Merge pull request #199 from SBRG/escher-fixes-195

Changes for v1.2

bigg_models/model_dumper.py

@@ -18,7 +18,7 @@
 def autodetect_model_polisher():
     """Return the path to ModelPolisher."""
     return abspath(join(dirname(__file__), '..', 'bin',
-                        'ModelPolisher-1.2.jar'))
+                        'ModelPolisher-1.3.jar'))
 
 
 def make_all_static_models():
@@ -96,7 +96,8 @@ def write_static_model(bigg_id, model_polisher_path=None):
                    '--compression-type=NONE',
                    '--check-mass-balance=true',
                    '--omit-generic-terms=false',
-                   '--log-level=INFO']
+                   '--log-level=INFO',
+                   '--include-any-uri=false']
         polish_result = call(command)
         print('Polishing finished in %.2f seconds' % (time.time() - t))
         if polish_result == 0:

bigg_models/templates/advanced_search.html

@@ -6,9 +6,9 @@ <h1 class="centered">Advanced Search</h1>
 
   <hr/>
   <h2>
-    Search Metabolites by External IDs
-    {% with question_title='Search Metabolites by External IDs'%}
-      {% with question_text='You can search for metabolites in the BiGG Database by entering an identifier from an external database. Use the dropdown menu to choose the external database, and enter the identifier in the Database ID box.'%}
+    Search Metabolites and Reactions by External IDs
+    {% with question_title='Search Metabolites and Reactions by External IDs'%}
+      {% with question_text='You can search for metabolites and reactions in the BiGG Database by entering an identifier from an external database. Use the dropdown menu to choose the external database, and enter the identifier in the Database ID box.'%}
         {% include 'question_mark.html' %}
       {% endwith %}
     {% endwith %}

bigg_models/templates/escher_div.html

@@ -7,8 +7,8 @@ <h2>
 		{% endwith %}
 	{% endwith %}
 </h2>
-<div id="map" class="escher-map"></div>  
-<a class="btn btn-default btn-md" href="https://escher.github.io/builder.html?map_name={{escher_maps[0]['map_name']}}" target="_blank">
+<div id="map" class="escher-map"></div>
+<a class="btn btn-default btn-md" href="https://escher.github.io/builder/index.html?enable_editing=true&map_name={{escher_maps[0]['map_name']}}" target="_blank">
   Open map in a new window
 </a>
 <a class="btn btn-default btn-md" href="https://escher.github.io/" target="_blank">

bigg_models/templates/escher_script.html

@@ -18,8 +18,11 @@
    })
    map_sel.selectAll('.reaction').on('click', function (d) {
      console.log('clicked ', d)
-     if (d.bigg_id)
-       window.location.href = '/models/{{model_bigg_id}}/reactions/' + d.bigg_id;
+     if (d.bigg_id) {
+       // Strip _copy1, etc
+       url = '/models/{{model_bigg_id}}/reactions/' + d.bigg_id.replace(/_copy[0-9]+$/, '')
+       window.location.href = url
+     }
    })
  }
 

bigg_models/version.py

@@ -1,5 +1,5 @@
 # BiGG Models follows semantic versioning, with the added requirement that
 # namespace changes only occur with major releases (e.g. 1.1.2 -> 2.0.0).
-__version__ = '1.1.0'
+__version__ = '1.2.0'
 # The BiGG Models web API is versioned separately.
 __api_version__ = 'v2'

bin/load_metanetx

@@ -33,7 +33,7 @@ files = {
     # XREF <tab> MNX_ID
     # bigg:10FTHF5GLUtl <tab> MNXR1
 
-    # 'reac_prop': 'reac_prop.tsv',
+    'reac_prop': 'reac_prop.tsv',
     # MNX_ID <tab> Equation <tab> Description <tab> Balance <tab> EC <tab> Source
 }
 
@@ -81,11 +81,15 @@ def main():
     update_synonyms(parse_xref('chem_xref', 'metabolite'), 'metabolite', session)
 
     # Update reactions
-    update_synonyms(parse_xref('reac_xref', 'reaction'), 'reaction', session)
+    reaction_xref = parse_xref('reac_xref', 'reaction')
+    reaction_xref = add_ec_numbers('reac_prop', reaction_xref)
+    update_synonyms(reaction_xref, 'reaction', session)
 
     # Update compartments
     # TODO compartment synonyms
 
+    session.close()
+
 
 def add_prefix(loc):
     """Add the MetaNetX url prefix."""
@@ -161,6 +165,37 @@ def update_synonyms(xref_dict, ref_type, session):
     print 'New %s synonyms: %d' % (ref_type, stats['not_found'])
 
 
+def add_ec_numbers(file_key, reaction_xref):
+    """Add EC numbers from the reaction properties file to the xref object.
+
+    """
+
+    # read the file
+    ec_numbers = {}
+    with open(join(data_dir, files[file_key]), 'r')  as f:
+        for line in f.readlines():
+            if line.strip().startswith('#') or line.strip() == '':
+                continue
+            split_line = [x.strip() for x in line.split('\t')]
+            # no ec number
+            if split_line[4].strip() == '':
+                continue
+            for ec in [x.strip() for x in split_line[4].split(';')]:
+                # ec_numbers[MNX_ID] = EC
+                ec_numbers[split_line[0]] = ec
+
+    for bigg_id, val in reaction_xref.iteritems():
+        if not 'mnx.equation' in val:
+            continue
+        for mnx_id in val['mnx.equation']:
+            if not mnx_id in ec_numbers:
+                continue
+            if not 'ec' in val:
+                val['ec'] = []
+            val['ec'].append(ec_numbers[mnx_id])
+
+    return reaction_xref
+
 def parse_xref(file_key, ref_type):
     """Read an xref file and generate a dict like this: