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import logging
import unittest
from base_utils import get_data_file, get_temp_dir
from pbcommand.models import ResolvedToolContract, ResolvedScatteredToolContractTask, ResolvedGatherToolContractTask
from pbcommand.pb_io import load_tool_contract_from
from pbcommand.resolver import resolve_scatter_tool_contract, resolve_gather_tool_contract
log = logging.getLogger(__name__)
class TestScatterResolver(unittest.TestCase):
FILE_NAME = "dev_scatter_fasta_app_tool_contract.json"
MAX_NCHUNKS = 7
MAX_NPROC = 9
INPUT_FILES = ['/tmp/file.fasta']
CHUNK_KEYS = ('$chunk.fasta_id')
TOOL_OPTIONS = {}
def test_sanity(self):
d = get_temp_dir("resolved-tool-contract")
tc = load_tool_contract_from(get_data_file(self.FILE_NAME))
rtc = resolve_scatter_tool_contract(tc, self.INPUT_FILES, d, d, self.MAX_NPROC, self.TOOL_OPTIONS, self.MAX_NCHUNKS, self.CHUNK_KEYS)
self.assertIsInstance(rtc, ResolvedToolContract)
self.assertIsInstance(rtc.task, ResolvedScatteredToolContractTask)
self.assertEqual(rtc.task.max_nchunks, 7)
class TestGatherResolver(unittest.TestCase):
FILE_NAME = "dev_gather_fasta_app_tool_contract.json"
MAX_NCHUNKS = 7
MAX_NPROC = 9
INPUT_FILES = ['/tmp/file.fasta.chunk.json']
CHUNK_KEY = '$chunk.filter_fasta_id'
TOOL_OPTIONS = {}
def test_sanity(self):
d = get_temp_dir("resolved-tool-contract")
tc = load_tool_contract_from(get_data_file(self.FILE_NAME))
rtc = resolve_gather_tool_contract(tc, self.INPUT_FILES, d, d, self.MAX_NPROC, self.TOOL_OPTIONS, self.CHUNK_KEY)
self.assertIsInstance(rtc, ResolvedToolContract)
self.assertIsInstance(rtc.task, ResolvedGatherToolContractTask)
self.assertEqual(rtc.task.chunk_key, self.CHUNK_KEY)
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