def collections():
"""
Show a filtered list of all tree collections in the system.
"""
view_dict = get_opentree_services_method_urls(request)
view_dict['maintenance_info'] = get_maintenance_info(request)
return view_dict
def collections():
"""
Show a filtered list of all tree collections in the system.
"""
view_dict = get_opentree_services_method_urls(request)
view_dict['maintenance_info'] = get_maintenance_info(request)
return view_dict
def create():
# Block (redirect) if we've suspended study editing
maintenance_info = get_maintenance_info(request)
if maintenance_info.get('maintenance_in_progress', False):
redirect(URL('curator', 'default', 'index', vars={"maintenance_notice":"true"}))
pass
view_dict = get_opentree_services_method_urls(request)
view_dict['message'] = "study/create"
return view_dict
def index():
"""
Offer creation (or uploading) of a name-mapping dataset
"""
response.view = 'tnrs.html'
view_dict = get_opentree_services_method_urls(request)
#view_dict['message'] = "This would appear at bottom of page.."
view_dict['maintenance_info'] = get_maintenance_info(request)
view_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
return view_dict
def create():
# Block (redirect) if we've suspended study editing
maintenance_info = get_maintenance_info(request)
if maintenance_info.get('maintenance_in_progress', False):
redirect(
URL('curator',
'default',
'index',
vars={"maintenance_notice": "true"}))
pass
view_dict = get_opentree_services_method_urls(request)
view_dict['message'] = "study/create"
return view_dict
def index():
"""
Show an introduction page for visitors, or personalized curation dashboard for
a logged-in user.
"""
#response.flash = T("Welcome to web2py!")
view_dict = get_opentree_services_method_urls(request)
view_dict['maintenance_info'] = get_maintenance_info(request)
if False: ## auth.is_logged_in():
# user is logged in, bounce to their personal dashboard
redirect(URL('dashboard'))
else:
# anonymous visitor, show a general info page
return view_dict
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['maintenance_info'] = get_maintenance_info(request)
#view_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
view_dict['studyID'] = request.args[0]
view_dict['latestSynthesisSHA'] = _get_latest_synthesis_sha_for_study_id(view_dict['studyID'])
view_dict['viewOrEdit'] = 'VIEW'
view_dict['userCanEdit'] = auth.is_logged_in() and True or False;
return view_dict
def index():
"""
Show an introduction page for visitors, or personalized curation dashboard for
a logged-in user.
"""
#response.flash = T("Welcome to web2py!")
view_dict = get_opentree_services_method_urls(request)
view_dict['maintenance_info'] = get_maintenance_info(request)
if False: ## auth.is_logged_in():
# user is logged in, bounce to their personal dashboard
redirect(URL('dashboard'))
else:
# anonymous visitor, show a general info page
return view_dict
def edit():
# Block (redirect) if we've suspended study editing
maintenance_info = get_maintenance_info(request)
if maintenance_info.get('maintenance_in_progress', False):
redirect(URL('curator', 'study', 'view',
vars={"maintenance_notice":"true"},
args=request.args))
# 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['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
view_dict['studyID'] = request.args[0]
view_dict['latestSynthesisSHA'] = _get_latest_synthesis_sha_for_study_id(view_dict['studyID'])
view_dict['viewOrEdit'] = 'EDIT'
return view_dict
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['maintenance_info'] = get_maintenance_info(request)
#view_dict['taxonSearchContextNames'] = fetch_current_TNRS_context_names(request)
view_dict['studyID'] = request.args[0]
view_dict['latestSynthesisSHA'] = _get_latest_synthesis_sha_for_study_id(
view_dict['studyID'])
view_dict['viewOrEdit'] = 'VIEW'
view_dict['userCanEdit'] = auth.is_logged_in() and True or False
return view_dict
def _get_latest_synthesis_sha_for_study_id(study_id):
# Fetch this SHA from treemachine. If not found in contributing studies, return None
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
return contributing_study_info.get(study_id, '')
except Exception, e:
# throw 403 or 500 or just leave it
raise HTTP(
500,
T('Unable to retrieve latest synthesis SHA for study {u}'.format(
u=study_id)))
def _get_latest_synthesis_details_for_study_id(study_id):
# Fetch the last synthesis SHA *and* any tree IDs (from this study) from
# treemachine. If the study is not found in contributing studies, return
# None for both.
try:
import json
import requests
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,
headers={
"Content-Type": "application/json"
},
data=json.dumps({'include_source_list': True})).text
source_dict = json.loads(source_list_response)['source_id_map']
# fetch the full source list, then look for this study and its trees
commit_SHA_in_synthesis = None
current_study_trees_included = []
#print(source_dict)
# ignore source descriptions (e.g. "ot_764@tree1"); just read the details
for source_details in source_dict.values():
if source_details.get('study_id', None) == study_id:
# this is the study we're interested in!
current_study_trees_included.append(source_details['tree_id'])
if commit_SHA_in_synthesis is None:
commit_SHA_in_synthesis = source_details['git_sha']
# keep checking, as each tree will have its own entry
return commit_SHA_in_synthesis, current_study_trees_included
except Exception, e:
# throw 403 or 500 or just leave it
raise HTTP(
500,
T('Unable to retrieve latest synthesis details for study {u}'.
format(u=study_id)))
def edit():
# Block (redirect) if we've suspended study editing
maintenance_info = get_maintenance_info(request)
if maintenance_info.get('maintenance_in_progress', False):
redirect(
URL('curator',
'study',
'view',
vars={"maintenance_notice": "true"},
args=request.args))
# 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['taxonSearchContextNames'] = fetch_current_TNRS_context_names(
request)
view_dict['studyID'] = request.args[0]
view_dict['latestSynthesisSHA'] = _get_latest_synthesis_sha_for_study_id(
view_dict['studyID'])
view_dict['viewOrEdit'] = 'EDIT'
return view_dict
def _get_latest_synthesis_sha_for_study_id( study_id ):
# Fetch this SHA from treemachine. If not found in contributing studies, return None
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
return contributing_study_info.get( study_id, '')
except Exception, e:
# throw 403 or 500 or just leave it
raise HTTP(500, T('Unable to retrieve latest synthesis SHA for study {u}'.format(u=study_id)))
def _get_latest_synthesis_details_for_study_id( study_id ):
# Fetch the last synthesis SHA *and* any tree IDs (from this study) from
# treemachine. If the study is not found in contributing studies, return
# None for both.
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 = "https:%s" % fetch_url
# as usual, this needs to be a POST (pass empty fetch_args)
source_list_response = fetch(fetch_url, data={'include_source_list':True})
source_dict = simplejson.loads( source_list_response )['source_id_map']
# fetch the full source list, then look for this study and its trees
commit_SHA_in_synthesis = None
current_study_trees_included = [ ]
#print(source_dict)
# ignore source descriptions (e.g. "ot_764@tree1"); just read the details
for source_details in source_dict.values():
if source_details.get('study_id', None) == study_id:
# this is the study we're interested in!
current_study_trees_included.append( source_details['tree_id'] )
if commit_SHA_in_synthesis is None:
commit_SHA_in_synthesis = source_details['git_sha']
# keep checking, as each tree will have its own entry
return commit_SHA_in_synthesis, current_study_trees_included
except Exception, e:
# throw 403 or 500 or just leave it
raise HTTP(500, T('Unable to retrieve latest synthesis details for study {u}'.format(u=study_id)))
def profile():
"""
shows a personalized profile for any user (default = the current logged-in user)
http://..../{app}/default/profile/[username]
"""
view_dict = get_opentree_services_method_urls(request)
view_dict['maintenance_info'] = get_maintenance_info(request)
# if the URL has a [username], try to load their information
if len(request.args) > 0:
# try to load a profile for the specified userid, using the GitHub API
specified_userid = request.args[0]
view_dict['userid'] = specified_userid
view_dict['active_user_found'] = False
# fetch the JSON for this user's activities
json_response = _fetch_github_api(
verb='GET', url='/users/{0}'.format(specified_userid))
error_msg = json_response.get('message', None)
view_dict['error_msg'] = error_msg
if error_msg:
# pass error to the page for display
print("ERROR FETCHING INFO FOR USERID: ", specified_userid)
print(error_msg)
view_dict['user_info'] = None
view_dict['opentree_activity'] = None
else:
# pass user info to the page for display
view_dict['user_info'] = json_response
activity = _get_opentree_activity(
userid=specified_userid,
username=view_dict['user_info'].get('name', specified_userid))
if activity:
view_dict['active_user_found'] = True
else:
view_dict['active_user_found'] = False
view_dict['error_msg'] = 'Not active in OpenTree'
view_dict['opentree_activity'] = activity
view_dict['is_current_user_profile'] = False
if view_dict['active_user_found'] == True and auth.is_logged_in():
current_userid = auth.user and auth.user.github_login or None
if specified_userid == current_userid:
view_dict['is_current_user_profile'] = True
return view_dict
else:
# No userid was provided in the URL. Instead, we should try to bounce to the
# current user's profile if they're logged in (or try to force a login).
if auth.is_logged_in():
current_userid = auth.user and auth.user.github_login or None
# redirect to the fully expanded profile URL
expanded_url = URL('curator',
'default',
'profile',
args=(current_userid, ),
vars=request.vars)
redirect(expanded_url)
else:
# try to force a login and return here
redirect(
URL('curator',
'user',
'login',
vars=dict(
_next=URL(args=request.args, vars=request.vars))))
def error():
view_dict = get_opentree_services_method_urls(request)
return view_dict
def _get_opentree_activity(userid=None, username=None):
# Fetch information about a user's studies, comments, and collections in the
# OpenTree project. If a dict was provided, add this information to it; else
# bundle up the information and return it directly
if not userid:
return None
activity_found = False
activity = {
'curator_since': None,
'comments': [],
'issues': [],
'added_studies': [],
'curated_studies': [],
'curated_studies_in_synthesis': [],
'added_collections': [],
'curated_collections': []
}
method_dict = get_opentree_services_method_urls(request)
# Use GitHub API to gather comments from this user, as shown in
# https://github.com/OpenTreeOfLife/feedback/issues/created_by/jimallman
# N.B. that this is limited to 100 most recent items!
all_comments = _fetch_github_api(
verb='GET',
url='/repos/OpenTreeOfLife/feedback/issues/comments?per_page=100')
for comment in all_comments:
if comment.get('user', None):
comment_author = comment.get('user').get('login')
if comment_author == userid:
activity.get('comments').append(comment)
activity_found = True
# Again, for all feedback issues created by them
# N.B. that this is probably limited to 100 most recent items!
created_issues = _fetch_github_api(
verb='GET',
url=
'/repos/OpenTreeOfLife/feedback/issues?state=all&creator={0}&per_page=100'
.format(userid))
activity['issues'] = created_issues
if len(created_issues) > 0:
activity_found = True
# 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_data = requests.post(url=fetch_url,
headers={
"Content-Type": "application/json"
},
data=json.dumps({'include_source_list':
True})).json()
source_id_map = source_data.get('source_id_map')
# N.B. We can ignore the munged ids in source_data['source_list']
contributing_study_info = {
} # build a dict with unique study IDs as keys, commit SHAs as values
for source_id, source_details in source_id_map.iteritems():
if 'taxonomy' in source_details:
continue
study_id = source_details.get('study_id')
commit_SHA_in_synthesis = source_details.get('git_sha')
contributing_study_info[study_id] = commit_SHA_in_synthesis
# Use oti to gather studies curated and created by this user.
fetch_url = method_dict['findAllStudies_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
all_studies = requests.post(
url=fetch_url,
headers={
"Content-Type": "application/json"
},
data=json.dumps({'verbose': True}) # include curator list
).json().get('matched_studies', [])
for study in all_studies:
study_curators = study['ot:curatorName']
# TODO: improve oti to handle multiple curator names!
if type(study_curators) is not list:
study_curators = [study_curators]
# NB - If there's no "display name" defined, look for their userid
if (username or userid) in study_curators:
activity_found = True
activity['curated_studies'].append(study)
# first curator name is its original contributor
if study_curators[0] == (username or userid):
activity['added_studies'].append(study)
# does this contribute to synthesis?
if contributing_study_info.has_key(study['ot:studyId']):
activity['curated_studies_in_synthesis'].append(study)
# Use oti to gather collections curated and created by this user.
fetch_url = method_dict['findAllTreeCollections_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
all_collections = requests.get(url=fetch_url).json()
for collection in all_collections:
# gather all participants and check against their GitHub userids
if userid == collection.get('creator', {}).get('login', None):
activity_found = True
activity['added_collections'].append(collection)
contributor_ids = [
c.get('login', None) for c in collection.get('contributors', [])
]
if userid in contributor_ids:
activity_found = True
activity['curated_collections'].append(collection)
if activity_found:
try:
# search the repo stats (for each phylesystem shard!) for their earliest contribution
earliest_activity_date = None # TODO: make this today? or tomorrow? MAXTIME?
fetch_url = method_dict['phylesystem_config_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
phylesystem_config = requests.get(url=fetch_url).json()
shard_list = phylesystem_config['shards']
# if GitHub is rebuilding stats cache for any shard, poke them all but ignore dates
rebuilding_cache = False
for shard in shard_list:
shard_name = shard['name']
shard_contributors = _fetch_github_api(
verb='GET',
url='/repos/OpenTreeOfLife/{0}/stats/contributors'.format(
shard_name))
if type(shard_contributors) is not list:
# Flag this, but try to fetch remaining shards (to nudge the cache)
rebuilding_cache = True
else:
for contrib_info in shard_contributors:
if contrib_info['author']['login'] == userid:
# look for the earliest week here
for week in contrib_info['weeks']:
if earliest_activity_date:
earliest_activity_date = min(
earliest_activity_date, week['w'])
else:
earliest_activity_date = week['w']
break # skip any remaining records
if rebuilding_cache:
activity[
'curator_since'] = 'Generating data, please try again in a moment...'
elif not earliest_activity_date:
activity[
'curator_since'] = 'This user has not curated any studies.'
else:
# show a very approximate date (stats are just weekly)
from datetime import datetime
d = datetime.fromtimestamp(earliest_activity_date)
activity['curator_since'] = d.strftime("%B %Y")
except:
# probably JSONDecodeError due to misconfiguration of the API server
activity[
'curator_since'] = "Unable to determine this user's first activity"
return activity
else:
return None
def error():
view_dict = get_opentree_services_method_urls(request)
return view_dict
def profile():
"""
shows a personalized profile for any user (default = the current logged-in user)
http://..../{app}/default/profile/[username]
"""
view_dict = get_opentree_services_method_urls(request)
view_dict['maintenance_info'] = get_maintenance_info(request)
# if the URL has a [username], try to load their information
if len(request.args) > 0:
# try to load a profile for the specified userid, using the GitHub API
specified_userid = request.args[0]
view_dict['userid'] = specified_userid
view_dict['active_user_found'] = False
# fetch the JSON for this user's activities
json_response = _fetch_github_api(verb='GET',
url='/users/{0}'.format(specified_userid))
error_msg = json_response.get('message', None)
view_dict['error_msg'] = error_msg
if error_msg:
# pass error to the page for display
print("ERROR FETCHING INFO FOR USERID: ", specified_userid)
print(error_msg)
view_dict['user_info'] = None
view_dict['opentree_activity'] = None
else:
# pass user info to the page for display
view_dict['user_info'] = json_response
activity = _get_opentree_activity(
userid=specified_userid,
username=view_dict['user_info'].get('name', specified_userid)
)
if activity:
view_dict['active_user_found'] = True
else:
view_dict['active_user_found'] = False
view_dict['error_msg'] = 'Not active in OpenTree'
view_dict['opentree_activity'] = activity
view_dict['is_current_user_profile'] = False
if view_dict['active_user_found'] == True and auth.is_logged_in():
current_userid = auth.user and auth.user.github_login or None
if specified_userid == current_userid:
view_dict['is_current_user_profile'] = True
return view_dict
else:
# No userid was provided in the URL. Instead, we should try to bounce to the
# current user's profile if they're logged in (or try to force a login).
if auth.is_logged_in():
current_userid = auth.user and auth.user.github_login or None
# redirect to the fully expanded profile URL
expanded_url = URL('curator', 'default', 'profile',
args=(current_userid,),
vars=request.vars)
redirect(expanded_url)
else:
# try to force a login and return here
redirect(URL('curator', 'user', 'login',
vars=dict(_next=URL(args=request.args, vars=request.vars))))
def _get_opentree_activity( userid=None, username=None ):
# Fetch information about a user's studies, comments, and collections in the
# OpenTree project. If a dict was provided, add this information to it; else
# bundle up the information and return it directly
if not userid:
return None
activity_found = False
activity = {
'curator_since': None,
'comments':[],
'issues': [],
'added_studies':[],
'curated_studies': [],
'curated_studies_in_synthesis': [],
'added_collections':[],
'curated_collections':[]
}
method_dict = get_opentree_services_method_urls(request)
# Use GitHub API to gather comments from this user, as shown in
# https://github.com/OpenTreeOfLife/feedback/issues/created_by/jimallman
# N.B. that this is limited to 100 most recent items!
all_comments = _fetch_github_api(verb='GET',
url='/repos/OpenTreeOfLife/feedback/issues/comments?per_page=100')
for comment in all_comments:
if comment.get('user', None):
comment_author = comment.get('user').get('login')
if comment_author == userid:
activity.get('comments').append( comment )
activity_found = True
# Again, for all feedback issues created by them
# N.B. that this is probably limited to 100 most recent items!
created_issues = _fetch_github_api(verb='GET',
url='/repos/OpenTreeOfLife/feedback/issues?state=all&creator={0}&per_page=100'.format(userid))
activity['issues'] = created_issues
if len(created_issues) > 0:
activity_found = True
# 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_data = requests.post(
url=fetch_url,
data={'include_source_list':True}
).json()
source_id_map = source_data.get('source_id_map')
# N.B. We can ignore the munged ids in source_data['source_list']
contributing_study_info = { } # build a dict with unique study IDs as keys, commit SHAs as values
for source_id, source_details in source_id_map.iteritems():
if 'taxonomy' in source_details:
continue
study_id = source_details.get('study_id')
commit_SHA_in_synthesis = source_details.get('git_sha')
contributing_study_info[ study_id ] = commit_SHA_in_synthesis
# Use oti to gather studies curated and created by this user.
fetch_url = method_dict['findAllStudies_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
all_studies = requests.post(
url=fetch_url,
data={'verbose': True} # include curator list
).json().get('matched_studies', [ ])
for study in all_studies:
study_curators = study['ot:curatorName']
# TODO: improve oti to handle multiple curator names!
if type(study_curators) is not list:
study_curators = [study_curators]
if username in study_curators:
activity_found = True
activity['curated_studies'].append(study)
# first curator name is its original contributor
if study_curators[0] == username:
activity['added_studies'].append(study)
# does this contribute to synthesis?
if contributing_study_info.has_key( study['ot:studyId'] ):
activity['curated_studies_in_synthesis'].append(study)
# Use oti to gather collections curated and created by this user.
fetch_url = method_dict['findAllTreeCollections_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
all_collections = requests.get(url=fetch_url).json()
for collection in all_collections:
# gather all participants and check against their GitHub userids
if userid == collection.get('creator', {}).get('login', None):
activity_found = True
activity['added_collections'].append(collection)
contributor_ids = [c.get('login', None) for c in collection.get('contributors', [ ])]
if userid in contributor_ids:
activity_found = True
activity['curated_collections'].append(collection)
if activity_found:
try:
# search the repo stats (for each phylesystem shard!) for their earliest contribution
earliest_activity_date = None # TODO: make this today? or tomorrow? MAXTIME?
fetch_url = method_dict['phylesystem_config_url']
if fetch_url.startswith('//'):
# Prepend scheme to a scheme-relative URL
fetch_url = "https:%s" % fetch_url
phylesystem_config = requests.get( url=fetch_url ).json()
shard_list = phylesystem_config['shards']
# if GitHub is rebuilding stats cache for any shard, poke them all but ignore dates
rebuilding_cache = False
for shard in shard_list:
shard_name = shard['name']
shard_contributors = _fetch_github_api(verb='GET',
url='/repos/OpenTreeOfLife/{0}/stats/contributors'.format(shard_name))
if type(shard_contributors) is not list:
# Flag this, but try to fetch remaining shards (to nudge the cache)
rebuilding_cache = True
else:
for contrib_info in shard_contributors:
if contrib_info['author']['login'] == userid:
# look for the earliest week here
for week in contrib_info['weeks']:
if earliest_activity_date:
earliest_activity_date = min(earliest_activity_date, week['w'])
else:
earliest_activity_date = week['w']
break # skip any remaining records
if rebuilding_cache:
activity['curator_since'] = 'Generating data, please try again in a moment...'
elif not earliest_activity_date:
activity['curator_since'] = 'This user has not curated any studies.'
else:
# show a very approximate date (stats are just weekly)
from datetime import datetime
d = datetime.fromtimestamp(earliest_activity_date)
activity['curator_since'] = d.strftime("%B %Y")
except:
# probably JSONDecodeError due to misconfiguration of the API server
activity['curator_since'] = "Unable to determine this user's first activity"
return activity
else:
return None
