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 = default_view_dict.copy()
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[
'startingNodeID'] = fetch_current_synthetic_tree_ids()
treeview_dict[
'taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
return treeview_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 = default_view_dict.copy()
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['startingNodeID'] = fetch_current_synthetic_tree_ids()
treeview_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
return treeview_dict
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 the_synthetic_tree():
# -*- coding: utf-8 -*-
from opentreewebapputil import (get_opentree_services_method_urls,
fetch_current_TNRS_context_names)
### required - do no delete
def user(): return dict(form=auth())
def download(): return response.download(request,db)
def call(): return service()
### end requires
default_view_dict = get_opentree_services_method_urls(request)
default_view_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
def index():
return default_view_dict
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 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 = default_view_dict.copy()
treeview_dict['viewer'] = 'argus'
treeview_dict['domSource'] = ''
treeview_dict['nodeID'] = ''
treeview_dict['nodeName'] = ''
treeview_dict['viewport'] = ''
treeview_dict['nudgingToLatestSyntheticTree'] = False
treeview_dict['incomingDomSource'] = 'none'
treeview_dict['showLegendOnLoad'] = request.vars.get('show-legend') or False
# 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', 'feedback', 'properties']: # TODO: add 'onezoom','phylet', others?
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]:
ds_and_node_id = request.args[1].split('@')
treeview_dict['domSource'] = ds_and_node_id[0]
if len(ds_and_node_id) > 1:
treeview_dict['nodeID'] = ds_and_node_id[1]
else:
treeview_dict['nodeName'] = request.args[1]
if len(request.args) > 2:
if not treeview_dict['nodeName']:
treeview_dict['nodeName'] = request.args[2]
# retrieve latest synthetic-tree ID (and its 'life' node ID)
# TODO: Only refresh this periodically? Or only when needed for initial destination?
latestSyntheticTreeVersion, startingNodeID = fetch_current_synthetic_tree_ids()
treeview_dict['draftTreeName'] = latestSyntheticTreeVersion
treeview_dict['startingNodeID'] = startingNodeID
# replace any invalid 'domSource' (typically this is "ottol" or a synth-tree version)
# with the latest synthetic tree version, and notify the user on the page
#
# N.B. that if this is unspecified ('none'), the user requested a shortened
# URL (e.g. https://tree.opentreeoflife.org/) that resolves to the latest
# synthetic tree.
incomingDomSource = treeview_dict.get('domSource', None) or latestSyntheticTreeVersion
treeview_dict['incomingDomSource'] = incomingDomSource
if incomingDomSource not in ('ottol', latestSyntheticTreeVersion, ):
treeview_dict['domSource'] = latestSyntheticTreeVersion
treeview_dict['nudgingToLatestSyntheticTree'] = True
# mark this as a redirect to a different resource
response.status = 303
# when all is said and done, do we have enough information to force the location?
if incomingDomSource and treeview_dict['nodeID']:
treeview_dict['forcedByURL'] = True
treeview_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
return treeview_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 = default_view_dict.copy()
treeview_dict['viewer'] = 'argus'
treeview_dict['domSource'] = ''
treeview_dict['nodeID'] = ''
treeview_dict['nodeName'] = ''
treeview_dict['viewport'] = ''
treeview_dict['nudgingToLatestSyntheticTree'] = False
treeview_dict['incomingDomSource'] = 'none'
# 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',]: # TODO: add 'onezoom','phylet', others?
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]
# retrieve latest synthetic-tree ID (and its 'life' node ID)
# TODO: Only refresh this periodically? Or only when needed for initial destination?
latestSyntheticTreeVersion, startingNodeID = fetch_current_synthetic_tree_ids()
treeview_dict['draftTreeName'] = latestSyntheticTreeVersion
treeview_dict['startingNodeID'] = startingNodeID
# replace any invalid 'domSource' (typically this is "ottol" or a synth-tree version)
# with the latest synthetic tree version, and notify the user on the page
#
# N.B. that if this is unspecified ('none'), the user requested a shortened
# URL (e.g. https://tree.opentreeoflife.org/) that resolves to the latest
# synthetic tree.
incomingDomSource = treeview_dict.get('domSource', None) or latestSyntheticTreeVersion
treeview_dict['incomingDomSource'] = incomingDomSource
if incomingDomSource not in ('ottol', latestSyntheticTreeVersion, ):
treeview_dict['domSource'] = latestSyntheticTreeVersion
treeview_dict['nudgingToLatestSyntheticTree'] = True
# mark this as a redirect to a different resource
response.status = 303
# when all is said and done, do we have enough information to force the location?
if incomingDomSource and treeview_dict['nodeID']:
treeview_dict['forcedByURL'] = True
treeview_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
return treeview_dict
