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Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit d540196f authored by LE GAC Renaud's avatar LE GAC Renaud
Browse files

Apply 2to3 converter to scripts.

parent eb83aeb7
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Showing with 56 additions and 70 deletions
scripts/_run_pytest.py
View file @ d540196f
# -*- coding: utf-8 -*-
""" NAME
_run_pytest -- private script
......
scripts/deploy.py
View file @ d540196f
# -*- coding: utf-8 -*-
""" NAME
deploy my_institute.csv
......@@ -85,7 +84,7 @@ def create_affiliation(opt):
"""
aff = raw_input("\tEnter the inspirehep identifier for your institute: ")
if not aff.isdigit():
print "\t\tERROR: invalid answer!"
print("\t\tERROR: invalid answer!")
# ........................................................................
#
......@@ -104,12 +103,12 @@ def create_affiliation(opt):
is_key_add = False
for key in keys:
if get_id(db.affiliation_keys, **key) is None:
print "\t\tAdding the affiliation keys '%s'" % key["key_u"]
print("\t\tAdding the affiliation keys '%s'" % key["key_u"])
db.affiliation_keys[0] = key
is_key_add = True
if not is_key_add:
print "\t\tAffiliation keys already exist!"
print("\t\tAffiliation keys already exist!")
def create_harvesters(opt, dfi, dfh):
......@@ -150,9 +149,9 @@ def create_harvesters(opt, dfi, dfh):
missings.append(elt)
if len(missings) > 0:
print "\n\tPlease define the collaborations in data/harvesters.csv:"
print("\n\tPlease define the collaborations in data/harvesters.csv:")
for elt in missings:
print "\t\t", elt
print("\t\t", elt)
print
sys.exit(1)
......@@ -163,8 +162,7 @@ def create_harvesters(opt, dfi, dfh):
#
recset = db(db.harvesters.id > 0)
if recset.count() > 0:
rep = \
raw_input("\n\tHarvesters already exist. Remove them all [y/N]: ")
rep = input("\n\tHarvesters already exist. Remove them all [y/N]: ")
if rep == "y":
for row in recset.iterselect(db.harvesters.id):
......@@ -177,7 +175,7 @@ def create_harvesters(opt, dfi, dfh):
for key, value in CONTROLLER_TO_CAT.iteritems():
id_category = get_id(db.categories, code=value)
if id_category is None:
print "\n\t\tERROR: category '%s' is not defined. exit" % value
print("\n\t\tERROR: category '%s' is not defined. exit" % value)
sys.exit(1)
CONTROLLER_TO_CAT[key] = id_category
......@@ -195,12 +193,12 @@ def create_harvesters(opt, dfi, dfh):
id_team = get_id(db.teams, team=team)
if id_team is None:
print "\n\t\tTeam '%s' is not defined. skip it!" % team
print("\n\t\tTeam '%s' is not defined. skip it!" % team)
continue
id_project = get_id(db.projects, project=project)
if id_project is None:
print "\n\t\tProject '%s' is not defined. skip it!" % project
print("\n\t\tProject '%s' is not defined. skip it!" % project)
continue
data = dict(id_teams=id_team, id_projects=id_project)
......@@ -315,23 +313,23 @@ def create_teams_projects(opt, dfi):
#
id_team = get_id(db.teams, team=team)
if id_team is None:
print "\n\t\tCreate team '%s'" % team
print("\n\t\tCreate team '%s'" % team)
id_team = db.teams.insert(team=team, domain=row.domain)
else:
print "\n\t\tteam '%s' already exist!" % team
print("\n\t\tteam '%s' already exist!" % team)
#
# project
#
id_project = get_id(db.projects, project=project)
if id_project is None:
print "\t\tCreate project '%s'" % project
print("\t\tCreate project '%s'" % project)
id_project = \
db.projects.insert(project=project, agencies="CNRS/IN2P3")
else:
print "\t\tproject '%s' already exist!" % project
print("\t\tproject '%s' already exist!" % project)
#
# relation team / project
......@@ -340,11 +338,11 @@ def create_teams_projects(opt, dfi):
get_id(db.organisation, id_teams=id_team, id_projects=id_project)
if rec_id is None:
print "\t\tCreate the relation %s/%s" % (team, project)
print("\t\tCreate the relation %s/%s" % (team, project))
db.organisation.insert(id_teams=id_team, id_projects=id_project)
else:
print "\t\tRelation %s/%s already exist!" % (team, project)
print("\t\tRelation %s/%s already exist!" % (team, project))
def harvesters(opt):
......@@ -362,7 +360,7 @@ def harvesters(opt):
- collection
"""
print "\tCollect definitions of harvesters", opt.path_harvesters
print("\tCollect definitions of harvesters", opt.path_harvesters)
# absolute path in the docker container
path = os.path.join(os.getcwd(),
......@@ -372,7 +370,7 @@ def harvesters(opt):
opt.path_harvesters)
if not os.path.exists(path):
print "\n\tFile {0} don't exist!".format(path)
print("\n\tFile {0} don't exist!".format(path))
sys.exit(1)
dh = (pd.read_csv(path)
......@@ -398,17 +396,17 @@ def insert_harvester(**data):
id_harvester = get_id(db.harvesters, **data)
if id_harvester is None:
print "\n\t\tCreate harvester"
print("\n\t\tCreate harvester")
db.harvesters.insert(**data)
else:
print "\n\t\tHarvester exist!"
print("\n\t\tHarvester exist!")
print "\t\t\t team:", db.teams[data["id_teams"]].team
print "\t\t\t project:", db.projects[data["id_projects"]].project
print "\t\t\t controller:", data["controller"]
print "\t\t\t host:", data["host"]
print "\t\t\t collection:", data["collections"]
print("\t\t\t team:", db.teams[data["id_teams"]].team)
print("\t\t\t project:", db.projects[data["id_projects"]].project)
print("\t\t\t controller:", data["controller"])
print("\t\t\t host:", data["host"])
print("\t\t\t collection:", data["collections"])
def institute(opt):
......@@ -429,7 +427,7 @@ def institute(opt):
- hal_hidden
"""
print "\tCollect parameters for the institute", opt.institute
print("\tCollect parameters for the institute", opt.institute)
# absolute path in the docker container
path = os.path.join(os.getcwd(),
......@@ -439,7 +437,7 @@ def institute(opt):
opt.institute)
if not os.path.exists(path):
print "\n\tFile {0} don't exist!".format(path)
print("\n\tFile {0} don't exist!".format(path))
sys.exit(1)
df = pd.read_csv(path)
......@@ -511,11 +509,11 @@ if __name__ == "__main__":
OPT = PARSER.parse_args()
if not (OPT.harvesters or OPT.teams or OPT.affiliation):
print "\n\tPlease select an option!"
print "\tPossible ones are --affiliation, --harvesters or --teams"
print("\n\tPlease select an option!")
print("\tPossible ones are --affiliation, --harvesters or --teams")
sys.exit(1)
print "\n%s\nStart deploy" % ("."*80,)
print("\n%s\nStart deploy" % ("."*80,))
DFI = institute(OPT)
DFH = harvesters(OPT)
......@@ -530,11 +528,11 @@ if __name__ == "__main__":
create_affiliation(OPT)
if OPT.commit:
print "\n\tChange are committed to the database."
print("\n\tChange are committed to the database.")
db.commit()
else:
print "\n\tDry run, the database is not modified."
print("\n\tDry run, the database is not modified.")
print "\nEnd deploy\n%s\n" % ("."*80, )
print("\nEnd deploy\n%s\n" % ("."*80, ))
sys.exit(0)
scripts/export_to_csv.py
View file @ d540196f
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" NAME
export-to-csv -- export table content as CSV file
......@@ -58,6 +56,6 @@ if __name__ == "__main__":
writer.writerow(row.as_dict())
# close
print 'Table "%s" exported to "%s"' % (args.table, args.file.name)
print('Table "%s" exported to "%s"' % (args.table, args.file.name))
args.file.close()
sys.exit(0)
scripts/import_from_csv.py
View file @ d540196f
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" NAME
import-from-csv -- import table content from CSV file
......@@ -53,6 +51,6 @@ if __name__ == "__main__":
db.commit()
# close
print 'File "%s" import in "%s"' % (args.file.name, args.table)
print('File "%s" import in "%s"' % (args.file.name, args.table))
args.file.close()
sys.exit(0)
scripts/limbra_status.py
View file @ d540196f
# -*- coding: utf-8 -*-
""" NAME
status
......@@ -71,7 +70,7 @@ if __name__ == "__main__":
for el in db().iterselect(year, count, groupby=year)}
if len(publications) == 0:
print json.dumps(data)
print(json.dumps(data))
sys.exit(0)
data["publications"] = publications
......@@ -115,5 +114,5 @@ if __name__ == "__main__":
#
# output and exit
#
print json.dumps(data)
print(json.dumps(data))
sys.exit(0)
scripts/statistics.py
View file @ d540196f
# -*- coding: utf-8 -*-
""" NAME
statistics
......@@ -24,6 +23,8 @@
R. Le Gac -- Mar 2015
"""
def do_labels(ax, xlabel, ylabel):
"""Deal with axes label.
......@@ -109,11 +110,9 @@ def savefig(ax, fn):
if __name__ == "__main__":
import matplotlib as mp
import re
import sys
from argparse import ArgumentParser, FileType
from invenio_tools import InvenioStore, Marc12
from argparse import ArgumentParser
from pandas import DataFrame
# command line options
......@@ -132,17 +131,16 @@ if __name__ == "__main__":
q_base = db.publications.year >= start_year
q_base = (q_base) & (db.publications.year <= end_year)
#--------------------------------------------------------------------------
# ........................................................................
#
# publications per domain and per year
#
#--------------------------------------------------------------------------
query = (q_base) & (db.publications.id_teams == db.teams.id)
rows = db(query).select(db.publications.year,
db.teams.domain,
count,
groupby= (db.publications.year, db.teams.domain))
db.teams.domain,
count,
groupby=(db.publications.year, db.teams.domain))
data = []
for row in rows:
......@@ -163,24 +161,23 @@ if __name__ == "__main__":
kind="bar",
stacked=True,
xlabel="",
ylabel=u'Nombre de publications / année')
ylabel='Nombre de publications / année')
ax.set_xticklabels(list(df.index), rotation=0)
fig = ax.get_figure()
fig.show()
#--------------------------------------------------------------------------
# ........................................................................
#
# publications per category per year
#
#--------------------------------------------------------------------------
query = (q_base) & (db.publications.id_categories == db.categories.id)
rows = db(query).select(db.publications.year,
db.categories.usual,
count,
groupby= (db.publications.year, db.categories.usual))
groupby=(db.publications.year, db.categories.usual))
data = []
for row in rows:
......@@ -197,7 +194,7 @@ if __name__ == "__main__":
df.columns = [el[1] for el in df.columns]
# one column per year -- normalize the row on the sum per year
df = df.T
df = df.T
for col in df.columns:
df[col] = df[col] / df[col].sum()
......@@ -205,25 +202,24 @@ if __name__ == "__main__":
df = df.T
# prepare the stack by ordering the category (conference, article, report)
df = df[[0,5,1,2,3,4,6]]
df = df[[0, 5, 1, 2, 3, 4, 6]]
ax = do_plot(df,
colormap="Pastel1",
kind="bar",
stacked=True,
xlabel="",
ylabel=u'Fraction / catégorie / année')
ylabel='Fraction / catégorie / année')
ax.set_xticklabels(list(df.index), rotation=0)
fig = ax.get_figure()
fig.show()
#--------------------------------------------------------------------------
# ........................................................................
#
# Fraction of harvested publication per year
#
#--------------------------------------------------------------------------
query = q_base
rows = db(query).select(db.publications.year,
......@@ -253,7 +249,7 @@ if __name__ == "__main__":
kind="bar",
stacked=True,
xlabel="",
ylabel=u'Fraction / entrepôt / année',
ylabel='Fraction / entrepôt / année',
ylim=[0, 1.2])
ax.set_xticklabels(list(df.index), rotation=0)
......@@ -261,11 +257,10 @@ if __name__ == "__main__":
fig = ax.get_figure()
fig.show()
#--------------------------------------------------------------------------
# ........................................................................
#
# Fraction of harvested publication per category
#
#--------------------------------------------------------------------------
query = (q_base) & (db.publications.id_categories == db.categories.id)
rows = db(query).select(db.categories.usual,
......@@ -299,7 +294,7 @@ if __name__ == "__main__":
kind="bar",
stacked=True,
xlabel="",
ylabel=u'Fraction / entrepôt / catégorie',
ylabel='Fraction / entrepôt / catégorie',
ylim=[0, 1.2])
ax.set_xticklabels([el.decode('utf-8') for el in df.index], rotation=12)
......@@ -307,11 +302,10 @@ if __name__ == "__main__":
fig = ax.get_figure()
fig.show()
#--------------------------------------------------------------------------
# ........................................................................
#
# Fraction of harvested publication per domain
#
#--------------------------------------------------------------------------
query = (q_base) & (db.publications.id_teams == db.teams.id)
rows = db(query).select(db.teams.domain,
......@@ -345,7 +339,7 @@ if __name__ == "__main__":
kind="bar",
stacked=True,
xlabel="",
ylabel=u'Fraction / entrepôt / domaine',
ylabel='Fraction / entrepôt / domaine',
ylim=[0, 1.2])
ax.set_xticklabels([el.decode('utf-8') for el in df.index], rotation=8)
......@@ -354,5 +348,5 @@ if __name__ == "__main__":
fig.show()
# close
raw_input('type CR to exit')
input('type CR to exit')
sys.exit(0)
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