Merge branch 'gitlab-ci' into develop

horkko · Aug 31, 2016 · 3c05668 · 3c05668
2 parents 4f1a031 + ab2fb23
commit 3c05668
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Showing 4 changed files with 5 additions and 22 deletions.
diff --git a/README.md b/README.md
@@ -146,6 +146,9 @@ Tests
 
 You can run tests by typing `nosetests`
 
+It is also possible to clone this repo into gitlab and run tests using gitlab-ci. There's a `.gitlab-ci.yml` available for
+this as well as a `Dockerfile` to run gitlab tests inside Docker.
+
 Status
 ======
 [![Build Status](https://travis-ci.org/horkko/biomaj-manager.svg?branch=master)](https://travis-ci.org/horkko/biomaj-manager)

diff --git a/biomajmanager/links.py b/biomajmanager/links.py
@@ -216,11 +216,6 @@ def _clone_structure(self, source=None, target=None, remove_ext=False):
             Utils.error("[%s] Can't create %s dir: %s (%s)" % (self.bank_name, end_target, str(err),
                                                                os.access(end_target, os.W_OK)))
 
-        # if not self.manager.get_verbose():
-        #     Utils.warn("Perms for %s: R(%s)W(%s)X(%s)" % (str(self.target), str(os.access(self.target, os.R_OK)),
-        #                                                   str(os.access(self.target, os.W_OK)),
-        #                                                   str(os.access(self.target, os.X_OK))))
-
         return True
 
     def _generate_dir_link(self, source=None, target=None, hard=False, fallback=None, requires=None):
@@ -389,24 +384,8 @@ def _prepare_links(self, source=None, target=None, get_deepest=False, fallback=N
                 Utils.verbose("[%s] Creating directory %s" % (bank_name, target))
             else:
                 try:
-                    if target.endswith('link_test'):
-                        import pwd
-                        import grp
-                        Utils.warn("[%s][prepare_links] We create dir %s" % (Utils.user(), target))
-                        Utils.warn("Perms for %s: R(%s)W(%s)X(%s) [%s]" % (str(target_dir),
-                                                                           str(os.access(target_dir, os.R_OK)),
-                                                                           str(os.access(target_dir, os.W_OK)),
-                                                                           str(os.access(target_dir, os.X_OK)),
-                                                                           str(os.stat(target_dir).st_uid)))
-                        stat_info = os.stat(target_dir)
-                        uid = stat_info.st_uid
-                        gid = stat_info.st_gid
-                        Utils.warn("[%s][prepare_links] Owner U:%s, G:%s" % (Utils.user(), str(pwd.getpwuid(uid)[0]),
-                                                                             str(grp.getgrgid(gid)[0])))
                     if not Manager.get_simulate():
                         os.makedirs(target)
-                        if target.endswith('link_test'):
-                            Utils.warn("[%s][prepare_links] Dir created: %s" % (Utils.user(), target))
                 except OSError as err:
                     Utils.error("[%s] Can't create %s dir: %s" % (bank_name, target, str(err)))
 

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 config = {
     'name': 'biomajmanager',
-    'version': '1.1.5',
+    'version': '1.1.6',
     'packages': find_packages(),
     'scripts': ['bin/biomaj-manager.py'],
     'url': 'https://github.com/horkko/biomaj-manager',

diff --git a/tests/gitlab-tests.sh b/tests/gitlab-tests.sh
@@ -24,6 +24,7 @@ sudo pip install git+https://github.com/svpino/rfeed#egg=rfeed
 
 # Run tests for biomaj-manager with DOCKER tests
 export LOGNAME='biomaj'
+export USER='biomaj'
 
 # Install BioMAJ Manager to test it later on
 cd /builds || { echo "Can't cd to /builds" && exit 1; }