diff --git a/sourmash/__main__.py b/sourmash/__main__.py index e9e2dfb4db..0e66b6ef1c 100644 --- a/sourmash/__main__.py +++ b/sourmash/__main__.py @@ -8,8 +8,8 @@ from .logging import error, set_quiet from .commands import (categorize, compare, compute, dump, import_csv, - gather, index, sbt_combine, search, - plot, watch, info, storage, migrate, multigather) + gather, index, sbt_combine, search, plot, watch, + info, storage, migrate, multigather, prepare) from .lca import main as lca_main from .sig import main as sig_main @@ -64,7 +64,9 @@ def main(): 'migrate': migrate, 'multigather': multigather, 'sig': sig_main, - 'signature': sig_main} + 'signature': sig_main, + 'prepare': prepare + } parser = argparse.ArgumentParser( description='work with compressed biological sequence representations') parser.add_argument('command', nargs='?') diff --git a/sourmash/commands.py b/sourmash/commands.py index 9e82b35a6e..0dd1160eb5 100644 --- a/sourmash/commands.py +++ b/sourmash/commands.py @@ -8,6 +8,8 @@ import os.path import sys import random +import tempfile +import tarfile import screed from .sourmash_args import SourmashArgumentParser @@ -1402,3 +1404,60 @@ def migrate(args): notify('saving SBT under "{}".', args.sbt_name) tree.save(args.sbt_name, structure_only=True) + + +def prepare(args): + from .sbt import parse_backend_args + from .sbt_storage import FSStorage + + parser = argparse.ArgumentParser() + parser.add_argument('sbt_name', help='name of SBT to prepare') + parser.add_argument('-x', help='new nodegraph size', default=1e5) + parser.add_argument('-b', "--backend", type=str, + help='Backend to convert to', + default='FSStorage') + args = parser.parse_args(args) + + notify('saving SBT under "{}".', args.sbt_name) + + backend, options = parse_backend_args(args.sbt_name, args.backend) + + with backend(*options) as storage: + is_tarfile = False + try: + tarfile.is_tarfile(args.sbt_name) + is_tarfile = True + except IOError: + pass + + if is_tarfile: + with tarfile.open(args.sbt_name, 'r') as t: + t.extractall('.') + args.sbt_name = next(f for f in t.getnames() + if f.endswith('.sbt.json')) + else: + with open(args.sbt_name, 'r:*') as f: + import json + temptree = json.load(f) + + if ((temptree['storage']['backend'] == 'IPFSStorage') and + (backend == FSStorage) and + ('preload' in temptree['storage']['args'])): + # Let's take a shortcut... The preload multihash contains the + # directory in the same structure FSStorage expects. + ipfs_args = temptree['storage']['args'] + multihash = ipfs_args.pop('preload') + + # TODO: in case the IPFS node is not available, need to + # fallback to read-only client + import ipfsapi + client = ipfsapi.connect(**ipfs_args) + + dirpath = os.path.join(storage.location, storage.subdir) + with tempfile.TemporaryDirectory() as temp: + client.get(multihash, filepath=temp) + shutil.rmtree(dirpath) + shutil.move(os.path.join(temp, multihash), dirpath) + + sbt = load_sbt_index(args.sbt_name, print_version_warning=False) + sbt.save(args.sbt_name, storage=storage) diff --git a/sourmash/sbt.py b/sourmash/sbt.py index c904cd716b..d7563243e5 100644 --- a/sourmash/sbt.py +++ b/sourmash/sbt.py @@ -410,8 +410,8 @@ def save(self, path, storage=None, sparseness=0.0, structure_only=False): 'args': self.factory.init_args() } - if not self.is_ready: - self._fill_internal() + if not self.is_ready and structure_only is False: + self._fill_internal_and_save(storage, sparseness) nodes = {} leaves = {} @@ -445,8 +445,6 @@ def save(self, path, storage=None, sparseness=0.0, structure_only=False): data['filename'] = node.save(data['filename']) - node.storage = storage - data['filename'] = node.save(data['filename']) if isinstance(node, Node): nodes[i] = data else: @@ -528,12 +526,15 @@ def _load_v1(jnodes, leaf_loader, dirname, storage, print_version_warning=True): raise ValueError("Empty tree!") sbt_nodes = {} + sbt_leaves = {} + + max_node = 0 sample_bf = os.path.join(dirname, jnodes[0]['filename']) ksize, tablesize, ntables = khmer.extract_nodegraph_info(sample_bf)[:3] factory = GraphFactory(ksize, tablesize, ntables) - for i, jnode in enumerate(jnodes): + for k, jnode in enumerate(jnodes): if jnode is None: continue @@ -542,13 +543,24 @@ def _load_v1(jnodes, leaf_loader, dirname, storage, print_version_warning=True): if 'internal' in jnode['name']: jnode['factory'] = factory sbt_node = Node.load(jnode, storage) + sbt_nodes[k] = sbt_node else: sbt_node = leaf_loader(jnode, storage) + sbt_leaves[k] = sbt_node - sbt_nodes[i] = sbt_node + max_node = max(max_node, k) tree = SBT(factory) tree._nodes = sbt_nodes + tree._leaves = sbt_leaves + tree._missing_nodes = {i for i in range(max_node) + if i not in sbt_nodes and i not in sbt_leaves} + + if print_version_warning: + error("WARNING: this is an old index version, please run `sourmash migrate` to update it.") + error("WARNING: proceeding with execution, but it will take longer to finish!") + + tree._fill_min_n_below() return tree @@ -562,6 +574,8 @@ def _load_v2(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru sbt_nodes = {} sbt_leaves = {} + max_node = 0 + sample_bf = os.path.join(dirname, nodes[0]['filename']) k, size, ntables = khmer.extract_nodegraph_info(sample_bf)[:3] factory = GraphFactory(k, size, ntables) @@ -580,9 +594,19 @@ def _load_v2(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru sbt_node = leaf_loader(node, storage) sbt_leaves[k] = sbt_node + max_node = max(max_node, k) + tree = cls(factory, d=info['d']) tree._nodes = sbt_nodes tree._leaves = sbt_leaves + tree._missing_nodes = {i for i in range(max_node) + if i not in sbt_nodes and i not in sbt_leaves} + + if print_version_warning: + error("WARNING: this is an old index version, please run `sourmash migrate` to update it.") + error("WARNING: proceeding with execution, but it will take longer to finish!") + + tree._fill_min_n_below() return tree @@ -623,7 +647,7 @@ def _load_v3(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru tree._nodes = sbt_nodes tree._leaves = sbt_leaves tree._missing_nodes = {i for i in range(max_node) - if i not in sbt_nodes and i not in sbt_leaves} + if i not in sbt_nodes and i not in sbt_leaves} if print_version_warning: error("WARNING: this is an old index version, please run `sourmash migrate` to update it.") @@ -667,9 +691,7 @@ def _load_v4(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru tree._nodes = sbt_nodes tree._leaves = sbt_leaves tree._missing_nodes = {i for i in range(max_node) - if i not in sbt_nodes and i not in sbt_leaves} - - tree.next_node = max_node + if i not in sbt_nodes and i not in sbt_leaves} if print_version_warning: error("WARNING: this is an old index version, please run `sourmash migrate` to update it.") @@ -679,7 +701,10 @@ def _load_v4(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru @classmethod def _load_v5(cls, info, leaf_loader, dirname, storage, print_version_warning=True): - nodes = {int(k): v for (k, v) in info['nodes'].items()} + nodes = {} + if 'nodes' in info: + nodes = {int(k): v for (k, v) in info['nodes'].items()} + leaves = {int(k): v for (k, v) in info['leaves'].items()} if not leaves: @@ -713,7 +738,7 @@ def _load_v5(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru tree._nodes = sbt_nodes tree._leaves = sbt_leaves tree._missing_nodes = {i for i in range(max_node) - if i not in sbt_nodes and i not in sbt_leaves} + if i not in sbt_nodes and i not in sbt_leaves} return tree @@ -743,6 +768,24 @@ def fill_min_n_below(node, *args, **kwargs): self._fill_up(fill_min_n_below) + def _fill_internal_and_save(self, storage, sparseness=0.0): + + def fill_nodegraphs_and_save(node, *args, **kwargs): + children = kwargs['children'] + for child in children: + if child.node is not None: + child.node.update(node) + + if isinstance(node, Node) and random() - sparseness > 0: + child.node.storage = storage + child.node.save(os.path.basename(node.name)) + + child.node.unload() + return True + + self._fill_up(fill_nodegraphs_and_save) + self.is_ready = True + def _fill_internal(self): def fill_nodegraphs(node, *args, **kwargs): @@ -944,6 +987,9 @@ def load(info, storage=None): new_node.metadata = info.get('metadata', {}) return new_node + def unload(self): + pass + def update(self, parent): parent.data.update(self.data) if 'min_n_below' in self.metadata: @@ -1008,6 +1054,9 @@ def load(cls, info, storage=None): path=info['filename'], storage=storage) + def unload(self): + pass + def filter_distance(filter_a, filter_b, n=1000): """ @@ -1040,20 +1089,18 @@ def filter_distance(filter_a, filter_b, n=1000): return distance / (8.0 * len(A) * n) -def convert_cmd(name, backend): - from .sbtmh import SigLeaf - +def parse_backend_args(name, backend): options = backend.split('(') backend = options.pop(0) backend = backend.lower().strip("'") if options: - print(options) - options = options[0].split(')') - options = [options.pop(0)] - #options = {} + print(options) + options = options[0].split(')') + options = [options.pop(0)] + #options = {} else: - options = [] + options = [] if backend.lower() in ('ipfs', 'ipfsstorage'): backend = IPFSStorage @@ -1076,6 +1123,14 @@ def convert_cmd(name, backend): else: error('backend not recognized: {}'.format(backend)) + return backend, options + + +def convert_cmd(name, backend_args): + from .sbtmh import SigLeaf + + backend, options = parse_backend_args(name, backend_args) + with backend(*options) as storage: sbt = SBT.load(name, leaf_loader=SigLeaf.load) sbt.save(name, storage=storage) diff --git a/sourmash/sbt_storage.py b/sourmash/sbt_storage.py index 05b601e2b5..adc26173cd 100644 --- a/sourmash/sbt_storage.py +++ b/sourmash/sbt_storage.py @@ -3,6 +3,7 @@ import abc from io import BytesIO import os +import urllib import tarfile @@ -103,10 +104,23 @@ def __init__(self, pin_on_add=True, **kwargs): import ipfsapi self.ipfs_args = kwargs self.pin_on_add = pin_on_add - self.api = ipfsapi.connect(**self.ipfs_args) + self.read_only = False + + if 'preload' in self.ipfs_args: + del self.ipfs_args['preload'] + + try: + self.api = ipfsapi.connect(**self.ipfs_args) + except ipfsapi.exceptions.ConnectionError: + self.api = ipfsapi.connect('ipfs.io', 80) + self.read_only = True def save(self, path, content): # api.add_bytes(b"Mary had a little lamb") + if self.read_only: + raise NotImplementedError('This is a read-only client. ' + 'Start an IPFS node to be able to save ' + 'data.') new_obj = self.api.add_bytes(content) if self.pin_on_add: self.api.pin_add(new_obj) diff --git a/tests/test-data/.sbt.v4/0107d767a345eff67ecdaed2ee5cd7ba b/tests/test-data/.sbt.v4/0107d767a345eff67ecdaed2ee5cd7ba new file mode 100644 index 0000000000..117edf2bf6 --- /dev/null +++ b/tests/test-data/.sbt.v4/0107d767a345eff67ecdaed2ee5cd7ba @@ -0,0 +1,522 @@ +[ + { + "class": "sourmash_signature", + "email": "titus@idyll.org", + "filename": "SRR453566_1.fastq.gz", + "hash_function": "0.murmur64", + "signatures": [ + { + "ksize": 31, + "max_hash": 0, + "md5sum": "0107d767a345eff67ecdaed2ee5cd7ba", + "mins": [ + 1877811749, + 1339603207230, + 5641354835174, + 10502027926594, + 11550845136154, + 12183113567732, + 14062071191653, + 14580861632266, + 18722876140337, + 20714320729467, + 22732389403804, + 24134363957219, + 30606147678309, + 30841792132441, + 31130970675642, + 32760645340554, + 33190965408032, + 33960067474598, + 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326362555166202, + 327401856042864, + 327430526220797, + 327717949035640, + 327729120445936 + ], + "molecule": "DNA", + "num": 500, + "seed": 42 + } + ], + "type": "mrnaseq", + "version": 0.4 + } +] \ No newline at end of file diff --git a/tests/test-data/.sbt.v5/internal.0 b/tests/test-data/.sbt.v5/internal.0 new file mode 100644 index 0000000000..e3f726a915 Binary files /dev/null and b/tests/test-data/.sbt.v5/internal.0 differ diff --git a/tests/test-data/.sbt.v5/internal.1 b/tests/test-data/.sbt.v5/internal.1 new file mode 100644 index 0000000000..8a25abfc88 Binary files /dev/null and b/tests/test-data/.sbt.v5/internal.1 differ diff --git a/tests/test-data/.sbt.v5/internal.2 b/tests/test-data/.sbt.v5/internal.2 new file mode 100644 index 0000000000..e87af3d701 Binary files /dev/null and b/tests/test-data/.sbt.v5/internal.2 differ diff --git a/tests/test-data/.sbt.v5/internal.3 b/tests/test-data/.sbt.v5/internal.3 new file mode 100644 index 0000000000..a24ae7ab15 Binary files /dev/null and b/tests/test-data/.sbt.v5/internal.3 differ diff --git a/tests/test-data/.sbt.v5/internal.4 b/tests/test-data/.sbt.v5/internal.4 new file mode 100644 index 0000000000..0cf699e295 Binary files /dev/null and b/tests/test-data/.sbt.v5/internal.4 differ diff --git a/tests/test-data/.sbt.v5/internal.5 b/tests/test-data/.sbt.v5/internal.5 new file mode 100644 index 0000000000..708a518a57 Binary files /dev/null and b/tests/test-data/.sbt.v5/internal.5 differ diff --git a/tests/test-data/ipfs_leaves.sbt.json b/tests/test-data/ipfs_leaves.sbt.json new file mode 100644 index 0000000000..24f56c7aea --- /dev/null +++ b/tests/test-data/ipfs_leaves.sbt.json @@ -0,0 +1 @@ +{"d": 2, "version": 5, "storage": {"backend": "IPFSStorage", "args": {}}, "factory": {"class": "GraphFactory", "args": [1, 100000, 4]}, "leaves": {"6": {"filename": "QmaW8C75VMgdrAVF8evR1FukPh3M4qCEPZK4ZLL7yJyMT8", "name": "6d6e87e1154e95b279e5e7db414bc37b", "metadata": "6d6e87e1154e95b279e5e7db414bc37b"}, "7": {"filename": "QmPArMUvrAK7spyH8WBp1gpExfbwG2Z4PMmCQVSaRNH5WE", "name": "60f7e23c24a8d94791cc7a8680c493f9", "metadata": "60f7e23c24a8d94791cc7a8680c493f9"}, "8": {"filename": "QmXd9x4L331soVHPBHMNeDbK73ugH2cXYoYCY8amFB2LZE", "name": "0107d767a345eff67ecdaed2ee5cd7ba", "metadata": "0107d767a345eff67ecdaed2ee5cd7ba"}, "9": {"filename": "QmWkR7Gj126x8u1kEf7z5WkGQzt4ib3yJyRYaGXL5Sk8t2", "name": "f71e78178af9e45e6f1d87a0c53c465c", "metadata": "f71e78178af9e45e6f1d87a0c53c465c"}, "10": {"filename": "QmesxNDT3P7bNhTLTaipFd6Gx6wx5SbbgW2jQfvUBdYYcS", "name": "f0c834bc306651d2b9321fb21d3e8d8f", "metadata": "f0c834bc306651d2b9321fb21d3e8d8f"}, "11": {"filename": "QmSKvxmECayQLwz77KwhsnFS8LevHZboHb3echuNxQYbWo", "name": "4e94e60265e04f0763142e20b52c0da1", "metadata": "4e94e60265e04f0763142e20b52c0da1"}, "12": {"filename": "QmVbeK97GQ6BYrv4wcn42RoiMKZonQLMY9THDgGujfAAo2", "name": "b59473c94ff2889eca5d7165936e64b3", "metadata": "b59473c94ff2889eca5d7165936e64b3"}}} diff --git a/tests/test-data/v4.sbt.json b/tests/test-data/v4.sbt.json new file mode 100644 index 0000000000..8b0a5f5100 --- /dev/null +++ b/tests/test-data/v4.sbt.json @@ -0,0 +1 @@ +{"d": 2, "version": 4, "storage": {"backend": "FSStorage", "args": {"path": ".sbt.v4"}}, "factory": {"class": "GraphFactory", "args": [1, 100000, 4]}, "nodes": {"0": {"filename": "internal.0", "name": "internal.0", "metadata": {"min_n_below": 500}}, "1": {"filename": "internal.1", "name": "internal.1", "metadata": {"min_n_below": 500}}, "2": {"filename": "internal.2", "name": "internal.2", "metadata": {"min_n_below": 500}}, "3": {"filename": "internal.3", "name": "internal.3", "metadata": {"min_n_below": 500}}, "4": {"filename": "internal.4", "name": "internal.4", "metadata": {"min_n_below": 500}}, "5": {"filename": "internal.5", "name": "internal.5", "metadata": {"min_n_below": 500}}, "6": {"filename": "6d6e87e1154e95b279e5e7db414bc37b", "name": "6d6e87e1154e95b279e5e7db414bc37b", "metadata": "6d6e87e1154e95b279e5e7db414bc37b"}, "7": {"filename": "60f7e23c24a8d94791cc7a8680c493f9", "name": "60f7e23c24a8d94791cc7a8680c493f9", "metadata": "60f7e23c24a8d94791cc7a8680c493f9"}, "8": {"filename": "0107d767a345eff67ecdaed2ee5cd7ba", "name": "0107d767a345eff67ecdaed2ee5cd7ba", "metadata": "0107d767a345eff67ecdaed2ee5cd7ba"}, "9": {"filename": "f71e78178af9e45e6f1d87a0c53c465c", "name": "f71e78178af9e45e6f1d87a0c53c465c", "metadata": "f71e78178af9e45e6f1d87a0c53c465c"}, "10": {"filename": "f0c834bc306651d2b9321fb21d3e8d8f", "name": "f0c834bc306651d2b9321fb21d3e8d8f", "metadata": "f0c834bc306651d2b9321fb21d3e8d8f"}, "11": {"filename": "4e94e60265e04f0763142e20b52c0da1", "name": "4e94e60265e04f0763142e20b52c0da1", "metadata": "4e94e60265e04f0763142e20b52c0da1"}, "12": {"filename": "b59473c94ff2889eca5d7165936e64b3", "name": "b59473c94ff2889eca5d7165936e64b3", "metadata": "b59473c94ff2889eca5d7165936e64b3"}}} diff --git a/tests/test_ipfs.py b/tests/test_ipfs.py new file mode 100644 index 0000000000..c2b3a9eb5c --- /dev/null +++ b/tests/test_ipfs.py @@ -0,0 +1,119 @@ +from __future__ import print_function, unicode_literals + +import os +import shutil + +import pytest + +from sourmash_lib import signature +from sourmash_lib.sbt import SBT, GraphFactory +from sourmash_lib.sbtmh import SigLeaf, search_minhashes +from sourmash_lib.sbt_storage import IPFSStorage, FSStorage + +from . import sourmash_tst_utils as utils + + +def test_sbt_ipfsstorage(tmpdir): + pytest.importorskip("ipfsapi") + + factory = GraphFactory(31, 1e5, 4) + + tree = SBT(factory) + + for f in utils.SIG_FILES: + sig = next(signature.load_signatures(utils.get_test_data(f))) + leaf = SigLeaf(os.path.basename(f), sig) + tree.add_node(leaf) + to_search = leaf + + print("*" * 60) + print("{}:".format(to_search.metadata)) + old_result = {str(s) for s in tree.find(search_minhashes, to_search.data, 0.1)} + print(*old_result, sep="\n") + + try: + with IPFSStorage() as storage: + tree.save(str(tmpdir.join("tree")), storage=storage) + except NotImplementedError: + pytest.xfail("Using a Read-only client for IPFS") + + with IPFSStorage() as storage: + tree = SBT.load( + str(tmpdir.join("tree")), leaf_loader=SigLeaf.load, storage=storage + ) + + print("*" * 60) + print("{}:".format(to_search.metadata)) + new_result = {str(s) for s in tree.find(search_minhashes, to_search.data, 0.1)} + print(*new_result, sep="\n") + + assert old_result == new_result + + +def test_storage_convert(tmpdir): + testdata = utils.get_test_data("v2.sbt.json") + testsbt = tmpdir.join("v2.sbt.json") + + shutil.copyfile(testdata, str(testsbt)) + shutil.copytree( + os.path.join(os.path.dirname(testdata), ".sbt.v2"), str(tmpdir.join(".sbt.v2")) + ) + + original = SBT.load(str(testsbt), leaf_loader=SigLeaf.load) + + args = ["storage", "convert", "-b", "ipfs", testsbt] + status, out, err = utils.runscript( + "sourmash", args, in_directory=str(tmpdir), fail_ok=True + ) + if not status and "ipfs.exceptions.ConnectionError" in err: + raise pytest.xfail("ipfs probably not running") + + ipfs = SBT.load(str(testsbt), leaf_loader=SigLeaf.load) + + assert len(original) == len(ipfs) + assert all(n1[1].name == n2[1].name for (n1, n2) in zip(original, ipfs)) + + args = [ + "storage", + "convert", + "-b", + """'TarStorage("{}")'""".format(tmpdir.join("v2.sbt.tar.gz")), + str(testsbt), + ] + status, out, err = utils.runscript("sourmash", args, in_directory=str(tmpdir)) + tar = SBT.load(str(testsbt), leaf_loader=SigLeaf.load) + + assert len(original) == len(tar) + assert all(n1[1].name == n2[1].name for (n1, n2) in zip(original, tar)) + + +def test_prepare_index(tmpdir): + pytest.importorskip("ipfsapi") + + try: + with IPFSStorage() as storage: + for f in utils.SIG_FILES: + with open(utils.get_test_data(f), 'rb') as data: + storage.save('', data.read()) + except NotImplementedError: + pytest.xfail("Using a Read-only client for IPFS") + + testdata = utils.get_test_data("ipfs_leaves.sbt.json") + testsbt = tmpdir.join("tree.sbt.json") + + shutil.copyfile(testdata, str(testsbt)) + + args = [ + "prepare", + str(testsbt), + ] + status, out, err = utils.runscript("sourmash", args, in_directory=str(tmpdir)) + prepared_sbt = SBT.load(str(testsbt), leaf_loader=SigLeaf.load) + assert not(isinstance(prepared_sbt.storage, IPFSStorage)) + assert isinstance(prepared_sbt.storage, FSStorage) + + sig = utils.get_test_data(utils.SIG_FILES[0]) + status, out, err = utils.runscript('sourmash', + ['search', sig, str(testsbt)], + in_directory=str(tmpdir)) + assert '3 matches:' in out diff --git a/tests/test_sbt.py b/tests/test_sbt.py index 139e2f25a4..9618aa1c7c 100644 --- a/tests/test_sbt.py +++ b/tests/test_sbt.py @@ -7,9 +7,8 @@ from sourmash import signature from sourmash.sbt import SBT, GraphFactory, Leaf, Node from sourmash.sbtmh import (SigLeaf, search_minhashes, - search_minhashes_containment) -from sourmash.sbt_storage import (FSStorage, TarStorage, - RedisStorage, IPFSStorage) + search_minhashes_containment) +from sourmash.sbt_storage import (FSStorage, TarStorage, RedisStorage) from . import sourmash_tst_utils as utils @@ -130,42 +129,25 @@ def search_transcript(node, seq, threshold): assert set(try3) == set([ 'd', 'e' ]), try3 -def test_tree_v1_load(): - tree_v1 = SBT.load(utils.get_test_data('v1.sbt.json'), - leaf_loader=SigLeaf.load) - - tree_cur = SBT.load(utils.get_test_data('v3.sbt.json'), +@pytest.mark.parametrize("old_version", + ['v1', 'v2', 'v3', 'v4']) +def test_tree_load_old_versions(old_version): + tree_old = SBT.load(utils.get_test_data(old_version + '.sbt.json'), leaf_loader=SigLeaf.load) - testdata1 = utils.get_test_data(utils.SIG_FILES[0]) - to_search = next(signature.load_signatures(testdata1)) - - results_v1 = {str(s) for s in tree_v1.find(search_minhashes_containment, - to_search, 0.1)} - results_cur = {str(s) for s in tree_cur.find(search_minhashes_containment, - to_search, 0.1)} - - assert results_v1 == results_cur - assert len(results_v1) == 4 - - -def test_tree_v2_load(): - tree_v2 = SBT.load(utils.get_test_data('v2.sbt.json'), - leaf_loader=SigLeaf.load) - - tree_cur = SBT.load(utils.get_test_data('v3.sbt.json'), + tree_cur = SBT.load(utils.get_test_data('v5.sbt.json'), leaf_loader=SigLeaf.load) testdata1 = utils.get_test_data(utils.SIG_FILES[0]) to_search = next(signature.load_signatures(testdata1)) - results_v2 = {str(s) for s in tree_v2.find(search_minhashes_containment, - to_search, 0.1)} + results_old = {str(s) for s in tree_old.find(search_minhashes_containment, + to_search, 0.1)} results_cur = {str(s) for s in tree_cur.find(search_minhashes_containment, to_search, 0.1)} - assert results_v2 == results_cur - assert len(results_v2) == 4 + assert results_old == results_cur + assert len(results_old) == 4 def test_tree_save_load(n_children): @@ -363,45 +345,6 @@ def test_sbt_tarstorage(): assert old_result == new_result -def test_sbt_ipfsstorage(): - ipfsapi = pytest.importorskip('ipfsapi') - - factory = GraphFactory(31, 1e5, 4) - with utils.TempDirectory() as location: - tree = SBT(factory) - - for f in utils.SIG_FILES: - sig = next(signature.load_signatures(utils.get_test_data(f))) - leaf = SigLeaf(os.path.basename(f), sig) - tree.add_node(leaf) - to_search = leaf - - print('*' * 60) - print("{}:".format(to_search.metadata)) - old_result = {str(s) for s in tree.find(search_minhashes, - to_search.data, 0.1)} - print(*old_result, sep='\n') - - try: - with IPFSStorage() as storage: - tree.save(os.path.join(location, 'tree'), storage=storage) - except ipfsapi.exceptions.ConnectionError: - pytest.xfail("ipfs not installed/functioning probably") - - with IPFSStorage() as storage: - tree = SBT.load(os.path.join(location, 'tree'), - leaf_loader=SigLeaf.load, - storage=storage) - - print('*' * 60) - print("{}:".format(to_search.metadata)) - new_result = {str(s) for s in tree.find(search_minhashes, - to_search.data, 0.1)} - print(*new_result, sep='\n') - - assert old_result == new_result - - def test_sbt_redisstorage(): redis = pytest.importorskip('redis') factory = GraphFactory(31, 1e5, 4) diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py index dcfe719a4a..15b208d058 100644 --- a/tests/test_sourmash.py +++ b/tests/test_sourmash.py @@ -3518,43 +3518,6 @@ def test_watch_coverage(): assert 'FOUND: genome-s10.fa.gz, at 1.000' in out -def test_storage_convert(): - import pytest - - with utils.TempDirectory() as location: - testdata = utils.get_test_data('v2.sbt.json') - shutil.copyfile(testdata, os.path.join(location, 'v2.sbt.json')) - shutil.copytree(os.path.join(os.path.dirname(testdata), '.sbt.v2'), - os.path.join(location, '.sbt.v2')) - testsbt = os.path.join(location, 'v2.sbt.json') - - original = SBT.load(testsbt, leaf_loader=SigLeaf.load) - - args = ['storage', 'convert', '-b', 'ipfs', testsbt] - status, out, err = utils.runscript('sourmash', args, - in_directory=location, fail_ok=True) - if not status and "ipfs.exceptions.ConnectionError" in err: - raise pytest.xfail('ipfs probably not running') - - ipfs = SBT.load(testsbt, leaf_loader=SigLeaf.load) - - assert len(original) == len(ipfs) - assert all(n1[1].name == n2[1].name - for (n1, n2) in zip(sorted(original), sorted(ipfs))) - - args = ['storage', 'convert', - '-b', """'TarStorage("{}")'""".format( - os.path.join(location, 'v2.sbt.tar.gz')), - testsbt] - status, out, err = utils.runscript('sourmash', args, - in_directory=location) - tar = SBT.load(testsbt, leaf_loader=SigLeaf.load) - - assert len(original) == len(tar) - assert all(n1[1].name == n2[1].name - for (n1, n2) in zip(sorted(original), sorted(tar))) - - def test_storage_convert_identity(): with utils.TempDirectory() as location: testdata = utils.get_test_data('v2.sbt.json')