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search.py
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search.py
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import os
import time
import json
import requests
from oti_search import OTISearch
from ConfigParser import SafeConfigParser
import urllib2
import sys
import traceback
import api_utils
# logger for indexing failures
_LOG = api_utils.get_logger(request, 'ot_api.default.v1')
def check_not_read_only():
if api_utils.READ_ONLY_MODE:
raise HTTP(403, json.dumps({"error": 1, "description": "phylesystem-api running in read-only mode"}))
return True
@request.restful()
def v1():
"The OpenTree API v1"
response.view = 'generic.json'
oti_base_url = api_utils.get_oti_base_url(request) # WAS conf.get("apis", "oti_base_url")
oti = OTISearch(oti_base_url)
def GET(kind, property_name, search_term,jsoncallback=None,callback=None,_=None,**kwargs):
""""OpenTree API methods relating to searching
Example:
http://localhost:8000/api/search/v1/tree/ot-ottTaxonName/Carex
http://localhost:8000/api/search/v1/node/ot-ottId/1000455
When searching for a property name ot:foo, ot-foo must be used
because web2py does not recognize URLs that contain a colon
other than specifying a port, even if URL encoded.
"""
opentree_docstore_url = _read_from_local_config(request, "apis", "opentree_docstore_url")
# support JSONP request from another domain
if jsoncallback or callback:
response.view = 'generic.jsonp'
# colons don't play nicely with GET requests
property_name = property_name.replace("-",":")
valid_kinds = ["study", "tree", "node"]
if kind in valid_kinds:
return oti.do_search(kind, property_name, search_term)
else:
raise HTTP(400,json.dumps({"error":1, "description":"not a valid property name"}))
return locals()
def nudgeStudyIndexOnUpdates():
""""Support method to update oti index in response to GitHub webhooks
This examines the JSON payload of a GitHub webhook to see which studies have
been added, modified, or removed. Then it calls oti's index service to
(re)index the NexSON for those studies, or to delete a study's information if
it was deleted from the docstore.
Finally, we clear the cached study list (response to find_studies with no args).
N.B. This depends on a GitHub webhook on the chosen docstore.
"""
if not check_not_read_only():
raise HTTP(500, "should raise from check_not_read_only")
opentree_docstore_url = _read_from_local_config(request, "apis", "opentree_docstore_url")
payload = request.vars
# get list of study ids to be added / modified / removed
try:
# how we nudge the index depends on which studies are new, changed, or deleted
added_study_ids = [ ]
modified_study_ids = [ ]
removed_study_ids = [ ]
# TODO: Should any of these lists override another? maybe use commit timestamps to "trump" based on later operations?
for commit in payload['commits']:
_harvest_study_ids_from_paths( commit['added'], added_study_ids )
_harvest_study_ids_from_paths( commit['modified'], modified_study_ids )
_harvest_study_ids_from_paths( commit['removed'], removed_study_ids )
# add and update treated the same, so merge
# also "flatten" each list to remove duplicates
add_or_update_ids = added_study_ids + modified_study_ids
add_or_update_ids = list(set(add_or_update_ids))
remove_ids = list(set(removed_study_ids))
except:
raise HTTP(400,json.dumps({"error":1, "description":"malformed GitHub payload"}))
if payload['repository']['url'] != opentree_docstore_url:
raise HTTP(400,json.dumps({"error":1, "description":"wrong repo for this API instance"}))
# get index URLs from config
otindex_base_url = api_utils.get_otindex_base_url(request)
# nexson_url_template only needed for oti method, not otindex
nexson_url_template = URL(r=request,
c="default",
f="v1",
args=["study", "%s"],
vars={'output_nexml2json': '0.0.0'},
scheme=True,
host=True,
url_encode=False)
# call both the oti and otindex methods
msg = ''
if len(add_or_update_ids) > 0:
# oti call
_otindex_add_update_studies( add_or_update_ids, otindex_base_url )
if len(remove_ids) > 0:
# oti call
# otindex call
_otindex_remove_studies( remove_ids, otindex_base_url )
# TODO: check returned IDs against our original list... what if something failed?
# Clear any cached study lists (both verbose and non-verbose)
api_utils.clear_matching_cache_keys(".*find_studies.*")
github_webhook_url = "%s/settings/hooks" % opentree_docstore_url
full_msg = """This URL should be called by a webhook set in the docstore repo:
<br /><br />
<a href="%s">%s</a><br />
<pre>%s</pre>
""" % (github_webhook_url, github_webhook_url, msg,)
if msg == '':
return full_msg
else:
raise HTTP(500, full_msg)
def _otindex_add_update_studies(add_or_update_ids, otindex_base_url):
if not check_not_read_only():
raise HTTP(500, "should raise from check_not_read_only")
nudge_url = "{o}/v3/studies/add_update".format(o=otindex_base_url)
# can call otindex with list of either github urls or study ids
payload = { "studies" : add_or_update_ids }
headers={"Content-Type": "application/json"}
resp = requests.post(nudge_url,
headers=headers,
data=json.dumps(payload),
allow_redirects=True)
msg = ''
try:
response = resp.json()
if len(response['failed_studies']) > 0:
f = response['failed_studies']
_LOG.warn("Could not update following studies: {s}".format(s=f))
except Exception as e:
msg = json.dumps({"description": "Unexpected error calling otindex: {}".format(e.message)})
return msg
def _otindex_remove_studies(remove_ids, otindex_base_url):
if not check_not_read_only():
raise HTTP(500, "should raise from check_not_read_only")
nudge_url = "{o}/v3/studies/remove".format(o=otindex_base_url)
# can call otindex with list of either github urls or study ids
payload = { "studies" : remove_ids }
headers={"Content-Type": "application/json"}
resp = requests.post(nudge_url,
headers=headers,
data=json.dumps(payload),
allow_redirects=True)
msg = ''
try:
response = resp.json()
if len(response['failed_studies']) > 0:
f = response['failed_studies']
_LOG.warn("Could not remove the following studies {s}".format(s=f))
except Exception as e:
msg = json.dumps({"description": "Unexpected error calling otindex: {}".format(e.message)})
return msg
def nudgeTaxonIndexOnUpdates():
""""Support method to update taxon index (taxomachine) in response to GitHub webhooks
This examines the JSON payload of a GitHub webhook to see which taxa have
been added, modified, or removed. Then it calls the appropriate index service to
(re)index these taxa, or to delete a taxon's information if it was deleted in
an amendment.
TODO: Clear any cached taxon list.
N.B. This depends on a GitHub webhook on the taxonomic-amendments docstore!
"""
if not check_not_read_only():
raise HTTP(500, "should raise from check_not_read_only")
amendments_repo_url = _read_from_local_config(request, "apis", "amendments_repo_url")
payload = request.vars
if payload['repository']['url'] != amendments_repo_url:
raise HTTP(400,json.dumps({"error":1, "description":"wrong repo for this API instance"}))
msg = ''
try:
# how we nudge the index depends on which taxa are new, changed, or deleted
added_ott_ids = [ ]
modified_ott_ids = [ ]
removed_ott_ids = [ ]
# TODO: Should any of these lists override another? maybe use commit timestamps to "trump" based on later operations?
for commit in payload['commits']:
_harvest_ott_ids_from_paths( commit['added'], added_ott_ids )
_harvest_ott_ids_from_paths( commit['modified'], modified_ott_ids )
_harvest_ott_ids_from_paths( commit['removed'], removed_ott_ids )
# "flatten" each list to remove duplicates
added_ott_ids = list(set(added_ott_ids))
modified_ott_ids = list(set(modified_ott_ids))
removed_ott_ids = list(set(removed_ott_ids))
except:
raise HTTP(400,json.dumps({"error":1, "description":"malformed GitHub payload"}))
# build a working URL, gather amendment body, and nudge the index!
amendments_api_base_url = api_utils.get_amendments_api_base_url(request)
if len(added_ott_ids) > 0:
nudge_url = "{b}v3/taxonomy/process_additions".format(b=amendments_api_base_url)
for ott_id in added_ott_ids:
# fetch the JSON body of each new amendment and submit it for indexing
fetch_url = "{b}v3/amendment/{i}".format(b=amendments_api_base_url, i=ott_id)
fetch_response = None
req = urllib2.Request(
url=fetch_url
)
try:
fetch_response = urllib2.urlopen(req).read()
# strip away metadata (version history, etc.)
amendment_blob = json.loads( fetch_response ).get('data')
except Exception, e:
# bail and report the error in webhook response
exc_type, exc_value, exc_traceback = sys.exc_info()
msg += """fetch of amendment failed!'
fetch_url: %s
fetch_response: %s
ott_id: %s
%s""" % (fetch_url, fetch_response, ott_id, traceback.format_exception(exc_type, exc_value, exc_traceback),)
break
# Extra weirdness required here, as neo4j needs an encoded *string*
# of the amendment JSON, within a second JSON wrapper :-/
POST_blob = {"addition_document": json.dumps(amendment_blob) }
POST_string = json.dumps(POST_blob)
nudge_response = None
req = urllib2.Request(
url=nudge_url,
data=POST_string,
headers={"Content-Type": "application/json"}
)
try:
# N.B. we don't expect anything interesting here, probably just an empty dict
nudge_response = urllib2.urlopen(req).read()
except Exception, e:
# report the error in webhook response
exc_type, exc_value, exc_traceback = sys.exc_info()
msg += """index amendments failed!'
nudge_url: %s
POST_data: %s
fetch_response: %s
nudge_response: %s
added_ott_ids: %s
%s""" % (nudge_url, POST_data, fetch_response, nudge_response, added_ott_ids, traceback.format_exception(exc_type, exc_value, exc_traceback),)
# LATER: add handlers for modified and removed taxa?
if len(modified_ott_ids) > 0:
raise HTTP(400,json.dumps({
"error":1,
"description":"We don't currently re-index modified taxa!"}))
if len(removed_ott_ids) > 0:
raise HTTP(400,json.dumps({
"error":1,
"description":"We don't currently re-index removed taxa!"}))
# N.B. If we had any cached amendment results, we'd clear them now
#api_utils.clear_matching_cache_keys(...)
github_webhook_url = "%s/settings/hooks" % amendments_repo_url
full_msg = """This URL should be called by a webhook set in the amendments repo:
<br /><br />
<a href="%s">%s</a><br />
<pre>%s</pre>
""" % (github_webhook_url, github_webhook_url, msg,)
if msg == '':
return full_msg
else:
raise HTTP(500, full_msg)
def _read_from_local_config(request, section_name, key_name):
app_name = request.application
conf = SafeConfigParser(allow_no_value=True)
if os.path.isfile("%s/applications/%s/private/localconfig" % (os.path.abspath('.'), app_name,)):
conf.read("%s/applications/%s/private/localconfig" % (os.path.abspath('.'), app_name,))
else:
conf.read("%s/applications/%s/private/config" % (os.path.abspath('.'), app_name,))
return conf.get(section_name, key_name)
def _harvest_study_ids_from_paths( path_list, target_array ):
for path in path_list:
path_parts = path.split('/')
if path_parts[0] == "study":
# skip any intermediate directories in docstore repo
study_id = path_parts[ len(path_parts) - 2 ]
target_array.append(study_id)
def _harvest_ott_ids_from_paths( path_list, target_array ):
for path in path_list:
path_parts = path.split('/')
# ignore changes to counter file, other directories, etc.
if path_parts[0] == "amendments":
# skip intermediate directories in docstore repo
amendment_file_name = path_parts.pop()
ott_id = amendment_file_name[:-5]
target_array.append(ott_id)