def create_shipit_commit(fbsource, shipit_projects, output_dir):
abs_output_dir = os.path.join(fbsource.path, output_dir)
with make_temp_dir(abs_output_dir):
for project in shipit_projects:
project_output_dir = os.path.join(abs_output_dir, project)
run_shipit(fbsource.path, project, project_output_dir)
with commit_to_hg(fbsource, output_dir, 'ShipIt-processed projects'):
bundle_info = get_local_repo_everstore_bundle_lego_dict(fbsource)
return bundle_info
def setUp(self):
# Create test directory
self.dir_ = utils.make_temp_dir()
# Make files and symlinks for tests
#
# File to link to 'test.txt'
self.filen = utils.make_file('test.txt',dirn=self.dir_)
# Absolute and relative links to this file
self.abslink = utils.make_symlink('abslink',self.filen,dirn=self.dir_)
self.rellink = utils.make_symlink('rellink',os.path.basename(self.filen),
dirn=self.dir_)
# A broken link (relative)
self.brklink = utils.make_symlink('brklink','missing.txt',
dirn=self.dir_)
# A bzipped file and a broken link that points to the uncompressed
# file name (an example of an "alternative target")
self.bzfilen = utils.make_file('test2.txt.bz2',dirn=self.dir_,
compress='bz2')
self.altlink = utils.make_symlink('altlink','test2.txt',dirn=self.dir_)
# A link that points outside of the temp dir (broken)
extfilen = os.path.normpath(os.path.join(self.dir_,'..','elsewhere','test3.txt'))
self.extlink = utils.make_symlink('extlink',extfilen,dirn=self.dir_)
def setUp(self):
# Create test directory
self.dir_ = utils.make_temp_dir()
# Add some files, directories and links
self.example_dir = utils.make_subdir(self.dir_,'example')
# Primary data that looks like SOLiD
d = utils.make_subdir(self.example_dir,'primary_data')
utils.make_file('test1.csfasta',dirn=d)
utils.make_file('test1_QV.qual',dirn=d)
utils.make_file('test2.csfasta',dirn=d)
utils.make_file('test2_QV.qual',dirn=d)
self.primary_data_dir = d
# Analysis with links to primary data
d = utils.make_subdir(self.example_dir,'analysis')
utils.make_symlink('test1.csfasta','../primary_data/test1.csfasta',dirn=d)
utils.make_symlink('test1_QV.qual','../primary_data/test1_QV.qual',dirn=d)
utils.make_symlink('test2.csfasta','../primary_data/test2.csfasta',dirn=d)
utils.make_symlink('test2_QV.qual','../primary_data/test2_QV.qual',dirn=d)
utils.make_file('test1.fastq',dirn=d)
utils.make_file('test2.fastq',dirn=d)
utils.make_file('test1_analysis.bam.bz2',dirn=d,compress='bz2')
utils.make_file('test2_analysis.bam.bz2',dirn=d,compress='bz2')
utils.make_file('organism.gff3',dirn=d)
self.analysis_dir = d
def setUp(self):
# Create test directory
self.dir_ = utils.make_temp_dir()
# -*- coding: utf-8 -*-
from time import time
import pytest
from land.copernicus.content.content.landfile import LandFileStore
from land.copernicus.content.content.api import LandFileApi
from utils import make_temp_dir
from utils import add_testfile
from utils import rm_testfile
make_temp_dir()
def test_api_add():
store = LandFileStore()
api = LandFileApi(store)
landfile = api.add(title=u'A title',
shortname='a-title',
description='desc')
assert landfile.title == u'A title'
assert landfile.shortname == 'a-title'
by_title = api.get('A title')
by_shortname = api.get_by_shortname('a-title')
by_prop = next(api.get_by_prop('description', 'desc'))
assert by_title is not None
from StringIO import StringIO
import pytest
from plone.i18n.normalizer.tests import base as i18n_base
from land.copernicus.content.browser.views import AdminLandFilesView
from land.copernicus.content.content.landfile import LandFileStore
from land.copernicus.content.content.api import LandFileApi
from utils import make_temp_dir
from utils import add_testfile
from utils import rm_testfile
make_temp_dir()
class Context(object):
landfiles = None
def __init__(self):
self.landfiles = LandFileStore()
self.fileCategories = ['Type', 'Country']
class Request(object):
form = None
def __init__(self, form):
self.form = form