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123 experiment key #126

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123 experiment key #126

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b720b1e
changed experiment arg to yaml key
beyzabozdag Dec 30, 2022
125fccc
modified md files
beyzabozdag Jan 2, 2023
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40 changes: 22 additions & 18 deletions distributed_pipeline_wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,11 +49,11 @@ def get_args():

# Season 12 and on should have a value for experiment set (e.g. sorghum, sunflower)
# For Season 11 it should be left '' (so no experiment dir is created)
parser.add_argument('-x',
'--experiment',
help='Experiment (e.g. Sorghum, Sunflower)',
type=str,
default='')
# parser.add_argument('-x',
# '--experiment',
# help='Experiment (e.g. Sorghum, Sunflower)',
# type=str,
# default='')

parser.add_argument('-c',
'--cctools_version',
Expand Down Expand Up @@ -249,7 +249,7 @@ def build_irods_path_to_sensor_from_yaml(yaml_dictionary, args):
sensor
)

experiment = args.experiment
experiment = yaml_dictionary['tags']['experiment']

# If level is greater than level zero, then we need to add
# two directories: .../expirment/date
Expand Down Expand Up @@ -296,7 +296,9 @@ def download_irods_input_dir(yaml_dictionary, date, args):

os.chdir(input_dir)

server_utils.download_files_from_cyverse(files=file_paths, experiment=args.experiment)
experiment = yaml_dictionary['tags']['experiment'] if yaml_dictionary['tags']['experiment'] else ""

server_utils.download_files_from_cyverse(files=file_paths, experiment=experiment)

# Step (2)

Expand All @@ -319,15 +321,15 @@ def find_matching_file_in_irods_dir(yaml_dictionary, date, args, irods_dl_dir):


args = get_args()
experiment = args.experiment
experiment = yaml_dictionary['tags']['experiment']
cyverse_datalevel = yaml_dictionary['paths']['cyverse']['input']['level']
prefix = yaml_dictionary['paths']['cyverse']['input']['prefix']
suffix = yaml_dictionary['paths']['cyverse']['input']['suffix']

all_files_in_dir = server_utils.get_filenames_in_dir_from_cyverse(irods_dl_dir)
# Now lets see if our file is in all_files_in_dir

if args.experiment:
if experiment:
date_sub = match = re.search(r'\d{4}-\d{2}-\d{2}', date)
date_sub = str(datetime.strptime(date_sub.group(), '%Y-%m-%d').date())
pattern = (prefix if prefix else "") + date_sub + (suffix if suffix else "")
Expand All @@ -344,7 +346,7 @@ def find_matching_file_in_irods_dir(yaml_dictionary, date, args, irods_dl_dir):
return None
if len(matching_files) > 1:

if args.experiment:
if experiment:
matching_files = [item for item in matching_files if date in item]

else:
Expand Down Expand Up @@ -1045,7 +1047,7 @@ def get_irods_data_path(yaml_dictionary):

#season_name = yaml_dictionary['tags']['season_name']
season_name = get_season_name()
experiment = args.experiment
experiment = yaml_dictionary['tags']['experiment']
sensor = yaml_dictionary['tags']['sensor']
cyverse_basename = yaml_dictionary['paths']['cyverse']['basename']
cyverse_datalevel = yaml_dictionary['paths']['cyverse']['output']['level']
Expand Down Expand Up @@ -1284,18 +1286,19 @@ def clean_inputs(date, yaml_dictionary):
def return_date_list(level_0_list):
args= get_args()
date_list = []
experiment = yaml_dictionary['tags']['experiment']
for item in level_0_list:
try:

if args.experiment:
if experiment:
match = re.search(r'\d{4}-\d{2}-\d{2}__\d{2}-\d{2}-\d{2}-\d{3}', item)
else:
match = re.search(r'\d{4}-\d{2}-\d{2}', item)

if match:
if args.experiment:
if experiment:
date = str(match.group())
date = '_'.join([date, args.experiment])
date = '_'.join([date, experiment])
else:
date = str(datetime.strptime(match.group(), '%Y-%m-%d').date())

Expand All @@ -1312,6 +1315,7 @@ def get_process_date_list(yaml_dictionary):
args= get_args()
basename = yaml_dictionary['paths']['cyverse']['basename']
input_level = yaml_dictionary['paths']['cyverse']['input']['level']
experiment = yaml_dictionary['tags']['experiment']

try:
pre, input_num = input_level.split('_')
Expand All @@ -1322,7 +1326,7 @@ def get_process_date_list(yaml_dictionary):

input_path = os.path.join(basename, yaml_dictionary['tags']['season_name'], input_level, yaml_dictionary['tags']['sensor'])

if args.experiment:
if experiment:
output_path = os.path.join(basename, yaml_dictionary['tags']['season_name'], output_level, yaml_dictionary['tags']['sensor'], args.experiment)

if int(str(yaml_dictionary['paths']['cyverse']['input']['level']).split('_')[1]) >= 1:
Expand All @@ -1335,10 +1339,10 @@ def get_process_date_list(yaml_dictionary):
level_0_list, level_1_list = [os.path.splitext(os.path.basename(item))[0].lstrip() for item in [line.rstrip() for line in os.popen(f'ils {input_path}').readlines()][1:]] \
,[os.path.splitext(os.path.basename(item))[0].lstrip() for item in [line.rstrip() for line in os.popen(f'ils {output_path}').readlines()][1:]]

if args.experiment:
if experiment:

level_0_list = [item for item in level_0_list if args.experiment in item]
level_1_list = [item for item in level_1_list if args.experiment in item]
level_0_list = [item for item in level_0_list if experiment in item]
level_1_list = [item for item in level_1_list if experiment in item]

level_0_dates, level_1_dates = return_date_list(level_0_list) \
, return_date_list(level_1_list)
Expand Down
1 change: 0 additions & 1 deletion docs/arguments.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
* Optional
* -hpc, --hpc | Download data using UA HPC data transfer node
* -d, --date | Test date/s to process (in YYYY-MM-DD format, i.e."2020-01-22")
* -x, --experiment | Experiment name (e.g. Sorghum, Sunflower)
* -c, --cctools_version | CCTools version to download and use for distributed computing
* -l, --local_cores | Number of cores to use for local processing
* --noclean | Do not delete local results
Expand Down
1 change: 1 addition & 0 deletions docs/yaml.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ Tags which will are used for documentation purposes. They include descriptions o
* [sensor] | Name of sensor being processed
* [season] | Season number (i.e. 10, 11, 12, etc)
* [season_name] | Season name as found on CyVerse (i.e. season_11_sorghum_yr_2020)
* [experiment] | Experiment name (i.e. Sorghum, Sunflower), empty if not specified
* [slack_notifications] | Send out Slack notifications
* [use] | Use notification system (True/False)
* [channel] | Slack channel on which to post
Expand Down
1 change: 1 addition & 0 deletions yaml_files/season_14/s14_rgb.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ tags:
sensor: stereoTop
season: 14
season_name: season_14_sorghum_yr_2022
experiment: sorghum
slack_notifications:
use: True
channel: gantry_data_updates
Expand Down