Commit 7ed010a8 authored by TROUSSELLIER Laurent's avatar TROUSSELLIER Laurent
Browse files

new constant, glob, gestion de certaines erreurs

parent 8fa4dd74
path,project,activity_id,institution_id,source_id,experiment_id,member_id,table_id,variable_id,grid_label,version,period_start,period_end,latest
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/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/tasmin/gn/v20190909/tasmin_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,tasmin,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/ta/gn/v20190909/ta_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,ta,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/rlut/gn/v20190909/rlut_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,rlut,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/psl/gn/v20190909/psl_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,psl,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/pr/gn/v20190909/pr_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,pr,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/zg/gn/v20190909/zg_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,zg,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/tasmax/gn/v20190909/tasmax_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,tasmax,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/rsuscs/gn/v20190909/rsuscs_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,rsuscs,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/rsus/gn/v20190909/rsus_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,rsus,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/ts/gn/v20190909/ts_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,ts,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/rsut/gn/v20190909/rsut_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,rsut,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
/bdd/CMIP6/PMIP/NUIST/NESM3/lig127k/r1i1p1f1/Amon/rsdscs/gn/v20190909/rsdscs_Amon_NESM3_lig127k_r1i1p1f1_gn_160001-169912.nc,CMIP6,PMIP,NUIST,NESM3,lig127k,r1i1p1f1,Amon,rsdscs,gn,v20190909,1600-01-01T00:00:00,1699-12-01T00:00:00,true
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......@@ -20,7 +20,7 @@ INPUT_SOURCES = {'CMIP6': ['/home/ltroussellier/dev_catalog/test3_gui/catalog/In
# 'CORDEX': ['/bdd/CORDEX/output/EUR-11/MOHC/.paths.txt', # CORDEX replicas (IDRIS)
# '/bdd/CORDEX/output/EUR-11/IPSL/.paths.txt' # CORDEX IPSL datasets (TGCC)
# ]}
INPUT_SOURCES_GRAN = {'CMIP6': "experiment_id", 'CMIP5': "experiment", 'CORDEX': "experiment" }
ALLOWED_PROJECTS = ['CMIP6', 'CMIP5', 'CORDEX']
CSV_EXTENSION = ".csv"
......
......@@ -16,6 +16,7 @@ from constants import *
from utils import *
import os
from glob import iglob
class Process(object):
"""
......@@ -47,9 +48,13 @@ class Process(object):
global drs
res = ""
entry_facets=None
debug = ""
#nbpath=0
with open(entry,"r") as fi :
for oneLine in fi :
#nbpath=nbpath+1
# Split entry into full file path and latest boolean.
path, latest = map(str.strip, oneLine.split())
#print(path, latest)
......@@ -58,21 +63,31 @@ class Process(object):
# Get facets from path.
facets = drs.get_facets_from_path(path)
#debug ="1"+str(facets)+"\n"
# Update facets from filename.
facets.update(drs.get_facets_from_filename(path.stem))
#debug = debug + "2"+str(facets)+"\n"
# Build CSV entry.
entry_facets = [facets[i] for i in drs.dir_keys]
#debug = debug + "3"+str(entry_facets)+"\n"
entry = [IPSL_DATA_ROOT + path.as_posix(), self.project]
entry.extend(entry_facets)
entry.extend([facets['period_start'], facets['period_end'], latest])
entry.extend([str(facets['period_start']), str(facets['period_end']), latest])
res=res+','.join(entry) + '\n'
#print("RES est remplit Normalement \n",res)
# Build catalog filename.
catdepth = entry_facets[:drs.dir_keys.index("experiment_id") + 1]
##### JUSTE POUR DEBUG
#global nbTot
#nbTot=nbTot+1
#print("NB:",nbTot, " pour le worker : ",os.getpid(),"nbre de path vu pour ce fichier: ",nbpath)
##### FIN POUR DEBUG
if entry_facets ==None:
return #il n'y a pas de path à tratier si bien qu'il n'est pas passé dans la boucleau dessus
raise Exception("On a entry_facets = None \n"+debug)
catdepth = entry_facets[:drs.dir_keys.index(INPUT_SOURCES_GRAN[self.project]) + 1]
catpath = os.path.join(self.outcat,
self.project,
'_'.join(catdepth))
......@@ -243,8 +258,8 @@ class Context(object):
# Set catalog depth.
# self.depth = args.depth
# Set sources
self.sources = INPUT_SOURCES[args.project]
# Set sources granularuty
self.sources_gran = INPUT_SOURCES_GRAN[args.project]
def __enter__(self):
return self
......@@ -253,6 +268,7 @@ class Context(object):
pass
drs = None
nbTot=0
def main():
"""
Run main program
......@@ -277,25 +293,37 @@ def main():
#r = Runner(ctx.threads)
with Pool(processes=ctx.threads) as pool:
for source in ctx.sources:
#for source in ctx.sources:
#print("mesource : ",source)
#FichList = [ f for f in os.listdir('.') if os.path.isfile(os.path.join('.',f)) ]
# Get total entires in a fast way for beautiful progress bar.
#total = int(subprocess.check_output(["wc", "-l", source]).split()[0])
total = len([ f for f in os.listdir(source) if os.path.isfile(os.path.join(source,f)) ])
#total = 1000# là je sais pas comment savoir combien il y en a ?
#chunksize = int(total/10)
# Instantiate pool of processes.
# Instantiate pool iterator with progress bar.
processes = tqdm(pool.imap(Process(ctx), get_files(source), chunksize=1), desc='Catalog generation',
total=total)
processes = pool.imap(Process(ctx), get_files(args.project, drs.dir_keys.index(INPUT_SOURCES_GRAN[args.project])+1))
#print("On va lancer ", len(processes), " ")
# Run processes in a dummy variable.
_ = [x for x in processes]
# Run the pool.
#r.run(ctx.sources, ctx)
def get_files(source):
def get_files(project,gran_index):
# Globbing pattern.
pattern = os.path.join("/bdd",project, '**/' * gran_index, '.paths.txt')
for nb,path in enumerate(iglob(pattern)):
# if nb> 500:
# return
yield path
#for path in iglob(pattern):
# yield path
def get_files_old(source):
FichList = [ f for f in os.listdir(source) if os.path.isfile(os.path.join(source,f)) ]
for filepath in FichList:
yield os.path.join(source,filepath)
......
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