mgrauer

import datetime
import os
import platform
import sys
import traceback
from typing import Optional


import click
from packaging.version import parse as parse_version

mgrauer

---
- name: Install Girder with qidw plugin
  hosts: all
  vars:
    ansible_python_interpreter: auto

  roles:
    - role: girder.mongodb
      vars:
        mongodb_data_path: /var/lib/mongodb

mgrauer

import json
import girder_client


GIRDER_URL = 'https://data.kitware.com/api/v1'
GIRDER_API_KEY = 'your_api_key_here'

gc = girder_client.GirderClient(apiUrl=GIRDER_URL)
gc.authenticate(apiKey=GIRDER_API_KEY)

mgrauer

collection_name = 'labs'
labs_collection = None
for col in gc.listCollection():
    if col['name'] == collection_name:
        labs_collection = col

if not labs_collection:
    labs_collection = gc.createCollection(collection_name)

mgrauer

import sys
import os
import subprocess

def get_frame_rate(filename):
    if not os.path.exists(filename):
        sys.stderr.write("ERROR: filename %r was not found!" % (filename,))
        return -1
    out = subprocess.check_output(["ffprobe",filename,"-v","0","-select_streams","v","-print_format","flat","-show_entries","stream=r_frame_rate"])
    rate = out.decode('utf-8').split('=')[1].strip()[1:-1].split('/')

mgrauer

# Find head of current branch and merge commit of last release
# Get merges in between
current_branch_head = '8dfeae34'
last_release_head = '3550d330'
cmd = 'git log --oneline --merges %s ^%s' % (current_branch_head, last_release_head)
import subprocess
merge_commits = subprocess.check_output(cmd, shell=True).split('\n')

# remove all merges of master or origin/master
master_merges = ["Merge branch 'master'", "Merge remote-tracking branch 'origin/master'"]

mgrauer

Include(gaussian.config.bms)
SetApp(gaussian @GaussianFilter)
SetAppOption(gaussian.inputImage ${cfg_inputImage})
SetAppOption(gaussian.outputImage ${cfg_outputImage})
SetAppOption(gaussian.sigma ${cfg_sigma})
CondorPostScript(gaussian ${cfg_exe} ${cfg_condorpostscript} ${cfg_output_directory} ${cfg_taskID})
Run(output ${gaussian})

mgrauer

Set(cfg_inputImage '/nfsmount/tmp/1/data/input.nrrd')
Set(cfg_outputImage '/nfsmount/data/output.nrrd')
Set(cfg_sigma '1.0')
Set(cfg_exe '/usr/bin/python')
Set(cfg_condorpostscript '/nfsmount/scripts/upload_pipeline_step_output.py')
Set(cfg_output_directory '/nfsmount/tmp/1')
Set(cfg_taskID 1)

mgrauer

Job job0 GaussianFilter.0.dagjob
SCRIPT POST job0 /usr/bin/python /nfsmount/scripts/upload_pipeline_step_output.py /nfsmount/tmp/1 1  $JOB $JOBID $RETURN

mgrauer

Universe       = vanilla
Output         = bmGrid.0.out.txt
Error          = bmGrid.0.error.txt
Log            = bmGrid.0.log.txt
Notification   = NEVER
Executable    = /nfsmount/bin/GaussianFilter
Arguments     = "'/nfsmount/data/input.nrrd' '/nfsmount/data/output.nrrd' -s 1.0"
Queue 1