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Remove pg-post-tasks and add common bash variable and functions
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| --- | ||
| - name: Ensure directory for bashrc common files | ||
| file: | ||
| state: directory | ||
| path: "{{ common_bashrc_dir }}" | ||
| - name: Template bashrc_common path | ||
| copy: | ||
| dest: "{{ common_bashrc_vars_file }}" | ||
| mode: 0755 | ||
| content: | | ||
| # slurm | ||
| export SINFO_FORMAT="{{ common_sinfo_format }}" | ||
| export SQUEUE_FORMAT="{{ common_squeue_format }}" | ||
| export SINFO_FORMAT="{{ common_sacct_format }}" | ||
| # helpful settings | ||
| export EDITOR=vim | ||
| HISTSIZE= | ||
| HISTFILESIZE= | ||
| {% if is_galaxy_head_node %} | ||
| # galaxy | ||
| export PGHOST='{{ db_address }}' | ||
| export PGDATABASE='galaxy' | ||
| export PGPORT='5432' | ||
| export GALAXY_CONFIG_DIR={{ galaxy_config_dir }} | ||
| export GALAXY_MUTABLE_CONFIG_DIR={{ galaxy_mutable_config_dir }} | ||
| export GALAXY_ROOT={{ galaxy_server_dir }} | ||
| export GALAXY_CONFIG_FILE={{ galaxy_config_file }} | ||
| export GALAXY_JWD_PATH="{{ galaxy_job_working_directory }}" | ||
| export GALAXY_LOG_DIR="{{ galaxy_log_dir }}" | ||
| export GALAXY_PULSAR_APP_CONF="{{ galaxy_pulsar_app_config_file }}" | ||
| {% endif %} | ||
| - name: Template common_bashrc path | ||
| copy: | ||
| dest: "{{ common_bashrc_functions_file }}" | ||
| mode: 0755 | ||
| content: | | ||
| # Common variables and functions for ubuntu and human users | ||
| {% if is_galaxy_head_node %} | ||
| # galaxy | ||
| jwd() { # print path of job working directory for job id | ||
| python "{{ common_bashrc_dir }}/get_jwd_path_galaxy.py" $1 | ||
| } | ||
| jwd-size() { | ||
| du -sh $(jwd $1) | ||
| } | ||
| go-jwd() { # go to job working directory for job id | ||
| cd $(jwd $1) | ||
| } | ||
| tail-stderr() { | ||
| stderr_filename=$(jwd $1)/outputs/tool_stderr | ||
| if [ ! -f $stderr_filename ]; then | ||
| echo "No stderr file for job $1"; | ||
| else | ||
| tail $stderr_filename; | ||
| fi | ||
| } | ||
| {% endif %} | ||
| {% if ansible_hostname in groups['pulsar_head_nodes'] %} | ||
| # pulsar | ||
| jwd() { # print path of job working directory for job id | ||
| echo {{ pulsar_staging_dir }}/${1} | ||
| } | ||
| jwd-size() { | ||
| du -sh $(jwd $1) | ||
| } | ||
| go-jwd() { # go to job working directory for job id | ||
| cd $(jwd $1) | ||
| } | ||
| tail-stderr() { | ||
| stderr_filename=$(jwd $1)/metadata/tool_stderr | ||
| if [ ! -f $stderr_filename ]; then | ||
| echo "No stderr file for job $1"; | ||
| else | ||
| tail $stderr_filename; | ||
| fi | ||
| } | ||
| {% endif %} | ||
| - name: Template helper scripts | ||
| template: | ||
| src: "bashrc/{{ item }}.j2" | ||
| dest: "{{ common_bashrc_dir }}/{{ item }}" | ||
| with_items: | ||
| - get_jwd_path_galaxy.py | ||
|
|
||
| - name: Add to .bashrc files | ||
| blockinfile: | ||
| marker: "# {mark} ANSIBLE MANAGED BLOCK (common role: source common bash env for users)" | ||
| dest: "/home/{{ item.name }}/.bashrc" | ||
| block: | | ||
| source {{ common_bashrc_vars_file }} | ||
| source {{ common_bashrc_functions_file }} | ||
| {% if is_galaxy_head_node %} | ||
| # galaxy (per user) | ||
| {% if item == 'ubuntu' %} | ||
| export PGUSER='galaxy' | ||
| {% elif 'tiaas_admin' in item.roles|d([]) %} | ||
| export PGUSER='tiaasadmin' | ||
| {% else %} | ||
| export PGUSER='reader' | ||
| {% endif %} | ||
| {% endif %} | ||
| with_items: "{{ machine_users + [{'name': 'ubuntu'}] }}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| import argparse | ||
| import os | ||
|
|
||
| def main(): | ||
| parser = argparse.ArgumentParser(description='Get job working directory from a job id') | ||
| parser.add_argument('job_id', type=int, help='Galaxy job id') | ||
| args = parser.parse_args() | ||
|
|
||
| prefix = os.environ.get("GALAXY_JWD_PATH") | ||
| if not prefix: | ||
| raise ValueError("Please set GALAXY_JWD_PATH environment variable") | ||
|
|
||
| jwd_path = get_jwd_path(args.job_id, prefix) | ||
| print(jwd_path) | ||
|
|
||
| def get_jwd_path(job_id, prefix): | ||
| if len(str(job_id)) > 6: # on production this is the case | ||
| nine_digit_id = '0'*(9-len(str(job_id))) + str(job_id) | ||
| return os.path.join(prefix, nine_digit_id[:3], nine_digit_id[3:6], str(job_id)) | ||
| elif len(str(job_id)) <= 6: | ||
| six_digit_id = '0'*(6-len(str(job_id))) + str(job_id) | ||
| return os.path.join(prefix, six_digit_id[:3], str(job_id)) | ||
|
|
||
|
|
||
| if __name__ == '__main__': | ||
| main() |
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