<commit_before>- name: install java7
  yum: name=java-1.7.0-openjdk-headless state=present

- name: install unzip
  yum: name=unzip state=present

- name: install maven
  yum: name=maven state=present

- name: install tomcat
  yum: name=tomcat state=present

- name: make sure phenotips is not a directory
  file: path=/var/lib/phenomecentral state=absent

- name: make sure phenomecentral is not a directory
  file: path=/var/lib/phenomecentral state=absent

- name: download phenomecentral zip
  get_url: 
    dest=/pc.zip 
    url={{ nexus_releases_url }}/org/phenomecentral/phenomecentral-standalone/{{ phenomecentral_version }}/{{ phenomecentral }}.zip

- name: unzip phenomecentral-standalone.zip
  unarchive: copy=no src=/pc.zip dest=/var/lib/ creates=/var/lib/{{ phenomecentral }} owner=tomcat group=tomcat

- name: link phenomcentral to unzipped phenomecentral
  file: src=/var/lib/{{ phenomecentral }} dest=/var/lib/phenomecentral state=link

- name: link data to /var/lib/phenotips
  file: src=/var/lib/phenomecentral/data dest=/var/lib/phenotips state=link

# SET UP TOMCAT
- name: copy tomcat config
  copy: src=catalina-root.xml dest=/etc/tomcat/Catalina/localhost/ROOT.xml owner=tomcat group=tomcat
<commit_msg>removing unnescessary link cleanups, instead forcing the link creation<commit_after>- name: install java7
  yum: name=java-1.7.0-openjdk-headless state=present

- name: install unzip
  yum: name=unzip state=present

- name: install maven
  yum: name=maven state=present

- name: install tomcat
  yum: name=tomcat state=present

- name: download phenomecentral zip
  get_url: 
    dest=/pc.zip 
    url={{ nexus_releases_url }}/org/phenomecentral/phenomecentral-standalone/{{ phenomecentral_version }}/{{ phenomecentral }}.zip

- name: unzip phenomecentral-standalone.zip
  unarchive: copy=no src=/pc.zip dest=/var/lib/ creates=/var/lib/{{ phenomecentral }} owner=tomcat group=tomcat

- name: link phenomcentral to unzipped phenomecentral
  file: src=/var/lib/{{ phenomecentral }} dest=/var/lib/phenomecentral state=link force=yes

- name: link data to /var/lib/phenotips
  file: src=/var/lib/phenomecentral/data dest=/var/lib/phenotips state=link force=yes

# SET UP TOMCAT
- name: copy tomcat config
  copy: src=catalina-root.xml dest=/etc/tomcat/Catalina/localhost/ROOT.xml owner=tomcat group=tomcat

{'fraction_non_alphanumeric': 0.11554982817869416, 'fraction_numerical': 0.003436426116838488, 'mean_word_length': 4.558472553699284, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 4}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '525894', 'n_tokens_mistral': 864, 'n_tokens_neox': 782, 'n_words': 192}