def edit():
#return dict(message="study/edit")
chosenLayout = request.vars.get('layout', None) # TOP, LEFT, RIGHT
if chosenLayout:
response.view = 'study/edit-%s.html' % chosenLayout #e eg, 'study/edit-RIGHT.html'
# TODO: fetch a fresh list of search contexts for TNRS? see working example in
# the header search of the main opentree webapp
view_dict = get_opentree_services_method_urls(request)
view_dict = get_opentree_services_method_urls(request)
return view_dict
def fetch_current_synthetic_tree_ids():
try:
# fetch the latest IDs as JSON from remote site
import simplejson
method_dict = get_opentree_services_method_urls(request)
fetch_url = method_dict['getDraftTreeID_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
fetch_args = {}
# this needs to be a POST (pass fetch_args or ''); if GET, it just describes the API
# N.B. that gluon.tools.fetch() can't be used here, since it won't send "raw" JSON data as treemachine expects
req = urllib2.Request(url=fetch_url,
data=simplejson.dumps(fetch_args),
headers={"Content-Type": "application/json"})
ids_response = urllib2.urlopen(req).read()
ids_json = simplejson.loads(ids_response)
draftTreeName = str(ids_json['synth_id']).encode('utf-8')
startNodeID = str(ids_json['root']['node_id']).encode('utf-8')
return (draftTreeName, startNodeID)
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message)
def fetch_current_synthetic_tree_ids():
try:
# fetch the latest IDs as JSON from remote site
import json
import requests
method_dict = get_opentree_services_method_urls(request)
fetch_url = method_dict['getDraftTreeID_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
fetch_args = {}
# this needs to be a POST (pass fetch_args or ''); if GET, it just describes the API
ids_json = requests.post(url=fetch_url,
data=json.dumps(fetch_args),
headers={
"Content-Type": "application/json"
}).json()
draftTreeName = str(ids_json['synth_id']).encode('utf-8')
startNodeID = str(ids_json['root']['node_id']).encode('utf-8')
return (draftTreeName, startNodeID)
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message)
def fetch_current_synthetic_tree_ids():
try:
# fetch the latest IDs as JSON from remote site
import simplejson
method_dict = get_opentree_services_method_urls(request)
fetch_url = method_dict['getDraftTreeID_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "http:%s" % fetch_url
fetch_args = {'startingTaxonOTTId': ""}
# this needs to be a POST (pass fetch_args or ''); if GET, it just describes the API
# N.B. that gluon.tools.fetch() can't be used here, since it won't send "raw" JSON data as treemachine expects
req = urllib2.Request(url=fetch_url, data=simplejson.dumps(fetch_args), headers={"Content-Type": "application/json"})
ids_response = urllib2.urlopen(req).read()
ids_json = simplejson.loads( ids_response )
draftTreeName = str(ids_json['draftTreeName']).encode('utf-8')
# Try to be compatible with different versions of treemachine
startNodeID = None
if 'startingNodeID' in ids_json:
startNodeID = str(ids_json['startingNodeID']).encode('utf-8')
elif 'startNodeID' in ids_json:
startNodeID = str(ids_json['startNodeID']).encode('utf-8')
return (draftTreeName, startNodeID)
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message)
def fetch_current_TNRS_context_names():
try:
# fetch the latest contextName values as JSON from remote site
from gluon.tools import fetch
import simplejson
method_dict = get_opentree_services_method_urls(request)
fetch_url = method_dict['getContextsJSON_url']
# as usual, this needs to be a POST (pass empty fetch_args)
contextnames_response = fetch(fetch_url, data='')
contextnames_json = simplejson.loads( contextnames_response )
# start with LIFE group (incl. 'All life'), and add any other ordered suggestions
ordered_group_names = unique_ordered_list(['LIFE','PLANTS','ANIMALS'] + [g for g in contextnames_json])
context_names = [ ]
for gname in ordered_group_names:
# allow for eventual removal or renaming of expected groups
if gname in contextnames_json:
context_names += [n.encode('utf-8') for n in contextnames_json[gname] ]
# draftTreeName = ids_json['draftTreeName'].encode('utf-8')
return (context_names)
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message)
def view():
"""
Allow any visitor to view (read-only!) a study on the 'master' branch
? OR can this include work-in-progress from a personal branch?
"""
response.view = 'study/edit.html'
view_dict = get_opentree_services_method_urls(request)
view_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names()
return view_dict
def index():
# interpret incoming URL as a tree view, in this format
# http://[hostname]/opentree/[{viewer}/]{domSource}@{nodeID}/{taxon name}
# some valid examples:
# http://opentree.com/opentree/argus/ottol@123456/H**o+sapiens
# http://opentree.com/opentree/ottol@123456/H**o+sapiens
# http://opentree.com/opentree/ottol@123456
#
# TODO: add another optional arg 'viewport', like so
# http://opentree.com/opentree/argus/0,23,100,400/ottol@123456/H**o+sapiens
# modify the normal view dictionary to include location+view hints from the URL
treeview_dict = get_opentree_services_method_urls(request)
treeview_dict['viewer'] = 'argus'
treeview_dict['domSource'] = ''
treeview_dict['nodeID'] = ''
treeview_dict['nodeName'] = ''
treeview_dict['viewport'] = ''
# add a flag to determine whether to force the viewer to this node (vs. using the
# browser's stored state for this URL, or a default starting node)
treeview_dict['forcedByURL'] = False
# handle the first arg (path part) found
if len(request.args) > 0:
if request.args[0] in ['argus','onezoom','phylet']:
treeview_dict['viewer'] = request.args[0]
elif '@' in request.args[0]:
treeview_dict['domSource'], treeview_dict['nodeID'] = request.args[0].split('@')
else:
# first arg is neither a viewer nor a proper node, which is a Bad Thing
raise HTTP(404)
if len(request.args) > 1:
if not treeview_dict['nodeID']:
#if (not treeview_dict['nodeID']) and '@' in request.args[1]:
treeview_dict['domSource'], treeview_dict['nodeID'] = request.args[1].split('@')
else:
treeview_dict['nodeName'] = request.args[1]
if len(request.args) > 2:
if not treeview_dict['nodeName']:
treeview_dict['nodeName'] = request.args[2]
# when all is said and done, do we have enough information to force the location?
if treeview_dict['domSource'] and treeview_dict['nodeID']:
treeview_dict['forcedByURL'] = True
# retrieve latest synthetic-tree ID (and its 'life' node ID)
# TODO: Only refresh this periodically? Or only when needed for initial destination?
treeview_dict['draftTreeName'], treeview_dict['lifeNodeID'], treeview_dict['startingNodeID'] = fetch_current_synthetic_tree_ids()
treeview_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names()
return treeview_dict
def download_subtree():
id_type = request.args(0) # 'ottol-id' or 'node-id'
node_or_ottol_id = request.args(1)
node_name = request.args(2)
import cStringIO
import contenttype as c
s = cStringIO.StringIO()
try:
# fetch the Newick tree as JSON from remote site
import requests
import json
json_headers = {
'content-type': 'application/json',
'accept': 'application/json',
}
method_dict = get_opentree_services_method_urls(request)
# use the appropriate web service for this ID type
fetch_url = method_dict['getDraftSubtree_url']
newick_text = 'NEWICK_NOT_FETCHED'
if id_type == 'ottol-id':
fetch_args = {'ott_id': int(node_or_ottol_id)}
else:
fetch_args = {'node_id': node_or_ottol_id}
fetch_args['format'] = 'newick'
fetch_args['height_limit'] = -1
# TODO: allow for dynamic height, based on max tips?
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
# apparently this needs to be a POST, or it just describes the API
tree_response = requests.post(fetch_url,
data=json.dumps(fetch_args),
headers=json_headers)
tree_json = tree_response.json()
newick_text = unicode(tree_json.get(
'newick', u'NEWICK_NOT_FOUND')).encode('utf-8')
s.write(newick_text)
except Exception, e:
# throw 403 or 500 or just leave it
if id_type == 'ottol-id':
s.write(
u'ERROR - Unable to fetch the Newick subtree for ottol id "%s" (%s):\n\n%s'
% (node_or_ottol_id, node_name, newick_text))
else:
s.write(
u'ERROR - Unable to fetch the Newick subtree for node id "%s" (%s):\n\n%s'
% (node_or_ottol_id, node_name, newick_text))
def download_subtree():
id_type = request.args(0) # 'ottol-id' or 'node-id'
node_or_ottol_id = request.args(1)
max_depth = request.args(2)
node_name = request.args(3)
import cStringIO
import contenttype as c
s = cStringIO.StringIO()
try:
# fetch the Newick tree as JSON from remote site
from gluon.tools import fetch
import simplejson
method_dict = get_opentree_services_method_urls(request)
# use the appropriate web service for this ID type
if id_type == 'ottol-id':
fetch_url = method_dict['getDraftTreeForOttolID_url']
fetch_args = {'ottId': node_or_ottol_id, 'maxDepth': max_depth}
else:
fetch_url = method_dict['getDraftTreeForNodeID_url']
fetch_args = {'nodeID': node_or_ottol_id, 'maxDepth': max_depth}
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "http:%s" % fetch_url
# apparently this needs to be a POST, or it just describes the API
tree_response = fetch(fetch_url, data=fetch_args)
tree_json = simplejson.loads(tree_response)
newick_text = str(tree_json['tree']).encode('utf-8')
s.write(newick_text)
except Exception, e:
# throw 403 or 500 or just leave it
if id_type == 'ottol-id':
s.write(
u'ERROR - Unable to fetch the Newick subtree for ottol id "%s" (%s) with max depth %s:\n\n%s'
% (node_or_ottol_id, node_name, max_depth, newick_text))
else:
s.write(
u'ERROR - Unable to fetch the Newick subtree for node id "%s" (%s) with max depth %s:\n\n%s'
% (node_or_ottol_id, node_name, max_depth, newick_text))
def download_subtree():
id_type = request.args(0) # 'ottol-id' or 'node-id'
node_or_ottol_id = request.args(1)
node_name = request.args(2)
import cStringIO
import contenttype as c
s=cStringIO.StringIO()
try:
# fetch the Newick tree as JSON from remote site
from gluon.tools import fetch
import simplejson
method_dict = get_opentree_services_method_urls(request)
# use the appropriate web service for this ID type
fetch_url = method_dict['getDraftSubtree_url']
newick_text = 'NEWICK_NOT_FETCHED'
if id_type == 'ottol-id':
fetch_args = {'ott_id': int(node_or_ottol_id)}
else:
fetch_args = {'node_id': node_or_ottol_id}
fetch_args['format'] = 'newick';
fetch_args['height_limit'] = -1; # TODO: allow for dynamic height, based on max tips?
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
# apparently this needs to be a POST, or it just describes the API
tree_response = fetch(fetch_url, data=fetch_args)
tree_json = simplejson.loads( tree_response )
newick_text = str(tree_json.get('newick', 'NEWICK_NOT_FOUND')).encode('utf-8');
s.write( newick_text )
except Exception, e:
# throw 403 or 500 or just leave it
if id_type == 'ottol-id':
s.write( u'ERROR - Unable to fetch the Newick subtree for ottol id "%s" (%s):\n\n%s' % (node_or_ottol_id, node_name, newick_text) )
else:
s.write( u'ERROR - Unable to fetch the Newick subtree for node id "%s" (%s):\n\n%s' % (node_or_ottol_id, node_name, newick_text) )
def download_subtree():
id_type = request.args(0) # 'ottol-id' or 'node-id'
node_or_ottol_id = request.args(1)
max_depth = request.args(2)
node_name = request.args(3)
import cStringIO
import contenttype as c
s=cStringIO.StringIO()
try:
# fetch the Newick tree as JSON from remote site
from gluon.tools import fetch
import simplejson
method_dict = get_opentree_services_method_urls(request)
# use the appropriate web service for this ID type
if id_type == 'ottol-id':
fetch_url = method_dict['getDraftTreeForOttolID_url']
fetch_args = {'ottId': node_or_ottol_id, 'maxDepth': max_depth}
else:
fetch_url = method_dict['getDraftTreeForNodeID_url']
fetch_args = {'nodeID': node_or_ottol_id, 'maxDepth': max_depth}
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "http:%s" % fetch_url
# apparently this needs to be a POST, or it just describes the API
tree_response = fetch(fetch_url, data=fetch_args)
tree_json = simplejson.loads( tree_response )
newick_text = str(tree_json['tree']).encode('utf-8');
s.write( newick_text )
except Exception, e:
# throw 403 or 500 or just leave it
if id_type == 'ottol-id':
s.write( u'ERROR - Unable to fetch the Newick subtree for ottol id "%s" (%s) with max depth %s:\n\n%s' % (node_or_ottol_id, node_name, max_depth, newick_text) )
else:
s.write( u'ERROR - Unable to fetch the Newick subtree for node id "%s" (%s) with max depth %s:\n\n%s' % (node_or_ottol_id, node_name, max_depth, newick_text) )
def fetch_current_synthetic_tree_ids():
try:
# fetch the latest IDs as JSON from remote site
from gluon.tools import fetch
import simplejson
method_dict = get_opentree_services_method_urls(request)
fetch_url = method_dict['getDraftTreeID_url']
fetch_args = {'startingTaxonName': "cellular organisms"}
# this needs to be a POST (pass fetch_args or ''); if GET, it just describes the API
ids_response = fetch(fetch_url, data=fetch_args)
ids_json = simplejson.loads( ids_response )
draftTreeName = ids_json['draftTreeName'].encode('utf-8')
lifeNodeID = ids_json['lifeNodeID'].encode('utf-8')
# IF we get a separate starting node ID, use it; else we'll start at 'life'
startingNodeID = ids_json.get('startingNodeID', lifeNodeID).encode('utf-8')
return (draftTreeName, lifeNodeID, startingNodeID)
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message, 'NO_STARTING_NODE_ID')
def fetch_current_synthesis_source_data():
json_headers = {
'content-type' : 'application/json',
'accept' : 'application/json',
}
try:
import requests
import json
method_dict = get_opentree_services_method_urls(request)
# fetch a list of all studies that contribute to synthesis
fetch_url = method_dict['getSynthesisSourceList_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
source_list_response = requests.post(fetch_url, data=json.dumps({'include_source_list':True}), headers=json_headers)
source_data = source_list_response.json()
source_id_list = source_data.get('source_list', [ ])
source_id_map = source_data.get('source_id_map')
# split these source descriptions, which are in the form '{STUDY_ID_PREFIX}_{STUDY_NUMERIC_ID}_{TREE_ID}_{COMMIT_SHA}'
contributing_study_info = { } # store (unique) study IDs as keys, commit SHAs as values
for source_id in source_id_list:
source_details = source_id_map.get( source_id )
if 'taxonomy' in source_details:
continue
study_id = source_details.get('study_id')
# N.B. assume that all study IDs have a two-letter prefix!
tree_id = source_details.get('tree_id')
commit_SHA_in_synthesis = source_details.get('git_sha')
# N.B. assume that any listed study has been used!
if study_id in contributing_study_info.keys():
contributing_study_info[ study_id ]['tree_ids'].append( tree_id )
else:
contributing_study_info[ study_id ] = {
'tree_ids': [ tree_id, ],
'commit_SHA_in_synthesis': commit_SHA_in_synthesis
}
# fetch the oti metadata (esp. DOI and full reference text) for each
fetch_url = method_dict['findAllStudies_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
study_metadata_response = requests.post(fetch_url, data=json.dumps({"verbose": True}), headers=json_headers)
# TODO: add more friendly label to tree metadata? if so, add "includeTreeMetadata":True above
study_metadata = study_metadata_response.json()
# filter just the metadata for studies contributing to synthesis
contributing_studies = [ ]
for study in study_metadata['matched_studies']:
# Add any missing study-ID prefixes (assume 'pg') so we can compare
# with the prefixed IDs provided by getSynthesisSourceList.
id_parts = study['ot:studyId'].split('_')
if len(id_parts) == 1:
prefixed_study_id = 'pg_%s' % study['ot:studyId']
else:
prefixed_study_id = study['ot:studyId']
if prefixed_study_id in contributing_study_info.keys():
contrib_info = contributing_study_info[ prefixed_study_id ]
# and commit SHA to support retrieval of *exact* Nexson from synthesis
study['commit_SHA_in_synthesis'] = contrib_info['commit_SHA_in_synthesis']
# add contributing tree ID(s) so we can directly link to (or download) them
study['tree_ids'] = contrib_info['tree_ids']
contributing_studies.append( study )
# sort these alphabetically by first author, then render in the page
contributing_studies.sort(key = lambda x: x.get('ot:studyPublicationReference'))
# TODO: encode data to utf-8?
## context_names += [n.encode('utf-8') for n in contextnames_json[gname] ]
# translate data-deposit DOIs/URLs into friendlier forms
for study in contributing_studies:
raw_deposit_doi = study.get('ot:dataDeposit', None)
if raw_deposit_doi:
study['friendlyDepositMessage'] = get_data_deposit_message(raw_deposit_doi)
return contributing_studies
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message)
ot_markdown_attributes = bleach.sanitizer.ALLOWED_ATTRIBUTES.copy()
ot_markdown_attributes.update(common_version_notes_attributes)
ot_cleaner = Cleaner(tags=ot_markdown_tags, attributes=ot_markdown_attributes)
### required - do no delete
def user(): return dict(form=auth())
def download(): return response.download(request,db)
def call(): return service()
### end requires
def index():
# bump to first About page in menu
redirect(URL('about', 'open-tree-of-life'))
# try grabbing shared data just once
default_view_dict = get_opentree_services_method_urls(request)
default_view_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
# NOTE that web2py should attempt to convert hyphens (dashes) in URLs into underscores
def open_tree_of_life():
# URL is /opentree/about/open-tree-of-life
return default_view_dict
def the_synthetic_tree():
# URL is /opentree/about/the-synthetic-tree
return default_view_dict
def the_source_tree_manager():
# URL is /opentree/about/the-source-tree-manager
return default_view_dict
def fetch_current_synthesis_source_data():
try:
from gluon.tools import fetch
import simplejson
method_dict = get_opentree_services_method_urls(request)
# fetch a list of all studies that contribute to synthesis
fetch_url = method_dict['getSynthesisSourceList_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "http:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
source_list_response = fetch(fetch_url, data='')
source_list = simplejson.loads( source_list_response )
# split these source descriptions, which are in the form '{STUDY_ID_PREFIX}_{STUDY_NUMERIC_ID}_{TREE_ID}_{COMMIT_SHA}'
contributing_study_info = { } # store (unique) study IDs as keys, commit SHAs as values
for source_desc in source_list:
if source_desc == 'taxonomy':
continue
source_parts = source_desc.split('_')
# add default prefix 'pg' to study ID, if not found
if source_parts[0].isdigit():
# prepend with default namespace 'pg'
study_id = 'pg_%s' % source_parts[0]
else:
study_id = '_'.join(source_parts[0:2])
if len(source_parts) == 4:
tree_id = source_parts[2]
commit_SHA_in_synthesis = source_parts[3]
else:
tree_id = source_parts[1]
if len(source_parts) == 3:
commit_SHA_in_synthesis = source_parts[2]
else:
commit_SHA_in_synthesis = None
if study_id in contributing_study_info.keys():
contributing_study_info[ study_id ]['tree_ids'].append( tree_id )
else:
contributing_study_info[ study_id ] = {
'tree_ids': [ tree_id, ],
'commit_SHA_in_synthesis': commit_SHA_in_synthesis
}
# fetch the oti metadata (esp. DOI and full reference text) for each
fetch_url = method_dict['findAllStudies_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "http:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
study_metadata_response = fetch(fetch_url, data={"verbose": True})
# TODO: add more friendly label to tree metadata? if so, add "includeTreeMetadata":True above
study_metadata = simplejson.loads( study_metadata_response )
# filter just the metadata for studies contributing to synthesis
contributing_studies = [ ]
for study in study_metadata:
# Add any missing study-ID prefixes (assume 'pg') so we can compare
# with the prefixed IDs provided by getSynthesisSourceList.
id_parts = study['ot:studyId'].split('_')
if len(id_parts) == 1:
prefixed_study_id = 'pg_%s' % study['ot:studyId']
else:
prefixed_study_id = study['ot:studyId']
if prefixed_study_id in contributing_study_info.keys():
contrib_info = contributing_study_info[ prefixed_study_id ]
# and commit SHA to support retrieval of *exact* Nexson from synthesis
study['commit_SHA_in_synthesis'] = contrib_info['commit_SHA_in_synthesis']
# add contributing tree ID(s) so we can directly link to (or download) them
study['tree_ids'] = contrib_info['tree_ids']
contributing_studies.append( study )
# sort these alphabetically by first author, then render in the page
contributing_studies.sort(key = lambda x: x.get('ot:studyPublicationReference'))
# TODO: encode data to utf-8?
## context_names += [n.encode('utf-8') for n in contextnames_json[gname] ]
# translate data-deposit DOIs/URLs into friendlier forms
from pprint import pprint
for study in contributing_studies:
raw_deposit_doi = study.get('ot:dataDeposit', None)
if raw_deposit_doi:
study['friendlyDepositMessage'] = get_data_deposit_message(raw_deposit_doi)
return contributing_studies
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message)
def call():
return service()
### end requires
def index():
# bump to first About page in menu
redirect(URL('about', 'open-tree-of-life'))
# try grabbing shared data just once
default_view_dict = get_opentree_services_method_urls(request)
default_view_dict[
'taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
# NOTE that web2py should attempt to convert hyphens (dashes) in URLs into underscores
def open_tree_of_life():
# URL is /opentree/about/open-tree-of-life
return default_view_dict
def privacy_policy():
# URL is /opentree/about/privacy-policy
return default_view_dict
def fetch_current_synthesis_source_data():
json_headers = {
'content-type': 'application/json',
'accept': 'application/json',
}
try:
import requests
import json
method_dict = get_opentree_services_method_urls(request)
# fetch a list of all studies that contribute to synthesis
fetch_url = method_dict['getSynthesisSourceList_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
source_list_response = requests.post(
fetch_url,
data=json.dumps({'include_source_list': True}),
headers=json_headers)
source_data = source_list_response.json()
source_id_list = source_data.get('source_list', [])
source_id_map = source_data.get('source_id_map')
# split these source descriptions, which are in the form '{STUDY_ID_PREFIX}_{STUDY_NUMERIC_ID}_{TREE_ID}_{COMMIT_SHA}'
contributing_study_info = {
} # store (unique) study IDs as keys, commit SHAs as values
for source_id in source_id_list:
source_details = source_id_map.get(source_id)
if 'taxonomy' in source_details:
continue
study_id = source_details.get('study_id')
# N.B. assume that all study IDs have a two-letter prefix!
tree_id = source_details.get('tree_id')
commit_SHA_in_synthesis = source_details.get('git_sha')
# N.B. assume that any listed study has been used!
if study_id in contributing_study_info.keys():
contributing_study_info[study_id]['tree_ids'].append(tree_id)
else:
contributing_study_info[study_id] = {
'tree_ids': [
tree_id,
],
'commit_SHA_in_synthesis': commit_SHA_in_synthesis
}
# fetch the oti metadata (esp. DOI and full reference text) for each
fetch_url = method_dict['findAllStudies_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
study_metadata_response = requests.post(fetch_url,
data=json.dumps(
{"verbose": True}),
headers=json_headers)
# TODO: add more friendly label to tree metadata? if so, add "includeTreeMetadata":True above
study_metadata = study_metadata_response.json()
# filter just the metadata for studies contributing to synthesis
contributing_studies = []
for study in study_metadata['matched_studies']:
# Add any missing study-ID prefixes (assume 'pg') so we can compare
# with the prefixed IDs provided by getSynthesisSourceList.
id_parts = study['ot:studyId'].split('_')
if len(id_parts) == 1:
prefixed_study_id = 'pg_%s' % study['ot:studyId']
else:
prefixed_study_id = study['ot:studyId']
if prefixed_study_id in contributing_study_info.keys():
contrib_info = contributing_study_info[prefixed_study_id]
# and commit SHA to support retrieval of *exact* Nexson from synthesis
study['commit_SHA_in_synthesis'] = contrib_info[
'commit_SHA_in_synthesis']
# add contributing tree ID(s) so we can directly link to (or download) them
study['tree_ids'] = contrib_info['tree_ids']
contributing_studies.append(study)
# sort these alphabetically by first author, then render in the page
contributing_studies.sort(
key=lambda x: x.get('ot:studyPublicationReference'))
# TODO: encode data to utf-8?
## context_names += [n.encode('utf-8') for n in contextnames_json[gname] ]
# translate data-deposit DOIs/URLs into friendlier forms
for study in contributing_studies:
raw_deposit_doi = study.get('ot:dataDeposit', None)
if raw_deposit_doi:
study['friendlyDepositMessage'] = get_data_deposit_message(
raw_deposit_doi)
return contributing_studies
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message)
def fetch_current_synthesis_source_data():
try:
from gluon.tools import fetch
import simplejson
method_dict = get_opentree_services_method_urls(request)
# fetch a list of all studies that contribute to synthesis
fetch_url = method_dict['getSynthesisSourceList_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "http:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
source_list_response = fetch(fetch_url, data='')
source_list = simplejson.loads( source_list_response )
# split these source descriptions, which are in the form '{STUDY_ID_PREFIX}_{STUDY_NUMERIC_ID}_{TREE_ID}_{COMMIT_SHA}'
contributing_study_info = { } # store (unique) study IDs as keys, commit SHAs as values
for source_desc in source_list:
if source_desc == 'taxonomy':
continue
source_parts = source_desc.split('_')
# add default prefix 'pg' to study ID, if not found
if source_parts[0].isdigit():
# prepend with default namespace 'pg'
study_id = 'pg_%s' % source_parts[0]
else:
study_id = '_'.join(source_parts[0:2])
if len(source_parts) == 4:
commit_SHA_in_synthesis = source_parts[3]
else:
commit_SHA_in_synthesis = None
contributing_study_info[ study_id ] = commit_SHA_in_synthesis
# fetch the oti metadata (esp. DOI and full reference text) for each
fetch_url = method_dict['findAllStudies_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "http:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
study_metadata_response = fetch(fetch_url, data={"verbose": True})
study_metadata = simplejson.loads( study_metadata_response )
# filter just the metadata for studies contributing to synthesis
contributing_studies = [ ]
for study in study_metadata:
# Add any missing study-ID prefixes (assume 'pg') so we can compare
# with the prefixed IDs provided by getSynthesisSourceList.
id_parts = study['ot:studyId'].split('_')
if len(id_parts) == 1:
prefixed_study_id = 'pg_%s' % study['ot:studyId']
else:
prefixed_study_id = study['ot:studyId']
if prefixed_study_id in contributing_study_info.keys():
# add commit SHA to support retrieval of *exact* Nexson from synthesis
study['commit_SHA_in_synthesis'] = contributing_study_info[ prefixed_study_id ];
contributing_studies.append( study )
# TODO: sort these alphabetically(?) and render in the page
## contributing_studies.sort(key = lambda x: x.get('ot:studyPublicationReference'))
# NO, apparently they're pre-sorted to reflect the importance of each study
# TODO: encode data to utf-8?
## context_names += [n.encode('utf-8') for n in contextnames_json[gname] ]
return contributing_studies
except Exception, e:
# throw 403 or 500 or just leave it
return ('ERROR', e.message)