diff --git a/coordinator/Processor.py b/coordinator/Processor.py
index 9341f71b14ded4150dbf435ee8d4a1ba4e670bf7..46d5c93fd9a0a33e1c34d2ac13d56cd3c5207966 100755
--- a/coordinator/Processor.py
+++ b/coordinator/Processor.py
@@ -512,7 +512,7 @@ class Processor:
endJob(status, ignore_inprogress = True, premature = False)
# files and directories that will be uploaded to public server
- FilesToSend = []
+ files_to_send = []
# files and directories that will be earmarked for removal after a
# successful job
@@ -550,7 +550,7 @@ class Processor:
# proc_description = universal_config['ProcessInJob']
proc_description = 'ProcessInJob'
try:
- proc_out = self.process_in_job(job_path, status, configjson, component)
+ proc_out: dict = self.process_in_job(job_path, status, configjson, component)
except:
self.logger.exception(f"Error in process_in_job")
status.reset('ERROR')
@@ -566,7 +566,7 @@ class Processor:
if 'output' in proc_out.keys():
append_item_to_list(
proc_out['output'],
- FilesToSend,
+ files_to_send,
proc_description,
status)
@@ -582,7 +582,7 @@ class Processor:
# proc_description = universal_config['ProcessEWSPlotting']
proc_description = 'ProcessEWSPlotting'
try:
- EWSPlottingOutputs = self.process_post_job(job_path, configjson)
+ ews_plotting_outputs = self.process_post_job(job_path, configjson)
except:
self.logger.exception(f"Error in {proc_description}()")
status.reset('ERROR')
@@ -590,10 +590,10 @@ class Processor:
self.logger.info('Finished with EWS-Plotting, appending images to list for transfer')
- if EWSPlottingOutputs:
+ if ews_plotting_outputs:
append_item_to_list(
- EWSPlottingOutputs,
- FilesToSend,
+ ews_plotting_outputs,
+ files_to_send,
proc_description,
status)
@@ -603,7 +603,7 @@ class Processor:
if not noupload:
try:
- ProcessorComponents.upload(universal_config, FilesToSend, component)
+ ProcessorComponents.upload(universal_config, files_to_send, component)
except IndexError:
status.reset('WARNING')
@@ -625,7 +625,7 @@ class Processor:
universal_config_extra['ServerPath'] = extra_path
try:
- ProcessorComponents.upload(universal_config_extra, FilesToSend, component)
+ ProcessorComponents.upload(universal_config_extra, files_to_send, component)
except IndexError:
status.reset('WARNING')
@@ -656,11 +656,11 @@ class Processor:
raise NotImplementedError
@abstractmethod
- def process_in_job(self, jobPath, status, configjson, component) -> object:
+ def process_in_job(self, jobPath, status, configjson, component) -> dict:
raise NotImplementedError
@abstractmethod
- def process_post_job(self, jobPath, configjson):
+ def process_post_job(self, jobPath, configjson) -> [str]:
raise NotImplementedError
@abstractmethod
diff --git a/coordinator/ProcessorComponents.py b/coordinator/ProcessorComponents.py
index f2e839138d6dcebb3b53c99d27807d44a5787581..2eb745b8668ca78270d56b25ecf1d2c9b9b690d0 100644
--- a/coordinator/ProcessorComponents.py
+++ b/coordinator/ProcessorComponents.py
@@ -12,10 +12,10 @@ from typing import List
# coordinator stages: pre, in (during) and plotting.
-# from ProcessorServer import (
-# process_pre_job_server_download,
-# upload
-# )
+from ProcessorServer import (
+ # process_pre_job_server_download,
+ upload
+)
from ProcessorUtils import (
add_filters_to_sublogger,
diff --git a/coordinator/ProcessorDeposition.py b/coordinator/ProcessorDeposition.py
index e84d5fcb8fdc9144fbcb085a90eba201e4da04a9..68fe833a65e1321bf95db569b5e8b811fe926e7c 100644
--- a/coordinator/ProcessorDeposition.py
+++ b/coordinator/ProcessorDeposition.py
@@ -28,11 +28,11 @@ class ProcessorDeposition(Processor):
return True
- def process_in_job(self, jobPath, status, configjson, component) -> object:
+ def process_in_job(self, jobPath, status, configjson, component) -> dict:
return self.process_in_job_dep(jobPath, status, configjson, component)
- def process_post_job(self, jobPath, configjson):
+ def process_post_job(self, jobPath, configjson) -> [str]:
return self.process_EWS_plotting_dep(jobPath, configjson)
@@ -108,7 +108,7 @@ class ProcessorDeposition(Processor):
return proc_out
- def process_EWS_plotting_dep(self, jobPath, config):
+ def process_EWS_plotting_dep(self, jobPath, config) -> [str]:
'''Returns a list of output files for transfer.'''
self.logger.info('started process_EWS_plotting_dep()')
@@ -125,7 +125,7 @@ class ProcessorDeposition(Processor):
deposition_data_file_name = Template(config['Deposition']['DataFileTemplate']).substitute(**config)
name_file_wildcard = f"{deposition_path}/{deposition_data_file_name}"
- EWSPlottingOutputGlobs = []
+ ews_plotting_output_globs = []
for region in regions:
@@ -164,26 +164,26 @@ class ProcessorDeposition(Processor):
depo_processor.process()
# check the output
- EWSPlottingOutputDir = f"{output_dir}/images/"
+ ews_plotting_output_dir = f"{output_dir}/images/"
#EWSPlottingOutputGlobs += [
# # daily plots
# f"{EWSPlottingOutputDir}Daily/deposition_{region.lower()}_*_daily_20*.png",
# # weekly plots
# f"{EWSPlottingOutputDir}Weekly/deposition_{region.lower()}_*_total_20*.png"]
- EWSPlottingOutputGlobs += [f"{EWSPlottingOutputDir}*"]
+ ews_plotting_output_globs += [f"{ews_plotting_output_dir}*"]
- EWSPlottingOutputGlobs = get_only_existing_globs(EWSPlottingOutputGlobs,inplace=False)
+ ews_plotting_output_globs = get_only_existing_globs(ews_plotting_output_globs, inplace = False)
# check there is some output from EWS-plotting
- if not EWSPlottingOutputGlobs:
+ if not ews_plotting_output_globs:
self.logger.error('EWS-Plotting did not produce any output')
raise RuntimeError
# provide list for transfer
- EWSPlottingOutputs = sorted([file for glob_str in EWSPlottingOutputGlobs for file in glob(glob_str)])
+ ews_plotting_outputs: [str] = sorted([file for glob_str in ews_plotting_output_globs for file in glob(glob_str)])
- return EWSPlottingOutputs
+ return ews_plotting_outputs
if __name__ == '__main__':
diff --git a/coordinator/ProcessorEnvironment.py b/coordinator/ProcessorEnvironment.py
index c927e41aa0a818f55e201d8941c2fc2d19d64e44..041ce5dc8841ac14eb370c431cba77f6f75f21cf 100644
--- a/coordinator/ProcessorEnvironment.py
+++ b/coordinator/ProcessorEnvironment.py
@@ -35,14 +35,14 @@ class ProcessorEnvironment(Processor):
return self.process_in_job_env2_0(jobPath, status, configjson, component)
- def process_post_job(self, jobPath, configjson):
+ def process_post_job(self, jobPath, configjson) -> [str]:
return self.process_EWS_plotting_env2_0(jobPath, configjson)
def __init__(self) -> None:
super().__init__()
- def process_in_job_env2_0(self, jobPath,status,config,component):
+ def process_in_job_env2_0(self, jobPath,status,config,component) -> dict:
'''Download met data from remote, prepare data, and run :class:`EnvSuitPipeline` pipeline.'''
self.logger.info('started process_in_job_env2_0()')
@@ -122,7 +122,7 @@ class ProcessorEnvironment(Processor):
run_params_dict[RUN_PARAMS.FILTER_FOR_COUNTRY_KEY] = "False"'''
#TODO test if this works
- def process_EWS_plotting_env2_0(self, jobPath,config):
+ def process_EWS_plotting_env2_0(self, jobPath,config) -> [str]:
'''Configures the plotting arguments and calls EWS-plotting as a python module.
Returns a list of output files for transfer.'''
@@ -134,7 +134,7 @@ class ProcessorEnvironment(Processor):
subregions = config['SubRegionNames']
- EWSPlottingOutputGlobs = []
+ ews_plotting_output_globs = []
# work on each region
for region in subregions:
@@ -176,27 +176,27 @@ class ProcessorEnvironment(Processor):
env_suit_processor.process()
# check the output
- EWSPlottingOutputDir = f"{output_dir}/images/"
+ ews_plotting_output_dir = f"{output_dir}/images/"
#EWSPlottingOutputGlobs += [
# # daily plots
# f"{EWSPlottingOutputDir}Daily/suitability_{region.lower()}_*_rust_daily_20*.png",
# # weekly plots
# f"{EWSPlottingOutputDir}Weekly/suitability_{region.lower()}_*_rust_total_20*.png"]
- EWSPlottingOutputGlobs += [f"{EWSPlottingOutputDir}*"]
+ ews_plotting_output_globs = [f"{ews_plotting_output_dir}*"]
# check the output
- EWSPlottingOutputGlobs = get_only_existing_globs(EWSPlottingOutputGlobs,inplace=False)
+ ews_plotting_output_globs = get_only_existing_globs(ews_plotting_output_globs,inplace=False)
# check there is some output from EWS-plotting
- if not EWSPlottingOutputGlobs:
+ if not ews_plotting_output_globs:
self.logger.error('EWS-Plotting did not produce any output')
raise RuntimeError
# provide list for transfer
- EWSPlottingOutputs = sorted([file for glob_str in EWSPlottingOutputGlobs for file in glob(glob_str)])
+ ews_plotting_outputs: [str] = sorted([file for glob_str in ews_plotting_output_globs for file in glob(glob_str)])
- return EWSPlottingOutputs
+ return ews_plotting_outputs
if __name__ == '__main__':
diff --git a/coordinator/ProcessorEpidemiology.py b/coordinator/ProcessorEpidemiology.py
index b26a20dca20bfc83574bad46c1bbb8410b0ff891..7ab4aa180650ddefcddeed5a244b12f8432659a5 100644
--- a/coordinator/ProcessorEpidemiology.py
+++ b/coordinator/ProcessorEpidemiology.py
@@ -45,11 +45,11 @@ class ProcessorEpidemiology(Processor):
return self.process_pre_job_epi(args)
- def process_in_job(self, jobPath, status, configjson, component) -> object:
+ def process_in_job(self, jobPath, status, configjson, component) -> dict:
return self.process_in_job_epi(jobPath, status, configjson, component)
- def process_post_job(self, jobPath, configjson):
+ def process_post_job(self, jobPath, configjson) -> [str]:
return self.process_EWS_plotting_epi(jobPath, configjson)
@@ -663,7 +663,7 @@ class ProcessorEpidemiology(Processor):
return proc_out
- def process_EWS_plotting_epi(self, jobPath,config):
+ def process_EWS_plotting_epi(self, jobPath,config) -> [str]:
'''Returns a list of output files for transfer.'''
self.logger.info('started process_EWS_plotting_epi()')
@@ -707,7 +707,7 @@ class ProcessorEpidemiology(Processor):
Path(ews_plot_dir).mkdir(parents=True, exist_ok=True)
# loop over diseases
- EWSPlottingOutputGlobs = []
+ ews_plotting_output_globs = []
for disease in diseases:
disease_short = disease.lower().replace('rust','')
@@ -772,21 +772,22 @@ class ProcessorEpidemiology(Processor):
epi_processor_2.process()
# check the output
- EWSPlottingOutputDir = f"{ews_plot_dir}/images/"
+ ews_plotting_output_dir = f"{ews_plot_dir}/images/"
# TODO: Make this smarter, connected to the results of EWSPlottingEPIBase.plot_epi()
- EWSPlottingOutputGlobs += [f"{EWSPlottingOutputDir}infection_{plotting_region_name_lower}_*{disease_short}*.png"]
+ ews_plotting_output_globs: [str] = []
+ ews_plotting_output_globs += [f"{ews_plotting_output_dir}infection_{plotting_region_name_lower}_*{disease_short}*.png"]
- EWSPlottingOutputGlobs = get_only_existing_globs(EWSPlottingOutputGlobs,inplace=False)
+ ews_plotting_output_globs = get_only_existing_globs(ews_plotting_output_globs,inplace=False)
# check there is some output from EWS-plotting
- if not EWSPlottingOutputGlobs:
+ if not ews_plotting_output_globs:
self.logger.error('EWS-Plotting did not produce any output')
raise RuntimeError
# provide to list for transfer
- EWSPlottingOutputs = [item for EWSPlottingOutput in EWSPlottingOutputGlobs for item in glob(EWSPlottingOutput)]
+ ews_plotting_outputs: [str] = [item for ews_plotting_output in ews_plotting_output_globs for item in glob(ews_plotting_output)]
- return EWSPlottingOutputs
+ return ews_plotting_outputs
if __name__ == '__main__':
diff --git a/coordinator/ProcessorSurveys.py b/coordinator/ProcessorSurveys.py
index 2bfffc66d9db9b164afee1bd63ec1b8b070c4666..2cda25ec07a00ed041be7ad8ed395e76048296a6 100644
--- a/coordinator/ProcessorSurveys.py
+++ b/coordinator/ProcessorSurveys.py
@@ -68,7 +68,7 @@ class ProcessorSurveys(Processor):
return self.process_in_job_survey(jobPath, status, configjson, component)
- def process_post_job(self, jobPath, configjson):
+ def process_post_job(self, jobPath, configjson) -> [str]:
return self.process_EWS_plotting_survey(jobPath, configjson)
diff --git a/coordinator/ProcessorUtils.py b/coordinator/ProcessorUtils.py
index 76ee3b64dbbcbd92631d3e7b4d2c07a0e712403e..cbcede7547f4e191073296017de5b0eac81af1f4 100644
--- a/coordinator/ProcessorUtils.py
+++ b/coordinator/ProcessorUtils.py
@@ -119,7 +119,8 @@ def open_and_check_config(configFile):
return config
-def get_only_existing_globs(file_globs,inplace=True):
+
+def get_only_existing_globs(file_globs: [str], inplace = True):
if inplace:
for i,fg in enumerate(file_globs):
diff --git a/coordinator/extra/ProcessorMetResample.py b/coordinator/extra/ProcessorMetResample.py
index 15d679c3b67731368a550405095a3b5a97d218d9..c8b1b943f0b837352b363853e93a78625dc9a821 100644
--- a/coordinator/extra/ProcessorMetResample.py
+++ b/coordinator/extra/ProcessorMetResample.py
@@ -23,9 +23,6 @@ from EpiModel.EpiUtils import (
parse_template_string)
from Processor import Processor
-from ProcessorServer import (
- get_data_from_server
-)
from ProcessorUtils import (
add_filters_to_sublogger,
calc_epi_date_range,