Merge pull request #132 from deNBI/dev

refactor(bioconda): playbook tasks now idempotent (#128)
deNBI · Aug 28, 2019 · fc4fef6 · fc4fef6
2 parents f7cede3 + c644452
commit fc4fef6
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Showing 3 changed files with 48 additions and 7 deletions.
diff --git a/VirtualMachineService/ancon/Playbook.py b/VirtualMachineService/ancon/Playbook.py
@@ -76,9 +76,21 @@ def copy_and_init(self, playbook_name, playbook_vars):
         def load_vars():
             if playbook_name == BIOCONDA:
                 for k, v in playbook_vars.items():
-                    if k == "string_line":
-                        data[playbook_name + "_tools"][k] = v.strip('\"')
-                        data[playbook_name + "_tools"]["timeout_length"] = str(len(v.split()) * 5) + "m"
+                    if k == "packages":
+                        p_array = []
+                        p_dict = {}
+                        for p in (v.strip('\"')).split():
+                            p_array.append(p.split("="))
+                        for p in p_array:
+                            p_dict.update(
+                                {
+                                    p[0]: {
+                                        "version": p[1],
+                                        "build": p[2]
+                                    }
+                                }
+                            )
+                        data[playbook_name + "_tools"][k] = p_dict
             if playbook_name == THEIA:
                 for k, v in playbook_vars.items():
                     if k == "version":

diff --git a/VirtualMachineService/ancon/playbooks/bioconda.yml b/VirtualMachineService/ancon/playbooks/bioconda.yml
@@ -5,24 +5,53 @@
     dest: "{{ bioconda_folders.install_script }}"
     mode: 0755
     timeout: 180
+    force: no
 
 - name: Install miniconda
   shell: "timeout 3m {{ bioconda_folders.install_script }} -b"
   args:
     executable: /bin/bash
     creates: "{{ bioconda_folders.conda_dir }}"
 
-- name: Add channels
-  shell: "timeout 2m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda config --add channels default && conda config --add channels bioconda && conda config --add channels conda-forge'"
+- name: Check for channels
+  shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda config --get channels'"
+  register: added_channels
+
+- name: Add default channel
+  shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda config --add channels default'"
   args:
     executable: /bin/bash
+  when: added_channels.stdout.find('default') == -1
+
+- name: Add bioconda channel
+  shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda config --add channels bioconda'"
+  args:
+    executable: /bin/bash
+  when: added_channels.stdout.find('bioconda') == -1
+
+- name: Add conda-forge channel
+  shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda config --add channels conda-forge'"
+  args:
+    executable: /bin/bash
+  when: added_channels.stdout.find('conda-forge') == -1
+
+- name: Check for environment
+  shell: "timeout 1m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda info -e'"
+  register: added_envs
 
 - name: Create environment
   shell: "timeout 2m bash -c 'source {{ bioconda_folders.conda_dir }}/bin/activate && conda create --yes -n {{ bioconda_tools.env }}'"
   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'"
+  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 {{ bioconda_tools.string_line }}'"
+  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 }}'"
   args:
     executable: /bin/bash
+  loop: "{{ lookup('dict', bioconda_tools.packages) }}"
+  when: added_packages.stdout.find(item.key) == -1
diff --git a/VirtualMachineService/ancon/playbooks/bioconda_vars_file.yml b/VirtualMachineService/ancon/playbooks/bioconda_vars_file.yml
@@ -1,5 +1,5 @@
 bioconda_tools:
-  string_line: ""
+  packages:
   env: "denbi"
   timeout_length: "5m"