Support for all Health Assessment figures

gcis_clients/gcis_client.py

@@ -108,7 +108,7 @@ class GcisClient(object):
         self.s.headers.update({'Accept': 'application/json'})
 
     @http_resp
-    def create_figure(self, report_id, chapter_id, figure, skip_images=False):
+    def create_figure(self, report_id, chapter_id, figure, skip_images=False, skip_upload=False):
         if figure.identifier in (None, ''):
             raise Exception('Invalid figure identifier', figure.identifier)
 
@@ -124,7 +124,7 @@ class GcisClient(object):
         if resp.status_code != 200:
             return resp
 
-        if figure.local_path is not None:
+        if not skip_upload and figure.local_path is not None:
             self.upload_figure_file(report_id, chapter_id, figure.identifier, figure.local_path)
 
         if skip_images is False:

gcis_clients/survey_client.py

@@ -6,6 +6,7 @@ import requests
 import re
 from os.path import join, basename
 import sys
+import traceback
 
 from gcis_clients.domain import Figure, Image, Dataset, Parent, Contributor, Person, Organization, Activity, Role
 import survey_transforms as trans
@@ -25,7 +26,7 @@ def get_credentials():
 
 
 def parse_title(graphic_title):
-    match = re.search('\d+\.\d+', graphic_title)
+    match = re.search('\w+\.\d+', graphic_title)
     if match:
         return match.group(0), graphic_title[match.end(0):].strip()
     else:
@@ -35,7 +36,20 @@ def parse_title(graphic_title):
 def populate_figure(fig_json):
     f = Figure({})
     try:
-        f.figure_num, f.title = parse_title(fig_json['graphics_title'])
+        if fig_json['graphics_title'].startswith('ES'):
+            title_fields = fig_json['graphics_title'].split('. ')
+            title = ' '.join(title_fields[1:])
+
+            f.ordinal = re.search('\d+', title_fields[0]).group(0)
+        else:
+            figure_num, title = parse_title(fig_json['graphics_title'])
+
+            if figure_num and figure_num.startswith('TSD'):
+                f.ordinal = figure_num.split('.')[1]
+            else:
+                f.figure_num = figure_num if figure_num else None
+
+        f.title = title
         f.identifier = fig_json['figure_id'] if fig_json['figure_id'] else re.sub('\W', '_', f.title).lower()
         f.create_dt = fig_json['graphics_create_date'].strip()
         if any(fig_json['period_record']):
@@ -43,7 +57,7 @@ def populate_figure(fig_json):
         f.lat_min, f.lat_max, f.lon_min, f.lon_max = fig_json['spatial_extent']
     except Exception, e:
         warning('Figure exception: ', e)
-
+        traceback.print_exc()
     return f
 
 

gcis_clients/survey_transforms.py

@@ -47,21 +47,29 @@ PARENT_SEARCH_HINTS = {
     'report': {
         'Climate Change Impacts in the United States: The Third National Climate Assessment': 'nca3',
         'Third National Climate Assessment': 'nca3',
-        'A conceptual framework for action on the social determinants of health': 'conceptual-framework-for-action-on-the-social-determinants-of-health'
+        'A conceptual framework for action on the social determinants of health': 'conceptual-framework-for-action-on-the-social-determinants-of-health',
+        'Regional Surface Climate Conditions in CMIP3 and CMIP5 for the United States: Differences, Similarities, and Implications for the U.S. National Climate Assessment.': 'noaa-techreport-nesdis-144',
+        '2012 Census of Agriculture': 'census-agriculture-2012'
     },
     'dataset': {
         'Global Historical Climatology Network - Daily': 'noaa-ncdc-ghcn-daily'
     },
     'article': {
-        'Projections of future temperature-attributable deaths in 209 U.S. cities using a cluster based Poisson approach': 'projections-of-future-temperature-attributable-deaths-in-209-us-cities',
+        'Projections of future temperature-attributable deaths in 209 U.S. cities using a cluster based Poisson approach': '10.1186/s12940-015-0071-2',
+        'Projections of future temperature-attributable deaths in 209 U.S. cities 1 using a cluster-based Poisson approach': '10.1186/s12940-015-0071-2',
         'A framework for examining climate driven changes to the seasonality and geographic range of coastal pathogens': '10.1016/j.crm.2015.03.002',
         'Effects of Ocean Warming on Growth and Distribution of Five Ciguatera-Associated Dinoflagellates in the Caribbean and Implications for Ciguatera Fish Poisoning': 'potential-effects-of-climate-change-on-growth-and-distribution-of-five-caribbean-gambierdiscus-species',
         'Effects of elevated CO2 on the protein concentration of food crops: a meta-analysis': '10.1111/j.1365-2486.2007.01511.x',
         'A new scenario framework for climate change research: the concept of shared socio-economic pathways': '10.1007/s10584-013-0905-2',
-        'Climate Change influences on the annual onset of Lyme disease in the United States': '10.1016/j.ttbdis.2015.05.005'
+        'Climate Change influences on the annual onset of Lyme disease in the United States': '10.1016/j.ttbdis.2015.05.005',
+        'The roads ahead: Narratives for shared socioeconomic pathways describing world futures in the 21st century': '10.1016/j.gloenvcha.2015.01.004'
     },
     'webpage': {
-        'Screenshot of: Social Vulnerability Index (SVI) Mapping Dashboard': '6d0ccc19-cdcc-4d56-acb7-d62f12611333'
+        'Screenshot of: Social Vulnerability Index (SVI) Mapping Dashboard': '6d0ccc19-cdcc-4d56-acb7-d62f12611333',
+        'Lyme Disease: Data and Statistics: Maps': '7206f315-04be-4536-9e10-70155edfada0',
+        'Risk of very large fires could increase sixfold by mid-century in the US': 'af962cb2-dd38-44f6-9b4e-7bef8577b92c',
+        'Flickr account: User: TeamSaintLouis. Album: Low Water on the Mississippi River': '9853a51e-b7c2-42c5-a201-d2f5c8527f52',
+        'USDA Biological Control of Pests Research Unit': '950835c0-2088-4f06-a61a-a809387d4930'
     },
     'book': {
         'Assessing Health Vulnerability to Climate Change: A Guide for Health Departments': ('report', 'assessing-health-vulnerability-to-climate-change-a-guide-for-health-departments')
@@ -130,18 +138,28 @@ ORG_IDS = {
 # contributing_agency
 
 PERSON_TRANSLATIONS = {
-    'Alexis Juliana': Person({'first_name': 'Alexis', 'last_name': 'St. Juliana'}),
+    'Alexis St. Juliana': Person({'id': 9934, 'first_name': 'Alexis', 'last_name': 'St. Juliana'}),
+    'Alexis Juliana': Person({'id': 9934, 'first_name': 'Alexis', 'last_name': 'St. Juliana'}),
     'Pat Dolwick': Person({'first_name': 'Patrick', 'last_name': 'Dolwick'}),
     'Alan Joyner': Person({'first_name': 'Alan', 'last_name': 'Joyner'}),
-    'Juli Trtanj': Person({'first_name': 'Juli M.', 'last_name': 'Trtanj'}),
-    'Stephanie Moore': Person({'first_name': 'Stephanie K.', 'last_name': 'Moore'}),
+    'Juli Trtanj': Person({'id': 1264, 'first_name': 'Juli M.', 'last_name': 'Trtanj'}),
+    'Juli M. Trtanj': Person({'id': 1264, 'first_name': 'Juli M.', 'last_name': 'Trtanj'}),
+    'Stephanie Moore': Person({'id': 9889, 'first_name': 'Stephanie K.', 'last_name': 'Moore'}),
+    'Stephanie K. Moore': Person({'id': 9889, 'first_name': 'Stephanie', 'last_name': 'Moore'}),
     'Steve Kibler': Person({'first_name': 'Steven R.', 'last_name': 'Kibler'}),
     'Jesse Bell': Person({'first_name': 'Jesse E.', 'last_name': 'Bell'}),
     'Dave Mills': Person({'first_name': 'David M.', 'last_name': 'Mills'}),
     'David Mills': Person({'first_name': 'David M.', 'last_name': 'Mills'}),
     'Lesley Crimmins)': Person({'first_name': 'Lesley', 'last_name': 'Jantarasami'}),
     'Allison Jantarasami)': Person({'first_name': 'Allison', 'last_name': 'Crimmins'}),
-    'Lewis Ziska': Person({'first_name': 'Lewis H.', 'last_name': 'Ziska'}),
+    'Lewis Ziska': Person({'id': 923, 'first_name': 'Lewis', 'last_name': 'Ziska'}),
+    'Jada Garofalo': Person({'id': 9885, 'first_name': 'Jada', 'last_name': 'F. Garofalo'}),
+    'Micah Hahn': Person({'id': 9886, 'first_name': 'Micah', 'last_name': 'Hahn'}),
+    'Jeanette Thurston': Person({'id': 9892, 'first_name': 'Jeanette', 'last_name': 'Thurston'}),
+    'Daniel Dodgen': Person({'id': 9908, 'first_name': 'Daniel', 'last_name': 'Dodgen'}),
+    'John Jacobs': Person({'id': 9888, 'first_name': 'John', 'last_name': 'Jacobs'}),
+    'Stephanie Herring': Person({'id': 8333, 'first_name': 'Stephanie', 'last_name': 'Herring'}),
+    'Tom Maycock': Person({'id': 10926, 'first_name': 'Tom', 'last_name': 'Maycock'})
 }
 
 CONTRIB_ROLES = {
@@ -153,6 +171,7 @@ CONTRIB_ROLES = {
     'Dave Mills': ('stratus-consulting', 'analyst'),
     'David Mills': ('stratus-consulting', 'analyst'),
     'Alexis Juliana': ('stratus-consulting', 'analyst'),
+    'Alexis St. Juliana': ('stratus-consulting', 'analyst'),
     'Neal Fann': ('us-environmental-protection-agency', 'analyst'),
     'Pat Dolwick': ('us-environmental-protection-agency', 'scientist'),
     'Lewis Ziska': ('us-department-agriculture', 'scientist'),
@@ -167,5 +186,8 @@ CONTRIB_ROLES = {
     'Daniel Dodgen': ('us-department-health-human-services', 'point_of_contact'),
     'Andrea Maguire': ('us-environmental-protection-agency', 'point_of_contact'),
     'Lesley Crimmins)': ('us-environmental-protection-agency', 'analyst'),
-    'Allison Jantarasami)': ('us-environmental-protection-agency', 'point_of_contact')
+    'Allison Jantarasami)': ('us-environmental-protection-agency', 'point_of_contact'),
+    'John Jacobs': ('national-oceanic-atmospheric-administration', 'scientist'),
+    'Stephanie Herring': ('national-oceanic-atmospheric-administration', 'scientist'),
+    'Tom Maycock': ('cooperative-institute-climate-satellites-nc', 'point_of_contact'),
 }

gcis_clients/sync_utils.py

@@ -38,14 +38,15 @@ def realize_contributors(gcis_client, contributors):
         person = cont.person
         org = cont.organization
 
-        name_matches = gcis_client.lookup_person(person.first_name + ' ' + person.last_name)
-        if len(name_matches) == 1:
-            person.id = name_matches[0][0]
-        elif len(name_matches) == 0:
-            warning('No ID found for ' + person.first_name + ' ' + person.last_name)
-        else:
-            warning('Ambiguous results for ' + person.first_name + ' ' + person.last_name)
-            warning(name_matches)
+        if not person.id:
+            name_matches = gcis_client.lookup_person(person.first_name + ' ' + person.last_name)
+            if len(name_matches) == 1:
+                person.id = name_matches[0][0]
+            elif len(name_matches) == 0:
+                warning('No ID found for ' + person.first_name + ' ' + person.last_name)
+            else:
+                warning('Ambiguous results for ' + person.first_name + ' ' + person.last_name)
+                warning(name_matches)
 
         if org and org.identifier in (None, '') and org.name not in (None, ''):
             warning('No ID found for ' + org.name)

setup.py

@@ -19,7 +19,7 @@ class PyTest(TestCommand):
 
 setup(
     name='GcisPyClient',
-    version='1.1',
+    version='1.1.1',
     author='Andrew Buddenberg',
     author_email='andrew.buddenberg@noaa.gov',
     packages=find_packages(),