Merge pull request #11 from SeqWare/feature/test_environment

Feature/test environment

.gitignore

@@ -0,0 +1 @@
+# Created by .ignore support plugin (hsz.mobi)

docker-test-start.yml

@@ -0,0 +1,28 @@
+--- 
+# file: docker-start.yml
+# This file is used for installing a seqware container
+
+- hosts: all
+  sudo: True
+  tasks:
+  - name: Start all required services
+    service: name={{ item }} state=restarted 
+    with_items: 
+     - postgresql
+     - hadoop-hdfs-datanode
+     - hadoop-hdfs-namenode
+     - hadoop-0.20-mapreduce-jobtracker
+     - hadoop-0.20-mapreduce-tasktracker
+     - oozie
+     - gridengine-master
+     - gridengine-exec
+  - name: Bump up control node memory allocation for high-mem machines
+    lineinfile: dest=~seqware/.seqware/settings regexp='^SW_CONTROL_NODE_MEMORY.*' line='SW_CONTROL_NODE_MEMORY=4000' state=present
+    when: ansible_memtotal_mb > 100000
+  - name: Redirect oozie working directory so that workflow runs are persisted
+    lineinfile: dest=~seqware/.seqware/settings regexp='^OOZIE_WORK_DIR.*' line='OOZIE_WORK_DIR=/datastore' state=present
+
+- hosts: all 
+  sudo: True
+  roles:
+    - { role: grid-engine, single_node: True , grid_engine_master: True }

roles/java/tasks/oracle8.yml

@@ -16,11 +16,49 @@
 
 - name: install java 8
   apt: name=oracle-java8-installer state=latest update-cache=yes force=yes
+  register: apt_result
   sudo: yes
 
+- name: Java | Set up Java
+  command: 'update-alternatives --install /usr/bin/java java /usr/lib/jvm/java-8-oracle/jre/bin/java 2000'
+  when: apt_result.changed
+
+- name: Java | Set up Java
+  command: 'update-alternatives --set java /usr/lib/jvm/java-8-oracle/jre/bin/java'
+  when: apt_result.changed
+
+- name: Java | Set up Jar
+  command: 'update-alternatives --install /usr/bin/jar jar /usr/lib/jvm/java-8-oracle/bin/jar 2000'
+  when: apt_result.changed
+
+- name: Java | Set up Jar
+  command: 'update-alternatives --set jar /usr/lib/jvm/java-8-oracle/bin/jar'
+  when: apt_result.changed
+
 - name: Java | Set JAVA_HOME
   lineinfile:
     line: 'JAVA_HOME=/usr/lib/jvm/java-8-oracle'
     dest: /etc/environment
     state: present
     create: yes
+
+- name: Java | Set JAVA_HOME
+  lineinfile:
+    line: 'export JAVA_HOME=/usr/lib/jvm/java-8-oracle'
+    dest: /etc/bash.bashrc
+    state: present
+    create: yes
+
+- name: Java | Set JAVA_HOME for root?
+  lineinfile:
+    line: 'export JAVA_HOME=/usr/lib/jvm/java-8-oracle'
+    dest: /root/.bash_profile
+    state: present
+    create: yes
+
+- name: Java | Really set JAVA_HOME for root?
+  lineinfile:
+    line: 'Defaults   env_keep += "JAVA_HOME"'
+    dest: /etc/sudoers
+    state: present
+    create: yes

roles/seqware-code/tasks/main.yml

@@ -75,19 +75,21 @@
     owner: "{{ user_name }}"
 
 - include: 'git.yml'
-  when: seqware_provider == "git"
+  when: seqware_provider == "git" and test_environment is undefined
 
 - include: 'artifactory.yml'
-  when: seqware_provider == "artifactory"
+  when: seqware_provider == "artifactory" and test_environment is undefined
 
 - name : Prime SeqWare script
   sudo_user: "{{ user_name }}"
   shell: "~{{ user_name }}/bin/seqware"
   register: script_prime
+  when: test_environment is undefined
   changed_when: "'Downloading' in script_prime.stdout"
 
 - name:  Setup script path in bash profile
   sudo: yes
+  when: test_environment is undefined
   lineinfile: 
     dest: ~{{ user_name }}/.bash_profile
     create: yes

roles/seqware-common-infrastructure/meta/main.yml

@@ -1,3 +1,3 @@
 ---
 dependencies:
-  - { role: java, java_provider: Cloudera }
+  - { role: java, java_provider: Oracle8 }

roles/seqware-master-infrastructure/tasks/main.yml

@@ -144,7 +144,7 @@
 - name:  Setup HDFS Shared Storage
   sudo: yes
   sudo_user: hdfs
-  command: "{{ item }}"
+  shell: "{{ item }}"
   when: "namenode_format.changed or 'No such file or directory' in hdfs_state.stderr"
   with_items: 
     - hadoop fs -mkdir /tmp

seqware-install.yml

@@ -65,7 +65,7 @@
     - { role: grid-engine, grid_engine_master: True }
     - { role: seqware-master-infrastructure }
     - { role: seqware-code }
-    - { role: seqware-webservice }
+    - { role: seqware-webservice, when: test_environment is undefined }
 
 - hosts: worker
   sudo: True
@@ -85,5 +85,5 @@
 - hosts: master
   sudo: True
   roles:
-    - { role: seqware-cron }
-    - { role: seqware-helloworld }
+    - { role: seqware-cron, when: test_environment is undefined }
+    - { role: seqware-helloworld, when: test_environment is undefined }