Removed log_file datasets and un-hidden json params (#33)

* bump version;removed log_file datasets and un-hidden json params

* update changelog

* fix integration test

* typo

* upgrade java vserion to 17 to support latest IRIDA

.github/workflows/ci-tests.yml

@@ -66,10 +66,10 @@ jobs:
           while ! mysqladmin ping -h"${{ env.MYSQL_HOST }}" -P"${{ env.MYSQL_PORT }}" --silent; do
             sleep 1
           done
-      - name: Set up JDK 11 # Installs java 11
+      - name: Set up JDK 17 # Installs java 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
       - name: MySQL Setup (SUDO) # Sets ONLY_FULL_GROUP_BY flag and gives runner privileges over database
         run: |
           sudo mysql -e "SET GLOBAL sql_mode=(SELECT REPLACE(@@sql_mode,'ONLY_FULL_GROUP_BY',''));" -h ${{ env.MYSQL_HOST }} -P ${{ env.MYSQL_PORT }} -p${{ env.MYSQL_ROOT_PASSWORD }};

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 All notable changes to irida-galaxy-importer will be documeted in this file.
 
+## 2.2.0
+* Removed log-file parameter and un hidden output parameter
+* Updated IRIDA's integration test java version from 11 to 17
+
 ## 2.1.0
 * Added in support for importing IRIDA files that are not available locally (i.e. in the cloud)
 * Switched from travisCI tests to Github Actions

irida_import/irida_import.xml.sample

@@ -1,10 +1,9 @@
-<tool add_galaxy_url="False" force_history_refresh="True" id="TOOL_ID" name="IRIDA" tool_type="data_source" version="2.1.0">
+<tool add_galaxy_url="False" force_history_refresh="True" id="TOOL_ID" name="IRIDA" tool_type="data_source" version="2.2.0">
     <description>server</description>
     <command detect_errors="exit_code"><![CDATA[
         PYTHONPATH="$__tool_directory__"
         python -m irida_import.main
         --json_parameter_file "${output}"
-        --log-file $log_file
         --history-id "$__app__.security.encode_id($output.history.id)"
     ]]></command>
     <inputs action="http://127.0.0.1:8080/projects" check_values="False" method="post">
@@ -15,8 +14,7 @@
     </inputs>
     <uihints minwidth="800" />
     <outputs>
-        <data format="auto" hidden="True" name="output" />
-        <data format="txt" label="IRIDA Export" name="log_file" />
+        <data format="auto" name="output" />
     </outputs>
     <options refresh="True" sanitize="False" />
 </tool>

irida_import/tests/integration/create_client.sql

@@ -9,4 +9,4 @@ INSERT INTO client_details_grant_types (client_details_id,grant_value) VALUES (2
 INSERT INTO client_details_scope (client_details_id,scope) VALUES (2,"read");
 
 -- user -- password encryption of `password1`
-INSERT INTO user (`createdDate`, `modifiedDate`, `email`, `firstName`, `lastName`, `locale`, `password`, `phoneNumber`, `username`, `enabled`, `system_role`, `credentialsNonExpired`) VALUES (now(), now() , '[email protected]', 'Jeffrey', 'Thiessen', 'en', '$2a$10$yvzFLxWA9m2wNQmHpJtWT.MRZv8qV8Mo3EMB6HTkDnUbi9aBrbWWW', '0000', 'jeff', 1, 'ROLE_ADMIN', 1);
+INSERT INTO user (`createdDate`, `modifiedDate`, `email`, `firstName`, `lastName`, `locale`, `password`, `phoneNumber`, `username`, `enabled`, `system_role`, `credentialsNonExpired`, `user_type`) VALUES (now(), now() , '[email protected]', 'Jeffrey', 'Thiessen', 'en', '$2a$10$yvzFLxWA9m2wNQmHpJtWT.MRZv8qV8Mo3EMB6HTkDnUbi9aBrbWWW', '0000', 'jeff', 1, 'ROLE_ADMIN', 1, 'TYPE_LOCAL');