Not using windows authentication + String[] parts = targetUserField.getText().split("/"); if (parts.length == 2) { dbSettings.user = parts[1]; dbSettings.domain = parts[0]; From 99d11d5a58ac2a4fd2946c551233233d109286b1 Mon Sep 17 00:00:00 2001 From: Maxim Moinat Date: Fri, 28 Jan 2022 17:19:28 +0100 Subject: [PATCH 4/7] add PDW as option for target database and use switch for target dbType --- .../ohdsi/whiteRabbit/WhiteRabbitMain.java | 52 +++++++++++-------- 1 file changed, 29 insertions(+), 23 deletions(-) diff --git a/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java index c0b006e1..b0a44fd8 100644 --- a/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java +++ b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java @@ -564,7 +564,7 @@ public void actionPerformed(ActionEvent e) { targetPanel.setLayout(new GridLayout(0, 2)); targetPanel.setBorder(BorderFactory.createTitledBorder("Target data location")); targetPanel.add(new JLabel("Data type")); - targetType = new JComboBox<>(new String[] { "Delimited text files", "MySQL", "Oracle", "SQL Server", "PostgreSQL" }); + targetType = new JComboBox<>(new String[] {"Delimited text files", "MySQL", "Oracle", "SQL Server", "PostgreSQL", "PDW"}); targetType.setToolTipText("Select the type of source data available"); targetType.addItemListener(event -> { targetIsFiles = event.getItem().toString().equals("Delimited text files"); @@ -943,30 +943,36 @@ private DbSettings getTargetDbSettings() { dbSettings.password = targetPasswordField.getText(); dbSettings.server = targetServerField.getText(); dbSettings.database = targetDatabaseField.getText(); - if (targetType.getSelectedItem().toString().equals("MySQL")) - dbSettings.dbType = DbType.MYSQL; - else if (targetType.getSelectedItem().toString().equals("Oracle")) - dbSettings.dbType = DbType.ORACLE; - else if (targetType.getSelectedItem().toString().equals("PostgreSQL")) - dbSettings.dbType = DbType.POSTGRESQL; - else if (targetType.getSelectedItem().toString().equals("SQL Server")) { - dbSettings.dbType = DbType.MSSQL; - if (targetUserField.getText().length() != 0) { // Not using windows authentication - String[] parts = targetUserField.getText().split("/"); - if (parts.length == 2) { - dbSettings.user = parts[1]; - dbSettings.domain = parts[0]; + switch(targetType.getSelectedItem().toString()) { + case "MySQL": + dbSettings.dbType = DbType.MYSQL; + break; + case "Oracle": + dbSettings.dbType = DbType.ORACLE; + break; + case "PostgreSQL": + dbSettings.dbType = DbType.POSTGRESQL; + break; + case "SQL Server": + dbSettings.dbType = DbType.MSSQL; + if (targetUserField.getText().length() != 0) { // Not using windows authentication + String[] parts = targetUserField.getText().split("/"); + if (parts.length == 2) { + dbSettings.user = parts[1]; + dbSettings.domain = parts[0]; + } } - } - } else if (targetType.getSelectedItem().toString().equals("PDW")) { - dbSettings.dbType = DbType.PDW; - if (targetUserField.getText().length() != 0) { // Not using windows authentication - String[] parts = targetUserField.getText().split("/"); - if (parts.length == 2) { - dbSettings.user = parts[1]; - dbSettings.domain = parts[0]; + break; + case "PDW": + dbSettings.dbType = DbType.PDW; + if (targetUserField.getText().length() != 0) { // Not using windows authentication + String[] parts = targetUserField.getText().split("/"); + if (parts.length == 2) { + dbSettings.user = parts[1]; + dbSettings.domain = parts[0]; + } } - } + break; } if (dbSettings.database.trim().length() == 0) { From a3ba570fe3b2521d230e700e25dd8e318ce1322c Mon Sep 17 00:00:00 2001 From: Jeff Sullivan Date: Tue, 1 Feb 2022 11:11:27 -0500 Subject: [PATCH 5/7] bump redshift jdbc to match pom. Closes #327 --- rabbit-core/src/main/java/org/ohdsi/databases/DBConnector.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rabbit-core/src/main/java/org/ohdsi/databases/DBConnector.java b/rabbit-core/src/main/java/org/ohdsi/databases/DBConnector.java index 15b467c7..af26acb0 100644 --- a/rabbit-core/src/main/java/org/ohdsi/databases/DBConnector.java +++ b/rabbit-core/src/main/java/org/ohdsi/databases/DBConnector.java @@ -71,7 +71,7 @@ public static Connection connectToRedshift(String server, String user, String pa if (!server.contains("/")) throw new RuntimeException("For Redshift, database name must be specified in the server field (:/?)"); try { - Class.forName("com.amazon.redshift.jdbc41.Driver"); + Class.forName("com.amazon.redshift.jdbc42.Driver"); } catch (ClassNotFoundException e1) { throw new RuntimeException("Cannot find JDBC driver. Make sure the file RedshiftJDBCx-x.x.xx.xxxx.jar is in the path"); } From f8f4be0dd85368d39733816f1e621964f850e781 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 2 Feb 2022 00:55:21 +0000 Subject: [PATCH 6/7] Bump postgresql from 42.3.1 to 42.3.2 in /rabbit-core Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.3.1 to 42.3.2. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.3.1...REL42.3.2) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- rabbit-core/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rabbit-core/pom.xml b/rabbit-core/pom.xml index 882e7ef2..9662489d 100644 --- a/rabbit-core/pom.xml +++ b/rabbit-core/pom.xml @@ -67,7 +67,7 @@ org.postgresql postgresql - 42.3.1 + 42.3.2 com.cedarsoftware From 3397d40512630c10e5791dec85e59f5181a58772 Mon Sep 17 00:00:00 2001 From: Maxim Moinat Date: Fri, 4 Feb 2022 12:56:29 +0100 Subject: [PATCH 7/7] bump version --- docs/index.html | 2 +- docs/index.md | 2 +- pom.xml | 2 +- rabbit-core/pom.xml | 2 +- rabbitinahat/pom.xml | 2 +- whiterabbit/pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/index.html b/docs/index.html index a9ee85ad..1e20518b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -327,7 +327,7 @@

Features

Latest version

-

v0.10.6

+

v0.10.7

diff --git a/docs/index.md b/docs/index.md index 53a8240d..cab00dd2 100644 --- a/docs/index.md +++ b/docs/index.md @@ -21,4 +21,4 @@ It comes with **RabbitInAHat**, an application for interactive design of an ETL - Rabbit in a Hat generates ETL specification document according to OMOP templatement according to OMOP template # Latest version -[**v0.10.6**](https://github.com/OHDSI/WhiteRabbit/releases/latest) +[**v0.10.7**](https://github.com/OHDSI/WhiteRabbit/releases/latest) diff --git a/pom.xml b/pom.xml index a7b4e19d..07bc7da6 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.ohdsi leporidae pom - 0.11.0-SNAPSHOT + 0.10.7 rabbitinahat whiterabbit diff --git a/rabbit-core/pom.xml b/rabbit-core/pom.xml index db7bd2d9..272d3e4e 100644 --- a/rabbit-core/pom.xml +++ b/rabbit-core/pom.xml @@ -5,7 +5,7 @@ leporidae org.ohdsi - 0.11.0-SNAPSHOT + 0.10.7 4.0.0 diff --git a/rabbitinahat/pom.xml b/rabbitinahat/pom.xml index b79ce2e5..5b6ab365 100644 --- a/rabbitinahat/pom.xml +++ b/rabbitinahat/pom.xml @@ -5,7 +5,7 @@ leporidae org.ohdsi - 0.11.0-SNAPSHOT + 0.10.7 4.0.0 diff --git a/whiterabbit/pom.xml b/whiterabbit/pom.xml index ccbc331d..50c50b58 100644 --- a/whiterabbit/pom.xml +++ b/whiterabbit/pom.xml @@ -5,7 +5,7 @@ leporidae org.ohdsi - 0.11.0-SNAPSHOT + 0.10.7 4.0.0