def test_memory_from_table(numpy):
table = asciitable.get_reader(numpy=numpy, Reader=asciitable.Daophot)
data = table.read('t/daophot.dat')
mem_table = asciitable.get_reader(Reader=asciitable.Memory, numpy=numpy)
mem_data = mem_table.read(data)
assert(data.dtype.names == mem_data.dtype.names)
_test_values_equal(data, mem_data, numpy)
mem_data = mem_table.read(mem_table)
assert(data.dtype.names == mem_data.dtype.names)
_test_values_equal(data, mem_data, numpy)
def test_write_table():
table = asciitable.get_reader(Reader=asciitable.Daophot)
data = table.read('t/daophot.dat')
for test_def in test_defs:
yield check_write_table, test_def, table
yield check_write_table, test_def, data
def test_write_table_no_numpy():
table = asciitable.get_reader(Reader=asciitable.Daophot, numpy=False)
data = table.read("t/daophot.dat")
for test_def in test_defs:
yield check_write_table, test_def, table
yield check_write_table, test_def, data
def test_write_table_no_numpy():
table = asciitable.get_reader(Reader=asciitable.Daophot, numpy=False)
data = table.read('t/daophot.dat')
for test_def in test_defs:
check_write_table(test_def, table)
check_write_table(test_def, data)
def test_custom_process_lines(numpy):
def process_lines(lines):
bars_at_ends = re.compile(r'^\| | \|$', re.VERBOSE)
striplines = (x.strip() for x in lines)
return [bars_at_ends.sub('', x) for x in striplines if len(x) > 0]
reader = asciitable.get_reader(delimiter='|', numpy=numpy)
reader.inputter.process_lines = process_lines
data = reader.read('t/bars_at_ends.txt')
assert_equal(data.dtype.names, ('obsid', 'redshift', 'X', 'Y', 'object', 'rad'))
assert_equal(len(data), 3)
def test_custom_process_line(numpy):
def process_line(line):
line_out = re.sub(r'^\|\s*', '', line.strip())
return line_out
reader = asciitable.get_reader(data_start=2, delimiter='|', numpy=numpy)
reader.header.splitter.process_line = process_line
reader.data.splitter.process_line = process_line
data = reader.read('t/nls1_stackinfo.dbout')
cols = get_testfiles('t/nls1_stackinfo.dbout')['cols']
assert_equal(data.dtype.names, cols[1:])
def __init__(self):
self.autoRerun = ""
self.parseKnownIssues = ""
self.errataName = ""
self.errataLname = ""
self.rerunedRSId = []
self.force = False
self.__parseArgs()
self.errataInfo = ErrataInfo(self.errataName, self.errataLname, False)
self.resultPath = "./result"
self.jobStatePath = "%s/%s.%s" % (self.resultPath, self.errataInfo.errataId, "jobstate")
genLogger.info("jobStatePath : %s", self.jobStatePath)
self.jobState = ConfigObj(self.jobStatePath, encoding="utf8")
if self.parseKnownIssues == "y":
self.knownIssuesPath = []
self.knownIssues = []
self.knownIssuesRPath = "./known_issues"
self.knownIssuesPath.append(
"%s/%s.%s" % (self.knownIssuesRPath, self.errataInfo.rhel_version, "known_issues")
)
self.knownIssuesPath.append(
"%s/RHEL-%s.%s" % (self.knownIssuesRPath, self.errataInfo.major, "known_issues")
)
for i in range(0, len(self.knownIssuesPath)):
str = "%d : %s" % (i, self.knownIssuesPath[i])
genLogger.info("knownIssuesPath%s" % str)
self.knownIssues.append(ConfigObj(self.knownIssuesPath[i], encoding="utf8"))
self.knownIssuesResult = "%s/%s.%s" % (self.resultPath, self.errataInfo.errataId, "knownIssues")
self.unknownIssuesResult = "%s/%s.%s" % (self.resultPath, self.errataInfo.errataId, "unknownIssues")
self.tableTemple = {
"Path": ["---"],
"TaskName": ["---"],
"TaskResult": ["---"],
"TaskStatus": ["---"],
"ResultPath": ["---"],
"PathResult": ["---"],
"Checked": ["---"],
}
self.columns = ["Path", "TaskName", "TaskResult", "TaskStatus", "ResultPath", "PathResult", "Checked"]
if not os.path.exists(self.knownIssuesResult):
asciitable.write(
self.tableTemple, self.knownIssuesResult, names=self.columns, Writer=asciitable.FixedWidth
)
if not os.path.exists(self.unknownIssuesResult):
asciitable.write(
self.tableTemple, self.unknownIssuesResult, names=self.columns, Writer=asciitable.FixedWidth
)
reader = asciitable.get_reader(Reader=asciitable.FixedWidth)
self.knownIssuesTable = reader.read(self.knownIssuesResult)
self.unknownIssuesTable = reader.read(self.unknownIssuesResult)
def run_ascii():
"""
Load records with asciitable.
* PyPy: OK. Development stopped (was moved into the Astropy project
as astropy.io.ascii).
* Source: https://github.com/taldcroft/asciitable
* Docs: Decent
* Independent: NumPy not required but recommended.
* Small: no
* Can specify column data types: yes. If trying to guess, will parse zips
as numbers.
* Can read in chunks: no
* Can skip columns: yes
* Can stream: no
* Return type: wrapper around file or iterable, each row is a tuple
* Memory usage: ~ 60 Mb
* Timing: around 0.7 sec
"""
import asciitable
import numpy
reader = asciitable.get_reader(
Reader=asciitable.FixedWidth,
header_start=None,
data_start=2,
col_starts=(0, 5, 7, 35, 36, 41, 48, 56, 59, 65, 66, 67, 71, 75, 78),
col_ends=(4, 6, 34, 35, 40, 47, 55, 58, 64, 65, 66, 70, 74, 77, 80),
names=(
'zip_code', 'state_code', 'city_name', 'zip_type',
'county_code', 'latitude', 'longitude', 'area_code',
'finance_code', 'city_official', 'facility', 'msa_code',
'pmsa_code', 'filler'
),
converters={
'zip_code': [asciitable.convert_numpy(numpy.str)]
},
include_names=(
'zip_code', 'state_code', 'city_name', 'county_code', 'latitude',
'longitude', 'area_code', 'msa_code', 'pmsa_code'
),
)
data = reader.read(
'data/ZIP.DAT'
)
records = 0
for row in data:
records += 1
print 'Records:', records
def test_read_normal_names(numpy):
"""Nice, typical fixed format table with col names provided"""
table = """
# comment (with blank line above)
| Col1 | Col2 |
| 1.2 | "hello" |
| 2.4 |'s worlds|
"""
reader = asciitable.get_reader(Reader=asciitable.FixedWidth,
names=('name1', 'name2'))
dat = reader.read(table)
assert_equal(reader.header.colnames, ('name1', 'name2'))
assert_almost_equal(dat[1][0], 2.4)
def test_read_normal_exclude(numpy):
"""Nice, typical fixed format table with col name excluded"""
table = """
# comment (with blank line above)
| Col1 | Col2 |
| 1.2 | "hello" |
| 2.4 |'s worlds|
"""
reader = asciitable.get_reader(Reader=asciitable.FixedWidth,
exclude_names=('Col1',))
dat = reader.read(table)
assert_equal(reader.header.colnames, ('Col2',))
assert_equal(dat[1][0], "'s worlds")
def test_read_weird(numpy):
"""Weird input table with data values chopped by col extent """
table = """
Col1 | Col2 |
1.2 "hello"
2.4 sdf's worlds
"""
reader = asciitable.get_reader(Reader=asciitable.FixedWidth)
dat = reader.read(table)
assert_equal(reader.header.colnames, ('Col1', 'Col2'))
assert_almost_equal(dat[1][0], 2.4)
assert_equal(dat[0][1], '"hel')
assert_equal(dat[1][1], "df's wo")
def test_custom_splitters(numpy):
reader = asciitable.get_reader(numpy=numpy)
reader.header.splitter = asciitable.BaseSplitter()
reader.data.splitter = asciitable.BaseSplitter()
f = 't/test4.dat'
data = reader.read(f)
testfile = get_testfiles(f)
assert_equal(data.dtype.names, testfile['cols'])
assert_equal(len(data), testfile['nrows'])
assert_almost_equal(data.field('zabs1.nh')[2], 0.0839710433091)
assert_almost_equal(data.field('p1.gamma')[2], 1.25997502704)
assert_almost_equal(data.field('p1.ampl')[2], 0.000696444029148)
assert_equal(data.field('statname')[2], 'chi2modvar')
assert_almost_equal(data.field('statval')[2], 497.56468441)
def test_read_normal(numpy):
"""Nice, typical fixed format table"""
table = """
# comment (with blank line above)
| Col1 | Col2 |
| 1.2 | "hello" |
| 2.4 |'s worlds|
"""
reader = asciitable.get_reader(Reader=asciitable.FixedWidth)
dat = reader.read(table)
assert_equal(reader.header.colnames, ('Col1', 'Col2'))
assert_almost_equal(dat[1][0], 2.4)
assert_equal(dat[0][1], '"hello"')
assert_equal(dat[1][1], "'s worlds")
def test_daophot_header_keywords(numpy):
reader = asciitable.get_reader(Reader=asciitable.DaophotReader, numpy=numpy)
table = reader.read('t/daophot.dat')
expected_keywords = (('NSTARFILE', 'test.nst.1', 'filename', '%-23s'),
('REJFILE', 'hello world', 'filename', '%-23s'),
('SCALE', '1.', 'units/pix', '%-23.7g'),)
for name, value, units, format_ in expected_keywords:
for keyword in reader.keywords:
if keyword.name == name:
assert_equal(keyword.value, value)
assert_equal(keyword.units, units)
assert_equal(keyword.format, format_)
break
else:
raise ValueError('Keyword not found')
def test_memory_from_LOL2(numpy):
data = [[1, 2, 3], [4, 5.2, 6.1], [8, 9, 'hello']]
mem_table = asciitable.get_reader(Reader=asciitable.Memory, numpy=numpy, names=('c1','c2','c3'))
mem_data = mem_table.read(data)
print(mem_data.dtype.names)
assert(mem_data.dtype.names == ('c1', 'c2', 'c3'))
if numpy:
assert(mem_data[0][0] == 1)
assert(mem_data[0][1] == 2)
assert(mem_data[0][2] == '3')
assert((mem_data['c2'] == np.array([2, 5.2, 9])).all())
assert((mem_data['c3'] == np.array([3, 6.1, 'hello'])).all())
else:
assert(mem_data[0] == [1, 2, 3])
assert(mem_data['c2'] == [2, 5.2, 9])
assert(mem_data['c3'] == [3, 6.1, 'hello'])
def test_ipac_read_types(numpy):
table = r"""\
| ra | dec | sai |-----v2---| sptype |
| real | float | l | real | char |
| unit | unit | unit | unit | ergs |
| null | null | null | null | -999 |
2.09708 2956 73765 2.06000 B8IVpMnHg
"""
reader = asciitable.get_reader(Reader=asciitable.Ipac, numpy=numpy)
dat = reader.read(table)
types = [asciitable.FloatType,
asciitable.FloatType,
asciitable.IntType,
asciitable.FloatType,
asciitable.StrType]
for (col, expected_type) in zip(reader.cols, types):
assert_equal(col.type, expected_type)
def run_ascii():
"""
Load records with asciitable.
* PyPy: OK. Development stopped (was moved into the Astropy project
as astropy.io.ascii).
* Source: https://github.com/taldcroft/asciitable
* Docs: Decent
* Independent: NumPy not required but recommended.
* Small: no
* Can specify column data types: yes. If trying to guess, will parse zips
as numbers.
* Can read in chunks: no
* Can skip columns: yes
* Can stream: no
* Return type: wrapper around file or iterable, each row is a tuple
* Memory usage: ~ 60 Mb
* Timing: around 0.7 sec
"""
import asciitable
import numpy
reader = asciitable.get_reader(
Reader=asciitable.FixedWidth,
header_start=None,
data_start=2,
col_starts=(0, 5, 7, 35, 36, 41, 48, 56, 59, 65, 66, 67, 71, 75, 78),
col_ends=(4, 6, 34, 35, 40, 47, 55, 58, 64, 65, 66, 70, 74, 77, 80),
names=('zip_code', 'state_code', 'city_name', 'zip_type',
'county_code', 'latitude', 'longitude', 'area_code',
'finance_code', 'city_official', 'facility', 'msa_code',
'pmsa_code', 'filler'),
converters={'zip_code': [asciitable.convert_numpy(numpy.str)]},
include_names=('zip_code', 'state_code', 'city_name', 'county_code',
'latitude', 'longitude', 'area_code', 'msa_code',
'pmsa_code'),
)
data = reader.read('data/ZIP.DAT')
records = 0
for row in data:
records += 1
print 'Records:', records
def test_memory_from_DOL(numpy):
data = {'c1': [1, 2, 3],
'c2': [4, 5.2, 6.1],
'c3': [8, 9, 'hello']}
mem_table = asciitable.get_reader(Reader=asciitable.Memory, numpy=numpy,
names=sorted(data.keys()))
mem_data = mem_table.read(data)
assert(mem_data.dtype.names == ('c1', 'c2', 'c3'))
if numpy:
assert(mem_data[0][0] == 1)
assert(mem_data[0][1] == 4)
assert(mem_data[0][2] == '8')
assert((mem_data['c2'] == np.array([4, 5.2, 6.1])).all())
assert((mem_data['c3'] == np.array([8, 9, 'hello'])).all())
else:
assert(mem_data[0] == [1, 4, 8])
assert(mem_data['c2'] == [4, 5.2, 6.1])
assert(mem_data['c3'] == [8, 9, 'hello'])
def test_types_from_dat(numpy):
if numpy:
converters = {'a': [asciitable.convert_numpy(np.float)],
'e': [asciitable.convert_numpy(np.str)]}
else:
converters = {'a': [asciitable.convert_list(float)],
'e': [asciitable.convert_list(str)]}
dat = asciitable.read(['a b c d e', '1 1 cat 2.1 4.2'], Reader=asciitable.Basic,
converters=converters, numpy=numpy)
reader = asciitable.get_reader(Reader=asciitable.Memory, numpy=numpy)
reader.read(dat)
print('numpy=%s' % numpy)
print('dat=%s' % repr(dat))
print('reader.table=%s' % repr(reader.table))
print('types=%s' % repr([x.type for x in reader.cols]))
assert_true(issubclass(reader.cols[0].type, asciitable.FloatType))
assert_true(issubclass(reader.cols[1].type, asciitable.IntType))
assert_true(issubclass(reader.cols[2].type, asciitable.StrType))
assert_true(issubclass(reader.cols[3].type, asciitable.FloatType))
assert_true(issubclass(reader.cols[4].type, asciitable.StrType))
def read_table2(readme, data):
reader = asciitable.get_reader(Reader=asciitable.Cds, readme=readme)
if asciitable.has_numpy:
reader.outputter = asciitable.NumpyOutputter()
return reader.read(data)
def test_comment_lines(numpy):
table = asciitable.get_reader(Reader=asciitable.RdbReader, numpy=numpy)
data = table.read('t/apostrophe.rdb')
assert_equal(table.comment_lines, ['# first comment', ' # second comment'])
"""
Test case for CDS table writing
Reads in an IPAC table and writes it out as a CDS table
Unfortunately, as of 7/7/11, IPAC tables do not have a 'descr' attribute
"""
import asciitable
# Generate an IPAC reader object
ipac_reader = asciitable.get_reader(Reader=asciitable.Ipac)
# Fill the IPAC reader from a table...
ipac_table = ipac_reader.read('t/ipac2.dat')
# create a CDS object
cds_writer = asciitable.get_writer(Writer=asciitable.Cds)
# write the ipac_reader Table using the CDS writer
# (I think there should be a wrapper for this...)
asciitable.write(ipac_reader,'t/ipac_convert_to_cds.cds',Writer=asciitable.Cds)
cds_reader = asciitable.get_reader(Reader=asciitable.Cds)
cds_table = cds_reader.read('t/cds2.dat')
asciitable.write(cds_reader,'t/cds_convert_to_cds.cds',Writer=asciitable.Cds)
test_read_ipaccds = cds_reader.read('t/ipac_convert_to_cds.cds')
print test_read_ipaccds
test_read_cdscds = cds_reader.read('t/cds_convert_to_cds.cds')
print test_read_cdscds[:5]