def __reload(self):
headers = {
'content-type': 'application/json',
'content-language': 'en-US',
'accept': 'application/json'
}
params = {'page_size': 1, 'page_number': 1}
if self.id() is not None:
methodurl = '/api/secure/' + self.type() + '/id:'
if isinstance(self.id(), list):
methodurl = methodurl + list2str(self.id())
if isinstance(self.id(), str):
methodurl = methodurl + self.id()
resp = self._connecthdr.get(methodurl=methodurl,
headers=headers,
payload=params)
results = resp.results()
if results is not None:
result = results[0]
g = Go(self._connecthdr, result.json())
self.__copy(g)
def genus(self,
genus_names=None,
page_size=PAGE_SIZE_DEFAULT,
page_number=PAGE_INDEX_DEFAULT
):
"""
Get OMXWare Genera by names .
Parameters:
:param genus_names: List of Genus names
:type genus_names: [str]
:param page_number: Page Number
:type page_number: int
:param page_size: Results page size
:type page_size: int
Returns:
:return: OmxResponse: Genus
"""
try:
self._init_omx_connection()
headers = {'content-type': 'application/json',
'content-language': 'en-US',
'accept': 'application/json'}
methodurl = "/api/secure/genus/"
params = {'page_size': page_size, 'page_number': page_number}
if genus_names is None:
raise InvalidParamsError("No Genus names passed")
if genus_names == 'all':
genus_names = None
if isinstance(genus_names, list):
params['name'] = list2str(genus_names)
if isinstance(genus_names, str):
params['name'] = [genus_names]
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
except InvalidParamsError as ex:
print("\nERROR: " + str(ex))
help(self.genus)
def ipr(self,
ids=None,
categories=None,
page_size=PAGE_SIZE_DEFAULT,
page_number=PAGE_INDEX_DEFAULT
):
"""
Get OMXWare IPRs by List of IPR Code(s) and/or Category name(s) .
Parameters:
:param ids: List of IPR IDs
:type ids: [str]
:param categories: List of IPR Categories.
:type categories: [str]
:param page_number: Page Number
:type page_number: int
:param page_size: Results page size
:type page_size: int
Returns:
:return: OmxResponse: Ipr
"""
try:
self._init_omx_connection()
headers = {'content-type': 'application/json',
'content-language': 'en-US',
'accept': 'application/json'}
params = {'page_size': page_size, 'page_number': page_number}
if ids is not None:
methodurl = "/api/secure/ipr/id:"
if isinstance(ids, list):
methodurl = methodurl + list2str(ids)
if isinstance(ids, str):
methodurl = methodurl + ids
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
methodurl = "/api/secure/ipr/"
if categories is None :
raise InvalidParamsError("No Categories or IPR Codes passed")
if isinstance(categories, list):
params['category'] = list2str(categories)
if isinstance(categories, str):
params['category'] = [categories]
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
except InvalidParamsError as ex:
print("\nERROR: " + str(ex))
help(self.ipr)
def go(self,
ids=None,
categories=None,
page_size=PAGE_SIZE_DEFAULT,
page_number=PAGE_INDEX_DEFAULT
):
"""
Get OMXWare GO Terms by List of GO ID(s) and/or Category name(s) .
Parameters:
:param ids: List of GO Term IDs
:type ids: [str]
:param categories: List of GO Term Categories. Must be one of { 'MOLECULAR_FUNCTION', 'BIOLOGICAL_PROCESS', 'CELLULAR_COMPONENT' }
:type categories: [str]
:param page_number: Page Number
:type page_number: int
:param page_size: Results page size
:type page_size: int
Returns:
:return: OmxResponse: Go
"""
try:
self._init_omx_connection()
headers = {'content-type': 'application/json',
'content-language': 'en-US',
'accept': 'application/json'}
params = {'page_size': page_size, 'page_number': page_number}
if ids is not None:
methodurl = "/api/secure/go/id:"
if isinstance(ids, list):
methodurl = methodurl + list2str(ids)
if isinstance(ids, str):
methodurl = methodurl + ids
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
methodurl = "/api/secure/go/"
if categories is None :
raise InvalidParamsError("No Categories or GO Term IDs passed")
if isinstance(categories, list):
params['category'] = list2str(categories)
if isinstance(categories, str):
params['category'] = [categories]
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
except InvalidParamsError as ex:
print("\nERROR: " + str(ex))
help(self.go)
def domains(self,
ids=None,
sequence=None,
genus_names=None,
protein_ids=None,
go_terms=None,
ipr_ids=None,
sequence_length=None,
page_size=PAGE_SIZE_DEFAULT,
page_number=PAGE_INDEX_DEFAULT
):
"""
Get OMXWare Domains.
Parameters:
:param ids: List of domain ids
:type ids: [str]
:param sequence: Domain sequence
:type sequence: str
:param genus_names: List of Genus names
:type genus_names: [str]
:param protein_ids: List of Protein ids
:type protein_ids: [str]
:param go_terms:
:type go_terms: [str]
:param ipr_ids:
:type ipr_ids: [str]
:param sequence_length:
:type sequence_length: str
:param page_number: (int): Page Number
:type page_number: int
:param page_size: (int): Results page size
:type page_size: int
Returns:
:return: OmxResponse: Domain
"""
try:
self._init_omx_connection()
headers = {'content-type': 'application/json',
'content-language': 'en-US',
'accept': 'application/json'}
params = {'page_size': page_size, 'page_number': page_number}
if ids is not None:
methodurl = "/api/secure/domains/id:"
if isinstance(ids, list):
methodurl = methodurl + list2str(ids)
if isinstance(ids, str):
methodurl = methodurl + ids
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
if sequence is not None:
methodurl = "/api/secure/domains/sequence:"
if isinstance(sequence, str):
methodurl = methodurl + sequence
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
methodurl = "/api/secure/domains/"
if isinstance(genus_names, list):
params['genus_name'] = list2str(genus_names)
if isinstance(genus_names, str):
params['genus_name'] = [genus_names]
if isinstance(protein_ids, list):
params['protein_id'] = list2str(protein_ids)
if isinstance(protein_ids, str):
params['protein_id'] = [protein_ids]
if isinstance(go_terms, list):
params['go_term'] = list2str(go_terms)
if isinstance(go_terms, str):
params['go_term'] = [go_terms]
if isinstance(ipr_ids, list):
params['ipr_id'] = list2str(ipr_ids)
if isinstance(ipr_ids, str):
params['ipr_id'] = [ipr_ids]
if isinstance(sequence_length, str):
params['sequence_length'] = [sequence_length]
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
except InvalidParamsError as ex:
print("\nERROR: " + str(ex))
help(self.domains)
def genomes(self,
ids=None,
genus_names=None,
genome_type=None,
genome_taxid=None,
created_before=None,
created_after=None,
modified_before=None,
modified_after=None,
page_size=PAGE_SIZE_DEFAULT,
page_number=PAGE_INDEX_DEFAULT
):
"""
Get OMXWare Genomes by List of Genome ID(s) and/or Genus name(s) .
Parameters:
:param ids: List of Genome IDs
:type ids: [str]
:param genus_names: List of Genus names
:type genus_names: [str]
:param genus_names: List of Genome Types. Must be one of { 'REFSEQ’, 'SRA’, ‘GENBANK’ }
:type genus_names: [str]
:param genus_names: List of Genome Tax ids
:type genus_names: [str]
:param created_before: Date - Created / Imported before. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY
:type created_before: [str]
:param created_after: Date - Created / Imported after. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY
:type created_after: [str]
:param modified_before: Date - Modified before. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY
:type modified_before: [str]
:param modified_after: Date - Modified after. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY
:type modified_after: [str]
:param page_number: Page Number
:type page_number: int
:param page_size: Results page size
:type page_size: int
Returns:
:return: OmxResponse: Genome
"""
try:
self._init_omx_connection()
headers = {'content-type': 'application/json',
'content-language': 'en-US',
'accept': 'application/json'}
params = {'page_size': page_size, 'page_number': page_number}
if ids is not None:
methodurl = "/api/secure/genomes/id:"
if isinstance(ids, list):
methodurl = methodurl + list2str(ids)
if isinstance(ids, str):
methodurl = methodurl + ids
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
methodurl = "/api/secure/genomes/"
if isinstance(genus_names, list):
params['name'] = list2str(genus_names)
if isinstance(genus_names, str):
params['name'] = [genus_names]
if isinstance(genome_type, list):
params['type'] = list2str(genome_type)
if isinstance(genome_type, str):
params['type'] = [genome_type]
if isinstance(genome_taxid, list):
params['taxid'] = list2str(genome_taxid)
if isinstance(genome_taxid, str) or isinstance(genome_taxid, int):
params['taxid'] = [genome_taxid]
created = []
modified = []
if created_before is not None and isinstance(created_before, str):
created.append('lte:'+created_before)
if created_after is not None and isinstance(created_after, str):
created.append('gte:'+created_after)
if len(created) > 0:
params['created'] = created
if modified_before is not None and isinstance(modified_before, str):
modified.append('lte:'+modified_before)
if modified_after is not None and isinstance(modified_after, str):
modified.append('gte:'+modified_after)
if len(modified) > 0:
params['modified'] = modified
resp = self.connection.get(methodurl=methodurl, headers=headers, payload=params)
return resp
except InvalidParamsError as ex:
print("\nERROR: " + str(ex))
help(self.genomes)