Dev (#147)

Dev

CHANGELOG.md

@@ -1,3 +1,14 @@
+##  (2019-10-08)
+
+### Bug Fixes
+
+* **delete-vm:**
+  *  deletes all security groups of server with the same name
+
+### Features
+
+* **bioconda:** init .bashrc and create alias for environment (#141)
+
 ##  (2019-09-11)
 
 

VirtualMachineService/VirtualMachineHandler.py

@@ -31,6 +31,7 @@
     from .ancon.Playbook import Playbook
 
 from openstack import connection
+from openstack import exceptions
 from deprecated import deprecated
 from keystoneauth1.identity import v3
 from keystoneauth1 import session
@@ -1138,13 +1139,20 @@ def delete_server(self, openstack_id):
                 raise serverNotFoundException
             self.logger.info(server)
             self.logger.info(server.name)
-            security_group = self.conn.network.find_security_group(name_or_id=openstack_id)
-            if security_group:
-                self.logger.info("Delete security group {}".format(openstack_id))
-                self.conn.compute.remove_security_group_from_server(server=server,
-                                                                    security_group=security_group)
-                self.conn.network.delete_security_group(security_group)
-            self.conn.compute.delete_server(server)
+            try:
+                security_groups = self.conn.network.security_groups(name=openstack_id)
+            except Exception as e:
+                self.logger.exception(e)
+            if security_groups is not None:
+                for sg in security_groups:
+                    self.logger.info("Delete security group {0}".format(openstack_id))
+                    self.conn.compute.remove_security_group_from_server(server=server,
+                                                                        security_group=sg)
+                    self.conn.network.delete_security_group(sg)
+                self.conn.compute.delete_server(server)
+            else:
+                return False
+
 
             return True
         except Exception as e:

VirtualMachineService/ancon/playbooks/bioconda.yml

@@ -35,22 +35,33 @@
     executable: /bin/bash
   when: added_channels.stdout.find('conda-forge') == -1
 
+- name: Init .bashrc for conda
+  shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda init'"
+  args:
+    executable: /bin/bash
+
 - name: Check for environment
   shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda info -e'"
   register: added_envs
 
+- name: Create alias for environment
+  shell: "echo $ALIAS_VARIABLE > ~/.bash_aliases"
+  environment:
+    ALIAS_VARIABLE: 'alias {{ bioconda_tools.env | quote }}="conda activate {{ bioconda_tools.env | quote }}"'
+  when: added_envs.stdout.find(bioconda_tools.env) == -1
+
 - name: Create environment
-  shell: "timeout 2m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda create --yes -n {{ bioconda_tools.env }}'"
+  shell: "timeout 2m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda create --yes -n {{ bioconda_tools.env | quote}}'"
   args:
     executable: /bin/bash
   when: added_envs.stdout.find(bioconda_tools.env) == -1
 
 - name: Check for installed packages
-  shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda activate {{ bioconda_tools.env }} && conda list'"
+  shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda activate {{ bioconda_tools.env | quote}} && conda list'"
   register: added_packages
 
 - name: Install chosen packages
-  shell: "timeout {{ bioconda_tools.timeout_length }} bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda activate {{ bioconda_tools.env }} && conda install --yes {{ item.key }}={{ item.value.version }}={{ item.value.build }}'"
+  shell: "timeout {{ bioconda_tools.timeout_length }} bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda activate {{ bioconda_tools.env | quote}} && conda install --yes {{ item.key }}={{ item.value.version }}={{ item.value.build }}'"
   args:
     executable: /bin/bash
   loop: "{{ q('dict', bioconda_tools.packages) }}"