Module rest_wrapper.rest_wrapper
Making use of the REST API (NeuroMorpho.org v7) to query the database.
Expand source code
"""Making use of the REST API (NeuroMorpho.org v7) to query the database."""
# python v2 or v3
try:
from urllib2 import urlopen, Request, URLError
except ImportError:
from urllib.request import urlopen, Request, URLError
import re, json, sys
# pseudo-constants
NEUROMORPHO_URL = "http://neuromorpho.org"
MAX_NEURONS_PER_PAGE = 500
def validate_response_code(response):
"""Checks response code from JSON request and print warning then exits
Keyword arguments:
response -- response of the issued JSON request
"""
code = response.getcode()
# success
if code == 200: return
# error codes
if code == 400:
print("Bad request, usually wrong parameters to select queries.")
elif code == 404:
print("Resource not found or does not exist")
elif code == 405:
print("Unsupported HTTP method used (No GET or POST request).")
elif code == 500:
print("Internal Server Error. Contact admin for assistance.")
sys.exit()
def check_api_health():
"""Checks if the REST API is available
Returns true if API is available or false otherwise
"""
url = "http://neuromorpho.org/api/health"
req = Request(url)
try:
response = urlopen(req)
if json.loads(response.read().decode('utf-8'))['status'] != "UP":
print("REST API not available.")
else:
return True
except URLError:
print("""
No network connectivity. A working internet connection is required.
Check with ISP and/or your local network infrastructure for failure.
""")
return False
def get_num_neurons(num_neurons):
"""Get number of neurons. API can handle only up to 500 neurons per page
Keyword arguments:
num_neurons -- number of neurons
"""
return num_neurons if (num_neurons != -1 and num_neurons < MAX_NEURONS_PER_PAGE) else MAX_NEURONS_PER_PAGE
def get_neuron_pages(num_neurons, total_pages):
"""
Get the number of neuron pages. API handles up to 500 neurons per page.
If more neurons than supported by the NeuroMorpho API (> 500), then
multiple pages need to be retrieved, otherwise one page is retrieved.
Keyword arguments:
num_neurons -- number of neurons
total_pages -- number of pages available when using numNeurons per page
"""
return min(total_pages, num_neurons / MAX_NEURONS_PER_PAGE if num_neurons > MAX_NEURONS_PER_PAGE else 1)
def get_swc_by_filter_rule_for_search_term(filter_string_list, search_term, num_neurons, index=-1):
"""Downloads n neurons by filterString and stores as SWC files
Keyword arguments:
filter_string_list -- the filter string as key value pairs
search_term-- the search term
num_neurons -- number of neurons
"""
if not check_api_health(): return
url = "%s/api/neuron/select?q=%s&" % (NEUROMORPHO_URL, search_term.replace("=", ":"))
pairs = []
if len(filter_string_list) == 1:
filter_string_list.replace(" ", "%20")
pairs = filter_string_list.split("=")
else:
for filterString in filter_string_list:
pairs = pairs + [fq.replace(" ", "%20").split("=") for fq in filterString]
url = url + "&".join(["fq=%s:%s" % (k, v) for (k, v) in pairs])
req = Request(url)
response = urlopen(req)
validate_response_code(response)
total_pages = json.loads(response.read().decode("utf-8"))['page']['totalPages']
num_neuron_pages = get_neuron_pages(num_neurons, total_pages)
count = 0
for page in range(0, num_neuron_pages):
url = url + "&size=%i&page=%i" % (num_neurons, page)
req = Request(url)
response = urlopen(req)
neurons = json.loads(response.read().decode("utf-8"))
num_neurons = len(neurons['_embedded']['neuronResources'])
count = 0
for neuron in range(0, num_neurons):
# get each file
if index == -1: get_swc_by_neuron_name(neurons['_embedded']['neuronResources'][neuron]['neuron_name'])
# get only file with index in this html view
if neuron - count == index:
get_swc_by_neuron_name(neurons['_embedded']['neuronResources'][neuron]['neuron_name'])
return neurons['_embedded']['neuronResources'][neuron]['neuron_name']
# increase count here
count = neuron + num_neurons
def get_swc_by_filter_rule_for_search_term_by_index(filterStringList, searchTerm, index):
"""Downloads the neuron by index which matches filter criteria and search term
Keyword arguments:
filterStringList -- the filter string as key value pairs
searchTerm -- the search term
index -- index of neuron of interest
"""
get_swc_by_filter_rule_for_search_term(filterStringList, searchTerm, -1, index)
def get_swc_by_neuron_index(neuronIndex):
"""Download a neuron by index and store it into a SWC file
Keyword arguments:
neronIndex -- the neuron index in the database
"""
if not check_api_health(): return
url = "%s/api/neuron/id/%i" % (NEUROMORPHO_URL, neuronIndex)
req = Request(url)
response = urlopen(req)
validate_response_code(response)
neuron_name = json.loads(response.read().decode("utf-8"))['neuron_name']
url = "%s/neuron_info.jsp?neuron_name=%s" % (NEUROMORPHO_URL, neuron_name)
html = urlopen(url).read().decode("utf-8")
p = re.compile(r'<a href=dableFiles/(.*)>Morphology File \(Standardized\)</a>', re.MULTILINE)
m = re.findall(p, html)
for match in m:
file_name = match.replace("%20", " ").split("/")[-1]
response = urlopen("%s/dableFiles/%s" % (NEUROMORPHO_URL, match))
with open(file_name, 'w') as f:
f.write(response.read().decode('utf-8'))
def get_swc_by_neuron_name(neuron_name):
"""Download the SWC file specified by the neuron's name
Keyword arguments:
neuron_name-- the neuron index in the database
"""
if not check_api_health(): return
url = "%s/neuron_info.jsp?neuron_name=%s" % (NEUROMORPHO_URL, neuron_name)
html = urlopen(url).read().decode("utf-8")
p = re.compile(r'<a href=dableFiles/(.*)>Morphology File \(Standardized\)</a>', re.MULTILINE)
m = re.findall(p, html)
file_name = None
for match in m:
file_name = match.replace("%20", " ").split("/")[-1]
response = urlopen("%s/dableFiles/%s" % (NEUROMORPHO_URL, match))
with open(file_name, 'w') as f:
f.write(response.read().decode('utf-8'))
# check for file name presence in database
if not file_name:
print("Neuron with name %s not found in NeuroMorpho.org database." % neuron_name)
return
return file_name
def get_swc_by_brain_region(brain_region, num_neurons=-1):
"""Download a specific number of SWC files specified by a region name
Keyword arguments:
brain_region -- the brain region
num_neurons -- how many neurons to retrieved (-1 means all neurons)
Note: Brain regions usually start in lowercase
"""
# check for API health
if not check_api_health():
return
# check if brain region found
if not brain_region[0].islower():
print("Warning: brain region does not start with lower case letter")
return
num_neurons = get_num_neurons(num_neurons)
url = "%s/api/neuron/select?q=brain_region:%s&size=%i" % (NEUROMORPHO_URL, brain_region, num_neurons)
req = Request(url)
response = urlopen(req)
validate_response_code(response)
total_pages = json.loads(response.read().decode("utf-8"))['page']['totalPages']
num_neuron_pages = get_neuron_pages(num_neurons, total_pages)
for page in range(0, num_neuron_pages):
url = "%s/api/neuron/select?q=brain_region:%s&size=%i&page=%i" % (
NEUROMORPHO_URL, brain_region, num_neurons, page)
req = Request(url)
response = urlopen(req)
neurons = json.loads(response.read().decode("utf-8"))
num_neurons = len(neurons['_embedded']['neuronResources'])
for neuron in range(0, num_neurons):
get_swc_by_neuron_name(neurons['_embedded']['neuronResources'][neuron]['neuron_name'])
def get_swc_by_archive_name(archive_name, num_neurons=-1):
"""Download a specific number of SWC files specified by an archive name
Keyword arguments:
archive_name -- the brain region
num_neurons -- how many neurons to retrieve (-1 means all neurons)
Note: Archive names usually start in uppercase
"""
# check for API health
if not check_api_health():
return
# check for archive name in database
if not archive_name[0].isupper():
print("Warning: archive name does not start with upper case letter")
return
num_neurons = get_num_neurons(num_neurons)
url = "%s/api/neuron/select?q=archive:%s&size=%i" % (NEUROMORPHO_URL, archive_name, num_neurons)
req = Request(url)
response = urlopen(req)
validate_response_code(response)
total_pages = json.loads(response.read().decode("utf-8"))['page']['totalPages']
num_neuron_pages = get_neuron_pages(num_neurons, total_pages)
for page in range(0, num_neuron_pages):
url = "%s/api/neuron/select?q=archive:%s&size=%i&page=%i" % (NEUROMORPHO_URL, archive_name, num_neurons, page)
req = Request(url)
response = urlopen(req)
neurons = json.loads(response.read().decode("utf-8"))
num_neurons = len(neurons['_embedded']['neuronResources'])
for neuron in range(0, num_neurons):
get_swc_by_neuron_name(neurons['_embedded']['neuronResources'][neuron]['neuron_name'])Functions
def check_api_health()-
Checks if the REST API is available
Returns true if API is available or false otherwise
Expand source code
def check_api_health(): """Checks if the REST API is available Returns true if API is available or false otherwise """ url = "http://neuromorpho.org/api/health" req = Request(url) try: response = urlopen(req) if json.loads(response.read().decode('utf-8'))['status'] != "UP": print("REST API not available.") else: return True except URLError: print(""" No network connectivity. A working internet connection is required. Check with ISP and/or your local network infrastructure for failure. """) return False def get_neuron_pages(num_neurons, total_pages)-
Get the number of neuron pages. API handles up to 500 neurons per page. If more neurons than supported by the NeuroMorpho API (> 500), then multiple pages need to be retrieved, otherwise one page is retrieved.
Keyword arguments: num_neurons – number of neurons total_pages – number of pages available when using numNeurons per page
Expand source code
def get_neuron_pages(num_neurons, total_pages): """ Get the number of neuron pages. API handles up to 500 neurons per page. If more neurons than supported by the NeuroMorpho API (> 500), then multiple pages need to be retrieved, otherwise one page is retrieved. Keyword arguments: num_neurons -- number of neurons total_pages -- number of pages available when using numNeurons per page """ return min(total_pages, num_neurons / MAX_NEURONS_PER_PAGE if num_neurons > MAX_NEURONS_PER_PAGE else 1) def get_num_neurons(num_neurons)-
Get number of neurons. API can handle only up to 500 neurons per page
Keyword arguments: num_neurons – number of neurons
Expand source code
def get_num_neurons(num_neurons): """Get number of neurons. API can handle only up to 500 neurons per page Keyword arguments: num_neurons -- number of neurons """ return num_neurons if (num_neurons != -1 and num_neurons < MAX_NEURONS_PER_PAGE) else MAX_NEURONS_PER_PAGE def get_swc_by_archive_name(archive_name, num_neurons=-1)-
Download a specific number of SWC files specified by an archive name
Keyword arguments: archive_name – the brain region num_neurons – how many neurons to retrieve (-1 means all neurons) Note: Archive names usually start in uppercase
Expand source code
def get_swc_by_archive_name(archive_name, num_neurons=-1): """Download a specific number of SWC files specified by an archive name Keyword arguments: archive_name -- the brain region num_neurons -- how many neurons to retrieve (-1 means all neurons) Note: Archive names usually start in uppercase """ # check for API health if not check_api_health(): return # check for archive name in database if not archive_name[0].isupper(): print("Warning: archive name does not start with upper case letter") return num_neurons = get_num_neurons(num_neurons) url = "%s/api/neuron/select?q=archive:%s&size=%i" % (NEUROMORPHO_URL, archive_name, num_neurons) req = Request(url) response = urlopen(req) validate_response_code(response) total_pages = json.loads(response.read().decode("utf-8"))['page']['totalPages'] num_neuron_pages = get_neuron_pages(num_neurons, total_pages) for page in range(0, num_neuron_pages): url = "%s/api/neuron/select?q=archive:%s&size=%i&page=%i" % (NEUROMORPHO_URL, archive_name, num_neurons, page) req = Request(url) response = urlopen(req) neurons = json.loads(response.read().decode("utf-8")) num_neurons = len(neurons['_embedded']['neuronResources']) for neuron in range(0, num_neurons): get_swc_by_neuron_name(neurons['_embedded']['neuronResources'][neuron]['neuron_name']) def get_swc_by_brain_region(brain_region, num_neurons=-1)-
Download a specific number of SWC files specified by a region name
Keyword arguments: brain_region – the brain region num_neurons – how many neurons to retrieved (-1 means all neurons)
Note: Brain regions usually start in lowercase
Expand source code
def get_swc_by_brain_region(brain_region, num_neurons=-1): """Download a specific number of SWC files specified by a region name Keyword arguments: brain_region -- the brain region num_neurons -- how many neurons to retrieved (-1 means all neurons) Note: Brain regions usually start in lowercase """ # check for API health if not check_api_health(): return # check if brain region found if not brain_region[0].islower(): print("Warning: brain region does not start with lower case letter") return num_neurons = get_num_neurons(num_neurons) url = "%s/api/neuron/select?q=brain_region:%s&size=%i" % (NEUROMORPHO_URL, brain_region, num_neurons) req = Request(url) response = urlopen(req) validate_response_code(response) total_pages = json.loads(response.read().decode("utf-8"))['page']['totalPages'] num_neuron_pages = get_neuron_pages(num_neurons, total_pages) for page in range(0, num_neuron_pages): url = "%s/api/neuron/select?q=brain_region:%s&size=%i&page=%i" % ( NEUROMORPHO_URL, brain_region, num_neurons, page) req = Request(url) response = urlopen(req) neurons = json.loads(response.read().decode("utf-8")) num_neurons = len(neurons['_embedded']['neuronResources']) for neuron in range(0, num_neurons): get_swc_by_neuron_name(neurons['_embedded']['neuronResources'][neuron]['neuron_name']) def get_swc_by_filter_rule_for_search_term(filter_string_list, search_term, num_neurons, index=-1)-
Downloads n neurons by filterString and stores as SWC files
Keyword arguments: filter_string_list – the filter string as key value pairs search_term– the search term num_neurons – number of neurons
Expand source code
def get_swc_by_filter_rule_for_search_term(filter_string_list, search_term, num_neurons, index=-1): """Downloads n neurons by filterString and stores as SWC files Keyword arguments: filter_string_list -- the filter string as key value pairs search_term-- the search term num_neurons -- number of neurons """ if not check_api_health(): return url = "%s/api/neuron/select?q=%s&" % (NEUROMORPHO_URL, search_term.replace("=", ":")) pairs = [] if len(filter_string_list) == 1: filter_string_list.replace(" ", "%20") pairs = filter_string_list.split("=") else: for filterString in filter_string_list: pairs = pairs + [fq.replace(" ", "%20").split("=") for fq in filterString] url = url + "&".join(["fq=%s:%s" % (k, v) for (k, v) in pairs]) req = Request(url) response = urlopen(req) validate_response_code(response) total_pages = json.loads(response.read().decode("utf-8"))['page']['totalPages'] num_neuron_pages = get_neuron_pages(num_neurons, total_pages) count = 0 for page in range(0, num_neuron_pages): url = url + "&size=%i&page=%i" % (num_neurons, page) req = Request(url) response = urlopen(req) neurons = json.loads(response.read().decode("utf-8")) num_neurons = len(neurons['_embedded']['neuronResources']) count = 0 for neuron in range(0, num_neurons): # get each file if index == -1: get_swc_by_neuron_name(neurons['_embedded']['neuronResources'][neuron]['neuron_name']) # get only file with index in this html view if neuron - count == index: get_swc_by_neuron_name(neurons['_embedded']['neuronResources'][neuron]['neuron_name']) return neurons['_embedded']['neuronResources'][neuron]['neuron_name'] # increase count here count = neuron + num_neurons def get_swc_by_filter_rule_for_search_term_by_index(filterStringList, searchTerm, index)-
Downloads the neuron by index which matches filter criteria and search term
Keyword arguments: filterStringList – the filter string as key value pairs searchTerm – the search term index – index of neuron of interest
Expand source code
def get_swc_by_filter_rule_for_search_term_by_index(filterStringList, searchTerm, index): """Downloads the neuron by index which matches filter criteria and search term Keyword arguments: filterStringList -- the filter string as key value pairs searchTerm -- the search term index -- index of neuron of interest """ get_swc_by_filter_rule_for_search_term(filterStringList, searchTerm, -1, index) def get_swc_by_neuron_index(neuronIndex)-
Download a neuron by index and store it into a SWC file
Keyword arguments: neronIndex – the neuron index in the database
Expand source code
def get_swc_by_neuron_index(neuronIndex): """Download a neuron by index and store it into a SWC file Keyword arguments: neronIndex -- the neuron index in the database """ if not check_api_health(): return url = "%s/api/neuron/id/%i" % (NEUROMORPHO_URL, neuronIndex) req = Request(url) response = urlopen(req) validate_response_code(response) neuron_name = json.loads(response.read().decode("utf-8"))['neuron_name'] url = "%s/neuron_info.jsp?neuron_name=%s" % (NEUROMORPHO_URL, neuron_name) html = urlopen(url).read().decode("utf-8") p = re.compile(r'<a href=dableFiles/(.*)>Morphology File \(Standardized\)</a>', re.MULTILINE) m = re.findall(p, html) for match in m: file_name = match.replace("%20", " ").split("/")[-1] response = urlopen("%s/dableFiles/%s" % (NEUROMORPHO_URL, match)) with open(file_name, 'w') as f: f.write(response.read().decode('utf-8')) def get_swc_by_neuron_name(neuron_name)-
Download the SWC file specified by the neuron's name
Keyword arguments: neuron_name– the neuron index in the database
Expand source code
def get_swc_by_neuron_name(neuron_name): """Download the SWC file specified by the neuron's name Keyword arguments: neuron_name-- the neuron index in the database """ if not check_api_health(): return url = "%s/neuron_info.jsp?neuron_name=%s" % (NEUROMORPHO_URL, neuron_name) html = urlopen(url).read().decode("utf-8") p = re.compile(r'<a href=dableFiles/(.*)>Morphology File \(Standardized\)</a>', re.MULTILINE) m = re.findall(p, html) file_name = None for match in m: file_name = match.replace("%20", " ").split("/")[-1] response = urlopen("%s/dableFiles/%s" % (NEUROMORPHO_URL, match)) with open(file_name, 'w') as f: f.write(response.read().decode('utf-8')) # check for file name presence in database if not file_name: print("Neuron with name %s not found in NeuroMorpho.org database." % neuron_name) return return file_name def validate_response_code(response)-
Checks response code from JSON request and print warning then exits Keyword arguments: response – response of the issued JSON request
Expand source code
def validate_response_code(response): """Checks response code from JSON request and print warning then exits Keyword arguments: response -- response of the issued JSON request """ code = response.getcode() # success if code == 200: return # error codes if code == 400: print("Bad request, usually wrong parameters to select queries.") elif code == 404: print("Resource not found or does not exist") elif code == 405: print("Unsupported HTTP method used (No GET or POST request).") elif code == 500: print("Internal Server Error. Contact admin for assistance.") sys.exit()