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import unittest
import tempfile, os
from tests.common import createTestFile, createTestGzip, createTestDbTable, readTestDbTable
from tol_data.gen_mapping_data import \
genData, readTaxonomyFile, readEolIdsFile, readWikidataDb, readPickedMappings, getEnwikiPageIds
class TestReadTaxonomyFile(unittest.TestCase):
def test_read(self):
with tempfile.TemporaryDirectory() as tempDir:
# Create temp taxonomy file
taxonomyFile = os.path.join(tempDir, 'taxonomy.tsv')
SEP = '\t|\t'
createTestFile(taxonomyFile, ''.join([
SEP.join(['uid', 'parent_uid', 'name', 'rank', 'sourceinfo', 'uniqueName', 'flags', '\n']),
SEP.join(['1', '2', 'one', 'species', 'ncbi:10', '', '', '\n']),
SEP.join(['2', '3', 'two', 'genus', 'ncbi:20,gbif:1', 'bananas', '', '\n']),
SEP.join(['10', '20', 'ten', 'family', 'if:10,if:100', '', '', '\n']),
SEP.join(['11', '100', 'eleven', '', 'igloo:1,ncbi:?', '', '', '\n'])
]))
# Run
nodeToSrcIds = {}
usedSrcIds = set()
readTaxonomyFile(taxonomyFile, nodeToSrcIds, usedSrcIds)
# Check
self.assertEqual(nodeToSrcIds, {
1: {'ncbi': 10},
2: {'ncbi': 20, 'gbif': 1},
10: {'if': 10},
})
self.assertEqual(usedSrcIds, {
('ncbi', 10),
('ncbi', 20),
('gbif', 1),
('if', 10)
})
class TestReadEolIdsFile(unittest.TestCase):
def test_read(self):
with tempfile.TemporaryDirectory() as tempDir:
# Create temp EOL IDs file
eolIdsFile = os.path.join(tempDir, 'ids.csv.gz')
createTestGzip(eolIdsFile, (
'node_id,resource_pk,resource_id,page_id,preferred_canonical_for_page\n'
'0,10,676,1,rhubarb\n' # EOL ID 1 with ncbi ID 10
'0,99,767,2,nothing\n' # EOL ID 2 with worms ID 99
'0,234,459,100,goat\n' # EOL ID 100 with gbif ID 234
'0,23,676,101,lemon\n' # EOL ID 101 with ncbi ID 23
))
# Create input maps
nodeToSrcIds = {
10: {'ncbi': 10},
20: {'ncbi': 23, 'gbif': 234}
}
# Run
usedSrcIds = {('ncbi', 10), ('gbif', 234), ('ncbi', 23)}
nodeToEolId = {}
readEolIdsFile(eolIdsFile, nodeToSrcIds, usedSrcIds, nodeToEolId)
# Check
self.assertEqual(nodeToEolId, {
10: 1,
20: 101,
})
class TestReadWikidataDb(unittest.TestCase):
def test_read(self):
with tempfile.TemporaryDirectory() as tempDir:
# Create temp wikidata db
wikidataDb = os.path.join(tempDir, 'taxon_srcs.db')
createTestDbTable(
wikidataDb,
'CREATE TABLE src_id_to_title (src TEXT, id INT, title TEXT, PRIMARY KEY(src, id))',
'INSERT INTO src_id_to_title VALUES (?, ?, ?)',
[
('ncbi', 1, 'one'),
('ncbi', 11, 'two'),
('gbif', 21, 'three'),
('if', 31, 'three'),
('ncbi', 2, 'four'),
('gbif', 1, 'five'),
('eol', 1, 'one'),
('eol', 2, 'three'),
('ncbi', 100, 'six'),
]
)
createTestDbTable(
wikidataDb,
'CREATE TABLE title_iucn (title TEXT PRIMARY KEY, status TEXT)',
'INSERT INTO title_iucn VALUES (?, ?)',
[
('one', 'least concern'),
('three', 'vulnerable'),
('six', 'extinct in the wild'),
]
)
# Create input maps
nodeToSrcIds = {
10: {'ncbi': 1},
20: {'ncbi': 11, 'gbif': 21, 'if': 31},
30: {'ncbi': 2, 'gbif': 1},
40: {'ncbi': 99},
}
usedSrcIds = {
('ncbi', 1), ('ncbi', 2), ('gbif', 1), ('ncbi', 11), ('gbif', 21), ('if', 31),
('eol', 10), ('ncbi', 99)
}
nodeToEolId = {
20: 100,
}
# Run
nodeToWikiTitle = {}
titleToIucnStatus = {}
readWikidataDb(wikidataDb, nodeToSrcIds, usedSrcIds, nodeToWikiTitle, titleToIucnStatus, nodeToEolId)
# Check
self.assertEqual(nodeToWikiTitle, {
10: 'one',
20: 'three',
30: 'four',
})
self.assertEqual(titleToIucnStatus, {
'one': 'least concern',
'three': 'vulnerable',
})
self.assertEqual(nodeToEolId, {
10: 1,
20: 100,
})
class TestReadPickedMappings(unittest.TestCase):
def test_read(self):
with tempfile.TemporaryDirectory() as tempDir:
# Create temp picked-mappings files
pickedMappings = {'eol': ['1.txt'], 'enwiki': ['2.txt', '3.txt']}
pickedMappingsContent = {'eol': [''], 'enwiki': ['', '']}
pickedMappingsContent['eol'][0] = (
'10|100\n'
'20|202\n'
)
pickedMappingsContent['enwiki'][0] = (
'12|abc\n'
'23|def\n'
)
pickedMappingsContent['enwiki'][1] = (
'15|ghi\n'
'35|jkl\n'
)
for src in pickedMappings:
for idx in range(len(pickedMappings[src])):
pickedMappings[src][idx] = os.path.join(tempDir, pickedMappings[src][idx])
createTestFile(pickedMappings[src][idx], pickedMappingsContent[src][idx])
# Create input maps
nodeToEolId = {
1: 1,
10: 66,
}
nodeToWikiTitle = {
10: 'one',
12: 'two',
35: 'goanna',
}
# Run
readPickedMappings(pickedMappings, nodeToEolId, nodeToWikiTitle)
# Check
self.assertEqual(nodeToEolId, {
1: 1,
10: 100,
20: 202,
})
self.assertEqual(nodeToWikiTitle, {
10: 'one',
12: 'abc',
23: 'def',
15: 'ghi',
35: 'jkl',
})
class TestReadGetEnwikiPageIds(unittest.TestCase):
def test_read(self):
with tempfile.TemporaryDirectory() as tempDir:
# Create temp dump index
dumpIndexDb = os.path.join(tempDir, 'dump_index.db')
createTestDbTable(
dumpIndexDb,
'CREATE TABLE offsets (title TEXT PRIMARY KEY, id INT UNIQUE, offset INT, next_offset INT)',
'INSERT INTO offsets VALUES (?, ?, ?, ?)',
[
('one', 1, 10, 100),
('two', 22, 10, 100),
('four', 3, 1000, 2000),
]
)
# Create input maps
nodeToWikiTitle = {
10: 'one',
20: 'two',
30: 'three',
}
# Run
titleToPageId = {}
getEnwikiPageIds(dumpIndexDb, nodeToWikiTitle, titleToPageId)
# Check
self.assertEqual(titleToPageId, {
'one': 1,
'two': 22,
})
class TestGenData(unittest.TestCase):
def test_mapping(self):
with tempfile.TemporaryDirectory() as tempDir:
# Create temp taxonomy file
taxonomyFile = os.path.join(tempDir, 'taxonomy.tsv')
SEP = '\t|\t'
createTestFile(taxonomyFile, ''.join([
SEP.join(['uid', 'parent_uid', 'name', 'rank', 'sourceinfo', 'uniqueName', 'flags', '\n']),
SEP.join(['1', '', '', '', 'ncbi:10', '', '', '\n']),
SEP.join(['2', '', '', '', 'ncbi:20,gbif:1', '', '', '\n']),
SEP.join(['3', '', '', '', 'ncbi:30,if:2', '', '', '\n']),
]))
# Create temp EOL IDs file
eolIdsFile = os.path.join(tempDir, 'ids.csv.gz')
createTestGzip(eolIdsFile, (
'node_id,resource_pk,resource_id,page_id,preferred_canonical_for_page\n'
'0,10,676,1,\n' # EOL ID 1 with ncbi ID 10
'0,30,676,2,\n' # EOL ID 2 with ncbi ID 30
))
# Create temp wikidata db
wikidataDb = os.path.join(tempDir, 'taxon_srcs.db')
createTestDbTable(
wikidataDb,
'CREATE TABLE src_id_to_title (src TEXT, id INT, title TEXT, PRIMARY KEY(src, id))',
'INSERT INTO src_id_to_title VALUES (?, ?, ?)',
[
('ncbi', 10, 'one'),
('gbif', 1, 'two'),
('eol', 100, 'two'),
('if', 2, 'three'),
]
)
createTestDbTable(
wikidataDb,
'CREATE TABLE title_iucn (title TEXT PRIMARY KEY, status TEXT)',
'INSERT INTO title_iucn VALUES (?, ?)',
[
('one', 'least concern'),
('three', 'vulnerable'),
]
)
# Create temp picked-mappings files
pickedMappings = {'eol': [], 'enwiki': ['w_ids.txt']}
pickedMappingsContent = {'eol': [], 'enwiki': ['']}
pickedMappingsContent['enwiki'][0] = (
'3|four\n'
)
for src in pickedMappings:
for idx in range(len(pickedMappings[src])):
pickedMappings[src][idx] = os.path.join(tempDir, pickedMappings[src][idx])
createTestFile(pickedMappings[src][idx], pickedMappingsContent[src][idx])
# Create temp dump index
dumpIndexDb = os.path.join(tempDir, 'dump_index.db')
createTestDbTable(
dumpIndexDb,
'CREATE TABLE offsets (title TEXT PRIMARY KEY, id INT UNIQUE, offset INT, next_offset INT)',
'INSERT INTO offsets VALUES (?, ?, ?, ?)',
[
('one', 1000, 1, 2),
('two', 2000, 1, 2),
('three', 3000, 1, 2),
('four', 4000, 1, 2),
]
)
# Create temp tree-of-life db
dbFile = os.path.join(tempDir, 'data.db')
createTestDbTable(
dbFile,
'CREATE TABLE nodes (name TEXT PRIMARY KEY, id TEXT UNIQUE, tips INT)',
'INSERT INTO nodes VALUES (?, ?, ?)',
[
('first', 'ott1', 10),
('second', 'ott2', 1),
('third', 'ott3', 2),
]
)
# Run
genData(taxonomyFile, eolIdsFile, wikidataDb, pickedMappings, dumpIndexDb, dbFile)
# Check
self.assertEqual(
readTestDbTable(dbFile, 'SELECT name, id from eol_ids'),
{
('first', 1),
('second', 100),
('third', 2),
}
)
self.assertEqual(
readTestDbTable(dbFile, 'SELECT name, id from wiki_ids'),
{
('first', 1000),
('second', 2000),
('third', 4000),
}
)
self.assertEqual(
readTestDbTable(dbFile, 'SELECT name, iucn from node_iucn'),
{
('first', 'least concern'),
}
)
|
