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application.properties

@@ -84,6 +84,7 @@ fastx_reverse_complement = /usr/bin/fastx_reverse_complement
 #ContaminationSearch.batch_options = -q unlimitq
 
 [resources]
+typo3_src = http://prdownloads.sourceforge.net/typo3/typo3_src+dummy-4.7.12.zip
 phix_bwa = /bank/bwadb/phi.fa
 ecoli_bwa = /bank/bwadb/ecoli536
 yeast_bwa = /bank/bwadb/yeast.nt

workflows/install/__init__.py

@@ -14,32 +14,36 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
+
 from subprocess import Popen, PIPE
-from jflow.workflow import Workflow
 import tempfile, os, sys, re, logging
+
+from jflow.workflow import Workflow
+
 from ng6.config_reader import NG6ConfigReader
-from os.path import expanduser
+
 
 class Install (Workflow):
     
     def process(self):
         
-        #typo3 variables
-        db_host ="localhost"
-        db_user ="root"
-        db_password ="root"
-        db_name ="t3"
+        # typo3 variables
+        ng6conf = NG6ConfigReader()
+        db_host, db_user, db_password, db_name = ng6conf.get_typo3_db_params()
+        
         db_tmp_name=db_name
         suffix_db = 1
-        home_path = expanduser("~")
         
+        # TODO: a modifier ce n'est pas jolie, utilise la path du file, tu le fera en 1 ligne!!
         if "/".join(sys.argv[0].split("/")[:-2])[0] != "/":
             ng6_path = str(os.getcwd()) + "/" +"/".join(sys.argv[0].split("/")[:-2])
         else:
             ng6_path = "/".join(sys.argv[0].split("/")[:-2])
         
+        # TODO: utililse os.path.join !!! ca c'est sous unix ...
         db_path = ng6_path +"/workflows/install/data_typo3/database.sql"
         
+        # TODO: web_dir doit etre un parametre
         web_dir="/var/www"
         save_data_path = NG6ConfigReader().get_save_directory()+"/data"
         unzip_binary_path=""
@@ -48,7 +52,8 @@ class Install (Workflow):
         
         # wget
         dummy_tmp = tempfile.NamedTemporaryFile(prefix = 'dummy_', suffix = '.zip').name
-        wget = ["wget", "--output-document", dummy_tmp, "http://prdownloads.sourceforge.net/typo3/typo3_src+dummy-4.7.12.zip"]
+        # TODO: j'ai mis le nom dans le .properties d'application c'est une ressource
+        wget = ["wget", "--output-document", dummy_tmp, self.get_resource("typo3_src")]
         p = Popen(wget, stdout=PIPE, stderr=PIPE)
         stdout, stderr = p.communicate()
         
@@ -60,11 +65,13 @@ class Install (Workflow):
         
         #rename typo3 folder
         typo3_dir = os.listdir(dummy_tmp_dir)[0]
+        # TODO: c'est quoi ce ng62 ??
         rename=["mv", dummy_tmp_dir+"/"+typo3_dir, dummy_tmp_dir+"/ng62"]
         p = Popen(rename, stdout=PIPE, stderr=PIPE)
         stdout, stderr = p.communicate()
         
         #link ng6 folder
+        # TODO: ne fait pas des links mais des cp
         slink_ext=["ln","-s", ng6_path+"/ui/nG6", dummy_tmp_dir+"/ng62/typo3conf/ext/nG6"]
         p = Popen(slink_ext, stdout=PIPE, stderr=PIPE)
         stdout, stderr = p.communicate()
@@ -129,6 +136,7 @@ class Install (Workflow):
             mysql_check_db= ["mysql", "--host=" + db_host, "--user=" + db_user, "--password=" + db_password, "-e", "SHOW DATABASES LIKE '" + db_tmp_name + "';" ]
             p_mysql_check_db = Popen(mysql_check_db, stdout=PIPE, stderr=PIPE)
             stdout, stderr = p_mysql_check_db.communicate()
+            # TODO: c'est quoi ce suffix_db ?
             suffix_db = suffix_db+1
             
         #Creating database typo3