def test_download_file(self):
url = "http://ndbserver.rutgers.edu/files/ftp/NDB/coordinates/na-chiral-correct/pdb5dg7.ent.gz"
file = DownloadHelper.download_file(url)
self.assertIsNotNone(file)
with self.assertRaises(FileNotFoundError):
url = "http://ndbserver.rutgers.edu/files/ftp/NDB/coordinates/na-chiral-correct/NotExistingOne.ent.gz"
DownloadHelper.download_file(url)
def test_download_file(self):
url = "http://ndbserver.rutgers.edu/files/ftp/NDB/coordinates/na-chiral-correct/pdb5dg7.ent.gz"
file = DownloadHelper.download_file(url)
self.assertIsNotNone(file)
with self.assertRaises(FileNotFoundError):
url = "http://ndbserver.rutgers.edu/files/ftp/NDB/coordinates/na-chiral-correct/NotExistingOne.ent.gz"
DownloadHelper.download_file(url)
def parse_search_report(html: str) -> SimpleResult:
"""To parse simple search report from html to SimpleResult
:param html: html string to parse
:type html: str
:return: simple search result
:rtype: SimpleResult
"""
result = SearchResult()
parser = NDBHtmlParser()
parser.analyze(html)
count_tag = parser.find_one('span', params={'id': 'numRec'})
file_tag = parser.find_one('a', after=count_tag, params={'id': 'fileGal'})
url = file_tag.attrs.get('href', '') if file_tag else ''
from ndb_adapter.ndb_download import DownloadHelper
file = DownloadHelper.download_file(NDBBase.siteUrl + url)
report = parse_xls(file)
try:
result.count = int(count_tag.data)
except (TypeError, ValueError, OverflowError, AttributeError):
pass
result.report = report
return result
def parse_search_report(html: str) -> SimpleResult:
"""To parse simple search report from html to SimpleResult
:param html: html string to parse
:type html: str
:return: simple search result
:rtype: SimpleResult
"""
result = SearchResult()
parser = NDBHtmlParser()
parser.analyze(html)
count_tag = parser.find_one('span', params={'id': 'numRec'})
file_tag = parser.find_one('a', after=count_tag, params={'id': 'fileGal'})
url = file_tag.attrs.get('href', '') if file_tag else ''
from ndb_adapter.ndb_download import DownloadHelper
file = DownloadHelper.download_file(NDBBase.siteUrl + url)
report = parse_xls(file)
try:
result.count = int(count_tag.data)
except (TypeError, ValueError, OverflowError, AttributeError):
pass
result.report = report
return result
def download(structure_id: str, download_type: DownloadType=DownloadType.Pdb,
save: bool=False, target_dir: str='') -> str:
"""Download PDB from NDB
:param download_type: file download type (default value is DownloadType.PDB)
:type download_type: DownloadType
:param target_dir: where to save file (default value is current dir)
:type target_dir: str
:param save: tells if file should be saved or not (default value = False)
:type save: bool
:param structure_id: structure NDB ID or PDB ID e.g. 4Z6C
:type structure_id: str
:return: string or None
:rtype: str
"""
return DownloadHelper.download(structure_id, download_type, save, target_dir)
def download(self, download_type: DownloadType = DownloadType.Pdb, save: bool = False, target_dir: str = '') -> str:
"""Download PDB from NDB
:param download_type: file download type (default value is DownloadType.PDB)
:type download_type: DownloadType
:param target_dir: where to save file (default value is current dir)
:type target_dir: str
:param save: tells if file should be saved or not (default value = False)
:type save: bool
:return: string or None
:rtype: str
"""
id_structure = self.pdb_id
if not self.pdb_id:
print("No pdb_id trying ndb_id")
id_structure = self.ndb_id
return DownloadHelper.download(id_structure, download_type, save, target_dir)
def download(structure_id: str,
download_type: DownloadType = DownloadType.Pdb,
save: bool = False,
target_dir: str = '') -> str:
"""Download PDB from NDB
:param download_type: file download type (default value is DownloadType.PDB)
:type download_type: DownloadType
:param target_dir: where to save file (default value is current dir)
:type target_dir: str
:param save: tells if file should be saved or not (default value = False)
:type save: bool
:param structure_id: structure NDB ID or PDB ID e.g. 4Z6C
:type structure_id: str
:return: string or None
:rtype: str
"""
return DownloadHelper.download(structure_id, download_type, save,
target_dir)
def test_download(self):
pdb_id = "5dg7"
file = DownloadHelper.download(pdb_id)
self.assertIsNotNone(file)
with self.assertRaises(AttributeError):
DownloadHelper.download("")
path = getcwd() + sep + "pdb" + pdb_id + ".ent"
DownloadHelper.download(pdb_id, save=True)
self.assertTrue(isfile(path))
remove(path)
for download_type in filter(lambda w: w is not DownloadType.CifStructureFactors, DownloadType):
file = DownloadHelper.download("5j0m", download_type)
self.assertTrue(file)
file = DownloadHelper.download("5DC3", DownloadType.CifStructureFactors)
self.assertTrue(file)
def test_download(self):
pdb_id = "5dg7"
file = DownloadHelper.download(pdb_id)
self.assertIsNotNone(file)
with self.assertRaises(AttributeError):
DownloadHelper.download("")
path = getcwd() + sep + "pdb" + pdb_id + ".ent"
DownloadHelper.download(pdb_id, save=True)
self.assertTrue(isfile(path))
remove(path)
for download_type in filter(
lambda w: w is not DownloadType.CifStructureFactors,
DownloadType):
file = DownloadHelper.download("5j0m", download_type)
self.assertTrue(file)
file = DownloadHelper.download("5DC3",
DownloadType.CifStructureFactors)
self.assertTrue(file)