add biotex properties generation

README.md

 # Wrap Biotex in API REST (python)
 
 This project aims to deploy an API Rest around BioTex. **BioTex is a Automated Term Extractor** (see [here](http://tubo.lirmm.fr/biotex/index.jsp) for more details)
+BioTex need a POS (Part of Speech) tagger. Its author suggest [TreeTagger](https://www.cis.uni-muenchen.de/~schmid/tools/TreeTagger/)
 
 This repository is based upon the work of **Jacques Fize** who build a python wrapper of Biotext (see [his repository](https://gitlab.irstea.fr/jacques.fize/biotex_python) for more details)
\ No newline at end of file

biotex-rest-deployment/ansible/playbook/roles/biotex-java/tasks/main.yml

@@ -24,31 +24,61 @@
     name:
       - openjdk-8-jdk
       
-- name: Prepare Download directory
-  become: yes
+- name: "POS : Prepare Download directory"
   file:
     state: directory
-    path: /root/ansible-dl
+    path: "~/TreeTagger"
 
 - name: "POS : Download TreeTagger"
   get_url: 
     url: "https://www.cis.uni-muenchen.de/~schmid/tools/TreeTagger/data/tree-tagger-linux-3.2.2.tar.gz"
-    dest: "~"
+    dest: "~/TreeTagger"
 
 - name: "POS : DownloadTreeTagger tagging scripts"
   get_url: 
     url: "https://www.cis.uni-muenchen.de/~schmid/tools/TreeTagger/data/tagger-scripts.tar.gz"
-    dest: "~"  
+    dest: "~/TreeTagger"  
 
 - name: "POS : Download TreeTagger install script"
   get_url: 
     url: "https://www.cis.uni-muenchen.de/~schmid/tools/TreeTagger/data/install-tagger.sh"
-    dest: "~"
+    dest: "~/TreeTagger"
 
 - name: "POS : Download French package"
   get_url: 
     url: "https://www.cis.uni-muenchen.de/~schmid/tools/TreeTagger/data/french.par.gz"
-    dest: "~"  
+    dest: "~/TreeTagger"  
 
 - name: "POS : install TreeTagger"
-  command: "sh ~/install-tagger.sh" 
\ No newline at end of file
+  shell: "cd TreeTagger && sh install-tagger.sh"
+
+- name: "biotex : Prepare Download directory"
+  file:
+    state: directory
+    path: "~/biotex"
+
+- name: "git clone biotex"
+  git:
+    repo: https://github.com/sifrproject/biotex.git
+    dest: "~/biotex"
+    version: maven #Branch maven for build
+    force: yes #otherwise, ansible error if repo existing in local
+
+- name: "Maven build"
+  shell: "cd biotex && mvn package"
+
+- name: "biotex : corpus directory"
+  file:
+    state: directory
+    path: "~/corpus"
+
+- name: "biotex : output directory"
+  file:
+    state: directory
+    path: "~/output"
+
+- name: "biotex: biotex.properties"
+  template:
+    src: templates/biotex.properties.j2
+    dest: "~/biotex/biotex.properties"
+

biotex-rest-deployment/ansible/playbook/roles/biotex-java/templates/biotex.properties.j2

+#source patterns directory
+biotex.source_patterns = {{ ansible_env.HOME }}/biotex/patterns
+biotex.source_dataset_reference = {{ ansible_env.HOME }}/biotex/dataSetReference
+biotex.source_stop_words = {{ ansible_env.HOME }}/biotex/stopWords
+biotex.source_treetagger = {{ ansible_env.HOME }}/TreeTagger
+
+biotex.output={{ ansible_env.HOME }}/output
+
+biotex.input_file={{ ansible_env.HOME }}/corpus/corpus.txt
+
+
+#(all|multi)
+biotex.type_of_terms=all
+
+#french, english or spanish
+biotex.language=french
+
+biotex.min_term_frequency=1
+
+#Default: 200
+biotex.number_of_patterns=200
+
+#For one document       :   LValue     CValue
+# For a set of documents :   LIDFValue  F-OCapi_A   F-OCapi_M   F-OCapi_S   F-TFIDF-C_A     F-TFIDF-C_M     F-TFIDF-C_S
+#                            TFIDF_A     TFIDF_M     TFIDF_S     Okapi_A     Okapi_M     Okapi_S
+biotex.measure=Okapi_A
+
+#1 = single file (only for LValue  or CValue)
+#2 = set of files (for LIDF-value or any measure)
+biotex.source_type=2