Orphaned commits on development - DO NOT MERGE

LICENSE.txt

@@ -1,7 +1,7 @@
-Copyright (c) 2013, Jonathan Rees
-Copyright (c) 2013, Mark Holder
-Copyright (c) 2013, Jim Allman
-Copyright (c) 2013, Stephen Smith
+Copyright (c) 2013-2016, Jonathan Rees
+Copyright (c) 2013-2016, Mark Holder
+Copyright (c) 2013-2016, Jim Allman
+Copyright (c) 2013-2016, Stephen Smith
 
 All rights reserved.
 

curator/controllers/collection.py

@@ -108,6 +108,17 @@ def load():
 def store():
     return dict(message="collection/store")
 
+def synthesis_dashboard():
+    """
+    Allow any visitor to view (read-only!) a queue of recent custom-synthesis runs
+    """
+    response.view = 'collection/synthesis_dashboard.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['userCanEdit'] = auth.is_logged_in() and True or False
+    return view_dict
+
 """ TODO: Adapt this for current collection status, based on new APIs """
 def _get_latest_synthesis_details_for_collection_id( collection_id ):
     # Fetch the last SHA for this collection that was used in the latest
@@ -137,15 +148,6 @@ def _get_latest_synthesis_details_for_collection_id( collection_id ):
         # Draft code is based on schema proposed in
         # https://github.com/OpenTreeOfLife/phylesystem-api/issues/228
 
-        # fetch the full source list, then look for this study and its trees
-        commit_SHA_in_synthesis = None
-        # if key (collection ID, e.g. "opentreeoflife/default") matches, read its details
-        for c_id, collection_details in source_dict.items():
-            if c_id == collection_id:
-                # this is the collection we're interested in!
-                commit_SHA_in_synthesis = collection_details['git_sha']
-        return commit_SHA_in_synthesis  # TODO: return more information?
-
         # fetch the full source list, then look for this collection and its SHA
         # if key (collection ID, e.g. "opentreeoflife/default") matches, read its details
         for c_id, collection_details in source_dict.items():
@@ -155,4 +157,5 @@ def _get_latest_synthesis_details_for_collection_id( collection_id ):
         return None
     except Exception, e:
         # throw 403 or 500 or just leave it
-        raise HTTP(500, T('Unable to retrieve latest synthesis details for collection {u}'.format(u=collection)))
+        ##raise HTTP(500, T('Unable to retrieve latest synthesis details for collection {u}'.format(u=collection_id)))
+        raise HTTP(500, T('Unable to retrieve latest synthesis details for collection {u}:\n\n{e}'.format(u=collection_id, e=e)))

curator/controllers/default.py

@@ -470,6 +470,7 @@ def to_nexson():
     _LOG = get_logger(request, 'to_nexson')
     if request.env.request_method == 'OPTIONS':
         raise HTTP(200, T('Preflight approved!'))
+
     orig_args = {}
     is_upload = False
     # several of our NexSON use "uploadid" instead of "uploadId" so we should accept either
@@ -622,7 +623,7 @@ def to_nexson():
                 try:
                     assert(os.path.exists(exe_path))
                 except:
-                    response.view = 'generic.json'; return {'hb':exe_path}
+                    #response.view = 'generic.json'; return {'hb':exe_path}
                     _LOG.warn("Could not find the 2nexml executable")
                     raise HTTP(501, T("Server is misconfigured for 2nexml conversion"))
                 invoc = [exe_path, '-f{f}'.format(f=inp_format), ]

curator/private/config.example

@@ -63,6 +63,9 @@ getContextForNames_url = {taxomachine_domain}/v3/tnrs/infer_context
 getSynthesisSourceList_url = {CACHED_treemachine_domain}/v3/tree_of_life/about
 getTaxonomicMRCAForNodes_url = {taxomachine_domain}/v3/taxonomy/mrca
 getDraftTreeMRCAForNodes_url = {treemachine_domain}/v3/tree_of_life/mrca
+findAllSynthesisRuns_url = https://ot38.opentreeoflife.org/v3/tree_of_life/list_custom_built_trees
+requestNewSynthesisRun_url = https://ot38.opentreeoflife.org/v3/tree_of_life/build_tree
+# TODO: This should start {treemachine_domain} OR {CACHED_treemachine_domain}
 findAllStudies_url = {CACHED_oti_domain}/v3/studies/find_studies
 # TODO: Can we use CACHED_oti_domain for this?
 singlePropertySearchForStudies_url = {oti_domain}/v3/studies/find_studies

curator/routes.py

@@ -0,0 +1,24 @@
+# -*- coding: utf-8 -*-
+
+# adapted from router.example.py
+
+# NOTE that this requires a parametric router in the web2py root directory.
+# Let's keep all the important stuff here, and just copy a minimal router
+# (SITE.routes.py) into the site root.
+
+# NOTE that this (app-specific) routes.py file mainly defines a router by the
+# same name. More general settings must be done in the main routes.py alongside
+# the web2py/applications/ directory
+#   root_static (for favicon.ico, robots.txt, etc)
+#   routes_onerror (defines error pages per app, per error code, or defaults)
+#   domain (maps domain names and ports to particular app)
+# See SITE.routes.py for recommended settings.
+
+routers = dict(
+    curator=dict(
+        # convert dashes (hyphens) in URLs to underscores in web2py controller+action names
+        map_hyphen=True,
+    ),
+)
+
+# see router.example.py for (many) more options!

curator/static/css/default.css

@@ -870,7 +870,13 @@ tr.after-shims th {
     position: relative;
     top: -8px;
 }
-.collection-move-panel {
+
+.form-horizontal.metadata-readonly .control-group {
+  margin-bottom: 12px;
+}
+
+.collection-move-panel,
+.synthrun-move-panel {
     position: absolute;
     margin-left: 2px;
     z-index: 1;
@@ -880,7 +886,8 @@ tr.after-shims th {
     -moz-box-shadow: 1px 2px 4px rgba(0, 0, 0, 0.5);
     box-shadow: 1px 2px 4px rgba(0, 0, 0, 0.5);
 }
-.collection-move-panel button {
+.collection-move-panel button,
+.synthrun-move-panel button {
     opacity: 1.0;
 }
 
@@ -1014,3 +1021,11 @@ form.skip-label * {
 form.skip-label *.non-fading {
     opacity: 1.0;
 }
+.loading-message {
+    display: inline-block; 
+    position: relative; 
+    top: -6px; 
+    left: 8px; 
+    color: #999; 
+    font-style: italic;
+}