common.py

"""
common helper functions
"""
import logging;
from datetime import *
import time
from enum import Enum

logger = logging.getLogger(__name__)
class State(Enum):
    DEFINED = "defined"
    STAGED = "staged"
    FETCHED = "fetched"
    PROCESSED = "processed"
    STORED = 'stored'
    VALIDATED = "validated"
    SCRUBBED = "scrubbed"
    PRE_ARCHIVING = "pre_archiving"
    PRE_ARCHIVED = "pre_archived"
    ARCHIVING = "archiving"
    ARCHIVED = "archived"
    FINISHED = "finished"
    FINISHING = "finishing"
    SUSPENDED = "suspended"
    DISCARDED = "discarded"
    FAILED = "failed"

verified_statusses = [State.STORED.value, State.VALIDATED.value, State.SCRUBBED.value, State.PRE_ARCHIVED,
                      State.ARCHIVED.value, State.FINISHED.value, State.SUSPENDED.value, State.DISCARDED.value]

processed_statusses = [State.PROCESSED.value, State.STORED.value, State.DISCARDED.value]

class SummaryFlavour(Enum):
    DEFAULT = "default"
    LINC_CALIBRATOR = "linc_calibrator"
    LINC_TARGET = "linc_target"
    IMAGING_COMPRESSION = "imaging_compression"

# this is a decorator that can be put in front (around) a function all to measure its execution time
def timeit(method):
    def timed(*args, **kw):
        ts = time.time()
        result = method(*args, **kw)
        te = time.time()
        if 'log_time' in kw:
            name = kw.get('log_name', method.__name__.upper())
            kw['log_time'][name] = int((te - ts) * 1000)
        else:
            print('execution time: %r  %2.2f ms' % \
                  (method.__name__, (te - ts) * 1000))
        return result
    return timed

def get_summary_flavour(task):
    """
    not every workflow has the same summary structure
    determine the flavour based on the selected task, and construct the html accordingly
    this could be made implicit in the future by adding a setting to the Workflow,
    but currently it is derived in a yucky way. But at least the yuck is confined to this function
    """

    summary_flavour = SummaryFlavour.DEFAULT.value

    # so... yikes... what distinguishes the summary flavours?
    workflow_uri = task.workflow.workflow_uri

    # for linc, look at the workflow_uri
    if "linc_calibrator" in workflow_uri:
        return SummaryFlavour.LINC_CALIBRATOR.value
    if "linc_target" in workflow_uri:
        return SummaryFlavour.LINC_TARGET.value

    try:
        summary = task.quality_json["summary"]
    except:
        # no summary found
        return None

    if 'details' in summary.keys():
        summary_flavour = SummaryFlavour.IMAGING_COMPRESSION.value

    return summary_flavour