def _find_indexer(type_module, type_name, type_version):
"""
Find the indexer function for the given object type within the indexer_directory list.
Returns:
Pair of indexer function and extra configuration data to pass as the last arg
"""
try:
return get_es_module(type_module, type_name, type_version)
except ModuleNotFound:
pass
# No indexer found for this type, check if there is a sdk indexer app
if type_module + '.' + type_name in config()['global']['sdk_indexer_apps']:
return (index_from_sdk, {})
return (generic_indexer(), {})
import os
import json
from src.utils.get_es_module import get_es_module
# Load test data
with open(os.path.join(os.path.dirname(__file__), 'data/taxon.json')) as fd:
data = json.load(fd)
(indexer, conf) = get_es_module('KBaseGenomeAnnotations', 'Taxon')
def test_taxon_indexer():
"""Valid indexing test"""
# Mock the request against the sample service
results = indexer(data['obj1'], data['ws_info1'], data['obj1'], conf)
for (idx, result) in enumerate(list(results)):
assert result == data['expected_result1'][idx]
import json
import tempfile
import shutil
from src.index_runner.es_indexers.annotated_metagenome_assembly import _index_ama
from src.utils.get_es_module import get_es_module
_DIR = os.path.dirname(os.path.realpath(__file__))
# Load test data
with open(os.path.join(_DIR, 'data/ama.json')) as fd:
data = json.load(fd)
with open(os.path.join(_DIR, 'data/ama_check_against.json')) as fd:
check_against = json.load(fd)
# Load module config
(indexer, conf) = get_es_module('KBaseMetagenomes', 'AnnotatedMetagenomeAssembly')
def test_annotated_metagenome_assembly_indexer():
# the annotated_metagenome_assembly 'check_against' data is really big, so we keep it in an external file
features_test_file = os.path.join(_DIR, "data", "features.json.gz")
info = data['obj']['info']
workspace_id = info[6]
object_id = info[0]
version = info[4]
ama_index = f"WS::{workspace_id}:{object_id}"
ver_ama_index = f"WSVER::{workspace_id}:{object_id}:{version}"
try:
tmp_dir = tempfile.mkdtemp()
features_path = os.path.join(tmp_dir, "features.json.gz")
import os
import json
from src.utils.get_es_module import get_es_module
_DIR = os.path.dirname(__file__)
# Load test data
with open(os.path.join(_DIR, 'data/genome.json')) as fd:
data = json.load(fd)
with open(os.path.join(_DIR, 'data/genome_check_against.json')) as fd:
check_against = json.load(fd)
# Load module config
(indexer, conf) = get_es_module('KBaseGenomes', 'Genome')
def test_genome_valid1():
"""Valid indexing test"""
results = indexer(data['obj1'], data['ws_info1'], data['obj1'], conf)
for (idx, result) in enumerate(list(results)):
assert result == check_against[idx]
import os
import json
from src.utils.get_es_module import get_es_module
# Load test data
with open(os.path.join(os.path.dirname(__file__), 'data/tree.json')) as fd:
data = json.load(fd)
(indexer, conf) = get_es_module('KBaseTrees', 'Tree')
def test_tree_indexer():
"""Valid indexing test"""
# Mock the request against the sample service
results = indexer(data['obj1'], data['ws_info1'], data['obj1'], conf)
for (idx, result) in enumerate(list(results)):
assert result == data['expected_result1'][idx]
"""
import json
import os
import pytest
import responses
from src.utils.config import config
from src.utils.get_es_module import get_es_module
_DIR = os.path.dirname(os.path.realpath(__file__))
# Load test data
with open(os.path.join(_DIR, 'data', 'narrative.json')) as fd:
data = json.load(fd)
# Load module config
(indexer, conf) = get_es_module('KBaseNarrative', 'Narrative')
def test_basic_valid():
"""Test the happy case."""
narr_obj = data['obj_valid']
ws_info = data['wsinfo_valid']
results = list(indexer(narr_obj, ws_info, {}, conf))
assert len(results) == 1
result = results[0]
assert result['_action'] == 'index'
assert result['index'] == 'narrative_2'
assert result['id'] == 'WS::33192:1'
doc = result['doc']
assert doc['narrative_title'] == 'Test fiesta'
assert not doc['is_narratorial']
import os
import json
from src.utils.get_es_module import get_es_module
# Load test data
with open(os.path.join(os.path.dirname(__file__), 'data/assembly.json')) as fd:
data = json.load(fd)
# Load module config
(indexer, conf) = get_es_module('KBaseGenomeAnnotations', 'Assembly')
def test_assembly_indexer():
"""Valid indexing test"""
# Mock the request against the sample service
results = indexer(data['obj1'], data['ws_info1'], data['obj1'], conf)
for (idx, result) in enumerate(list(results)):
assert result == data['expected_result1'][idx]
import os
import json
from src.utils.get_es_module import get_es_module
# Load test data
with open(os.path.join(os.path.dirname(__file__), 'data/reads.json')) as fd:
data = json.load(fd)
(indexer, conf) = get_es_module('KBaseFile', 'PairedEndLibrary')
def test_reads_valid1():
"""Valid reads indexing test"""
results = indexer(data['obj1'], data['ws_info1'], data['obj1'], conf)
for (idx, result) in enumerate(list(results)):
assert result == data['expected_result1'][idx]
import json
import os
import responses
from src.utils.config import config
from src.utils.get_es_module import get_es_module
# Load test data
with open(os.path.join(os.path.dirname(__file__), 'data/sample_set.json')) as fd:
data = json.load(fd)
(indexer, conf) = get_es_module('KBaseSets', 'SampleSet')
@responses.activate
def test_sample_set_indexer1():
# Mock the request that checks for an existing sample
url = config()['elasticsearch_url'] + '/search2.sample/_doc/SMP::1:1'
responses.add(responses.GET, url, json={'found': False})
# Mock the request against the sample service
responses.add(responses.POST, config()['sample_service_url'], json=data['sample_service_resp1'])
results = indexer(data['obj1'], data['ws_info1'], data['obj1'], conf)
for (idx, result) in enumerate(list(results)):
assert result == data['expected_result1'][idx]