Commit 80d21431 authored by Jerome Mariette's avatar Jerome Mariette
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parent f4e94e99
......@@ -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
......
......@@ -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
......
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