def index():
#####
# grab the install-time variables...
#
c = _get_nexson_proc_conf(request)
nexsons_dir = c['nexsons_dir']
response.title = 'List of known study status pages'
dd = get_default_dir_dict(nexsons_dir)
x = os.listdir(nexsons_dir)
study_list = []
for study_id in x:
try:
study_id_as_int = int(study_id)
study_list.append((study_id_as_int, study_id))
except:
continue
study_list.sort()
study_status_list = []
for study_id_as_int, study_id in study_list:
paths = get_processing_paths_from_prefix(study_id, **dd)
check_lock_policy = LockPolicy()
check_lock_policy.early_exit_if_locked = True
nexson_path = paths['nexson']
study_link = URL(a=request.application,
c=request.controller,
f='status',
args=[study_id])
el = { 'study_id': study_id,
'status_link': study_link,
'has_status': False,
'message_link_list': []
}
lockfile = nexson_path + '.studylock'
study_was_locked, owns_study_lock = check_lock_policy.wait_for_lock(lockfile)
try:
treemachine_log_path = paths['treemachine_log']
status_json = paths['status_json']
if study_was_locked:
el['message']='The status is being assessed.'
elif not target_is_dirty([nexson_path, treemachine_log_path], [status_json]):
el['has_status'] = True
el['message'] = 'Status is available'
else:
processing_launched_ts = paths['launched_study_proc']
if os.path.exists(processing_launched_ts) and target_is_dirty([processing_launched_ts], [status_json]):
# the study is not currently being processed, the status_json is out of date, and the status_json is younger than
# the 'study processing has been launched flag' This means that the processing failed
# We don't want to fall through hear and launch again, because that could
# lead to lots of processing getting launched as a problematic case repeatedly fails
el['message'] = 'Error in status assessment. Please add this study id (%s) to the following issue tracking document (if it is not already listed):' % study_id
el['message_link_list'] = [('Study/status problems document.', 'https://docs.google.com/spreadsheet/ccc?key=0AnYfNFYgyCWkdGRhUGNlbE8xVk9UNE1SV1NDTzBCdEE#gid=0')]
else:
el['message']= 'The status of this study has not been assessed. Click on the study # to start processing.'
finally:
check_lock_policy.remove_lock()
study_status_list.append(el)
return {'study_status_list' : study_status_list}
def index():
#####
# grab the install-time variables...
#
c = _get_nexson_proc_conf(request)
nexsons_dir = c['nexsons_dir']
response.title = 'List of known study status pages'
dd = get_default_dir_dict(nexsons_dir)
x = os.listdir(nexsons_dir)
study_list = []
for study_id in x:
try:
study_id_as_int = int(study_id)
study_list.append((study_id_as_int, study_id))
except:
continue
study_list.sort()
study_status_list = []
for study_id_as_int, study_id in study_list:
paths = get_processing_paths_from_prefix(study_id, **dd)
check_lock_policy = LockPolicy()
check_lock_policy.early_exit_if_locked = True
nexson_path = paths['nexson']
study_link = URL(a=request.application,
c=request.controller,
f='status',
args=[study_id])
el = {
'study_id': study_id,
'status_link': study_link,
'has_status': False,
'message_link_list': []
}
lockfile = nexson_path + '.studylock'
study_was_locked, owns_study_lock = check_lock_policy.wait_for_lock(
lockfile)
try:
treemachine_log_path = paths['treemachine_log']
status_json = paths['status_json']
if study_was_locked:
el['message'] = 'The status is being assessed.'
elif not target_is_dirty([nexson_path, treemachine_log_path],
[status_json]):
el['has_status'] = True
el['message'] = 'Status is available'
else:
processing_launched_ts = paths['launched_study_proc']
if os.path.exists(processing_launched_ts) and target_is_dirty(
[processing_launched_ts], [status_json]):
# the study is not currently being processed, the status_json is out of date, and the status_json is younger than
# the 'study processing has been launched flag' This means that the processing failed
# We don't want to fall through hear and launch again, because that could
# lead to lots of processing getting launched as a problematic case repeatedly fails
el['message'] = 'Error in status assessment. Please add this study id (%s) to the following issue tracking document (if it is not already listed):' % study_id
el['message_link_list'] = [(
'Study/status problems document.',
'https://docs.google.com/spreadsheet/ccc?key=0AnYfNFYgyCWkdGRhUGNlbE8xVk9UNE1SV1NDTzBCdEE#gid=0'
)]
else:
el['message'] = 'The status of this study has not been assessed. Click on the study # to start processing.'
finally:
check_lock_policy.remove_lock()
study_status_list.append(el)
return {'study_status_list': study_status_list}
def status():
study_id = request.args(0)
if study_id is None:
raise HTTP(404)
emit_json = study_id.lower().endswith('.json')
study_id = study_id.split('.')[0]
try:
ls = long(study_id)
assert ls > 0
except:
raise HTTP(404)
#####
# grab the install-time variables...
#
c = _get_nexson_proc_conf(request)
nexsons_dir = c['nexsons_dir']
treemachine_domain = c['treemachine_domain']
study_to_status_script = c['study_to_status_script']
force_phylografter_reload = request.get_vars.get('fetchnexson') is not None
response.title = 'Status page for study ' + str(study_id)
dd = get_default_dir_dict(nexsons_dir)
paths = get_processing_paths_from_prefix(study_id, **dd)
check_lock_policy = LockPolicy()
check_lock_policy.early_exit_if_locked = True
nexson_path = paths['nexson']
lockfile = nexson_path + '.studylock'
study_was_locked, owns_study_lock = check_lock_policy.wait_for_lock(
lockfile)
try:
treemachine_log_path = paths['treemachine_log']
status_json = paths['status_json']
if study_was_locked:
return {
'has_status':
False,
'message':
'The processing of the information for this study is underway. Once it is complete the status will be displayed when this page reloads.'
}
## the study is not currently being processed
if not force_phylografter_reload:
if not target_is_dirty([nexson_path, treemachine_log_path],
[status_json]):
rich_log = json.load(open(status_json, 'rU'))
rich_log['force_fetch_url'] = URL(
a=request.application,
c=request.controller,
f=request.function,
args=[study_id],
vars=dict(fetchnexson='True'))
if emit_json:
return response.json(rich_log)
rich_log['has_status'] = True
return rich_log
else:
processing_launched_ts = paths['launched_study_proc']
if os.path.exists(processing_launched_ts) and target_is_dirty(
[processing_launched_ts], [status_json]):
# the study is not currently being processed, the status_json is out of date, and the status_json is younger than
# the 'study processing has been launched flag' This means that the processing failed
# We don't want to fall through hear and launch again, because that could
# lead to lots of processing getting launched as a problematic case repeatedly fails
return {
'has_status':
False,
'message':
'The processing of the information for this study appears to have failed. Please add this study id (%s) to the following issue tracking document (if it is not already listed):'
% study_id,
'message_link_list':
[('Study/status problems document.',
'https://docs.google.com/spreadsheet/ccc?key=0AnYfNFYgyCWkdGRhUGNlbE8xVk9UNE1SV1NDTzBCdEE#gid=0'
)],
}
finally:
check_lock_policy.remove_lock()
invoc = [
sys.executable,
study_to_status_script,
treemachine_domain,
'-d%s' % nexsons_dir,
'-t', # run through treemachine if necessary
'-s', # create the status JSON
study_id
]
if force_phylografter_reload:
invoc.extend(['-l', '-n'])
subprocess.Popen(invoc)
return {
'has_status':
False,
'message':
'The process of fetching the latest information for this study from phylografter has begun. Once it is complete the status will be displayed when this page reloads.'
}
# we will get here if:
# 1. we are not fetching NexSON from phylografter,
# 2. we have not detected a lock indicating that the study is being processed, and
# 3. the status_json is out of date
subprocess.Popen(invoc)
return {
'has_status':
False,
'message':
'The process of analyzing previously downloaded information for this study is underway. Once it is complete the status will be displayed when this page reloads.'
}
def status():
study_id = request.args(0)
if study_id is None:
raise HTTP(404)
emit_json = study_id.lower().endswith('.json')
study_id = study_id.split('.')[0]
try:
ls = long(study_id)
assert ls > 0
except:
raise HTTP(404)
#####
# grab the install-time variables...
#
c = _get_nexson_proc_conf(request)
nexsons_dir = c['nexsons_dir']
treemachine_domain = c['treemachine_domain']
study_to_status_script = c['study_to_status_script']
force_phylografter_reload = request.get_vars.get('fetchnexson') is not None
response.title = 'Status page for study ' + str(study_id)
dd = get_default_dir_dict(nexsons_dir)
paths = get_processing_paths_from_prefix(study_id, **dd)
check_lock_policy = LockPolicy()
check_lock_policy.early_exit_if_locked = True
nexson_path = paths['nexson']
lockfile = nexson_path + '.studylock'
study_was_locked, owns_study_lock = check_lock_policy.wait_for_lock(lockfile)
try:
treemachine_log_path = paths['treemachine_log']
status_json = paths['status_json']
if study_was_locked:
return {'has_status': False,
'message': 'The processing of the information for this study is underway. Once it is complete the status will be displayed when this page reloads.'}
## the study is not currently being processed
if not force_phylografter_reload:
if not target_is_dirty([nexson_path, treemachine_log_path], [status_json]):
rich_log = json.load(open(status_json, 'rU'))
rich_log['force_fetch_url'] = URL(a=request.application,
c=request.controller,
f=request.function,
args=[study_id], vars=dict(fetchnexson='True'))
if emit_json:
return response.json(rich_log)
rich_log['has_status'] = True
return rich_log
else:
processing_launched_ts = paths['launched_study_proc']
if os.path.exists(processing_launched_ts) and target_is_dirty([processing_launched_ts], [status_json]):
# the study is not currently being processed, the status_json is out of date, and the status_json is younger than
# the 'study processing has been launched flag' This means that the processing failed
# We don't want to fall through hear and launch again, because that could
# lead to lots of processing getting launched as a problematic case repeatedly fails
return {'has_status': False,
'message': 'The processing of the information for this study appears to have failed. Please add this study id (%s) to the following issue tracking document (if it is not already listed):' % study_id,
'message_link_list': [('Study/status problems document.', 'https://docs.google.com/spreadsheet/ccc?key=0AnYfNFYgyCWkdGRhUGNlbE8xVk9UNE1SV1NDTzBCdEE#gid=0')],
}
finally:
check_lock_policy.remove_lock()
invoc = [sys.executable,
study_to_status_script,
treemachine_domain,
'-d%s' % nexsons_dir,
'-t', # run through treemachine if necessary
'-s', # create the status JSON
study_id
]
if force_phylografter_reload:
invoc.extend(['-l', '-n'])
subprocess.Popen(invoc)
return {'has_status': False,
'message': 'The process of fetching the latest information for this study from phylografter has begun. Once it is complete the status will be displayed when this page reloads.'}
# we will get here if:
# 1. we are not fetching NexSON from phylografter,
# 2. we have not detected a lock indicating that the study is being processed, and
# 3. the status_json is out of date
subprocess.Popen(invoc)
return {'has_status': False,
'message': 'The process of analyzing previously downloaded information for this study is underway. Once it is complete the status will be displayed when this page reloads.'}