Adding a command for showing cells

- Fixing WormBaseIDSetter -- was skipping too many lines and not normalizing cell names
- Small update to uses of OWM._conf

Author: mwatts15

Diff for: examples/default.conf

@@ -1,5 +1,5 @@
 {
-    "rdf.source" : "lazy_pickle",
+    "rdf.source" : "zodb",
     "rdf.store_conf" : "../.owm/worm.db",
     "imports_context_id": "http://openworm.org/data/imports",
     "rdf.upload_block_statement_count" : 50

Diff for: owmeta/bundle.py

@@ -242,7 +242,7 @@ def __init__(self, ident, bundles_directory=None, version=None, conf=None, remot
             bundles_directory = expanduser(p('~', '.owmeta', 'bundles'))
         self.bundles_directory = bundles_directory
         if not conf:
-            conf = {'rdf.source': 'lazy_pickle'}
+            conf = {'rdf.source': 'zodb'}
         self.version = version
         self.remotes = remotes
         self._given_conf = conf

Diff for: owmeta/cli_hints.py

@@ -185,4 +185,11 @@
             },
         },
     },
+    'owmeta.commands.biology.CellCmd': {
+        'show': {
+            (METHOD_NAMED_ARG, 'cell_name_or_id'): {
+                'names': ['cell_name_or_id'],
+            },
+        },
+    },
 }

Diff for: owmeta/command.py

@@ -27,6 +27,7 @@
 from .command_util import (IVar, SubCommand, GeneratorWithData, GenericUserError,
                            DEFAULT_OWM_DIR)
 from .commands.bundle import OWMBundle
+from .commands.biology import CellCmd
 from .context import Context, DEFAULT_CONTEXT_KEY, IMPORTS_CONTEXT_KEY
 from .capability import provide
 from .capabilities import FilePathProvider
@@ -588,7 +589,7 @@ def edit(self, context=None, format=None, editor=None, list_formats=False):
         from subprocess import call
         if context is None:
             ctx = self._parent._default_ctx
-            ctxid = self._parent._conf()[DEFAULT_CONTEXT_KEY]
+            ctxid = self._parent._conf(DEFAULT_CONTEXT_KEY)
         else:
             ctx = Context(ident=context, conf=self._parent._conf())
             ctxid = context
@@ -722,6 +723,8 @@ class OWM(object):
 
     registry = SubCommand(OWMRegistry)
 
+    cell = SubCommand(CellCmd)
+
     def __init__(self, owmdir=None):
         self.progress_reporter = default_progress_reporter
         self.message = lambda *args, **kwargs: print(*args, **kwargs)
@@ -1390,7 +1393,7 @@ def list_contexts(self):
 
     @property
     def rdf(self):
-        return self._conf()['rdf.graph']
+        return self._conf('rdf.graph')
 
     def commit(self, message):
         '''

Diff for: owmeta/commands/biology.py

@@ -0,0 +1,56 @@
+import six
+
+from ..command_util import GeneratorWithData
+from ..cell import Cell
+
+
+class CellCmd(object):
+    '''
+    Commands for dealing with biological cells
+    '''
+
+    def __init__(self, parent, *args, **kwargs):
+        self._parent = parent
+
+    def show(self, cell_name_or_id, context=None):
+        '''
+        Show information about the cell
+
+        Parameters
+        ----------
+        cell_name_or_id : str
+            Cell name or Cell URI
+        context : str
+            Context to search in. Optional, defaults to the default context.
+        '''
+
+        if not context:
+            ctx = self._parent._default_ctx
+        else:
+            ctx = Context(context)
+
+        def helper():
+            for cell in ctx.stored(Cell).query(name=cell_name_or_id).load():
+                yield cell
+                break
+            else: # no break
+                uri = self._parent._den3(cell_name_or_id)
+                for x in ctx.stored(Cell)(ident=uri).load():
+                    yield cell
+
+        def fmt_text(cell):
+            try:
+                sio = six.StringIO()
+
+                nm = self._parent._conf('rdf.namespace_manager')
+                print('%s(%s)' % (cell.__class__.__name__, nm.normalizeUri(cell.identifier)), file=sio)
+                print('    Lineage name: %s' % cell.lineageName(), file=sio)
+                print('    Name: %s' % cell.name(), file=sio)
+                print('    WormBase ID: %s' % cell.wormbaseID(), end='', file=sio)
+                return sio.getvalue()
+            except AttributeError:
+                res = str(cell)
+                L.error('Failed while creating formatting string representation for %s', res)
+                return res
+
+        return GeneratorWithData(helper(), text_format=fmt_text)

Diff for: owmeta/data_trans/wormbase.py

@@ -243,7 +243,8 @@ class WormbaseIDSetter(CSVDataTranslator):
     def translate(self, data_source, cells_source):
         """ Upload muscles and the neurons that connect to them """
         res = self.make_new_output((data_source,))
-        with self.make_reader(data_source, skipinitialspace=True, skipheader=True, skiplines=1, dict_reader=True) as csvreader:
+        with self.make_reader(data_source, skipinitialspace=True, skipheader=True,
+                skiplines=1, dict_reader=True) as csvreader:
             # TODO: Improve this evidence by going back to the actual research
             #       by using the wormbase REST API in addition to or instead of the CSV file
             with res.evidence_context(Evidence=Evidence, Website=Website) as ctx:
@@ -252,10 +253,11 @@ def translate(self, data_source, cells_source):
                 ctx.Evidence(reference=doc, supports=doc_ctx.rdf_object)
 
             for num, line in enumerate(csvreader):
-                if num < 2:  # skip rows with no data
+                if num < 1:  # skip rows with no data
                     continue
 
-                cell = cells_source.data_context.stored(Cell).query(name=line['Cell'])
+                cell_name = normalize_cell_name(line['Cell'])
+                cell = cells_source.data_context.stored(Cell).query(name=cell_name)
                 for loaded_cell in cell.load():
                     doc_ctx(loaded_cell).wormbaseID(line['WormBase ID'])
 

Diff for: readme.conf

@@ -1,5 +1,5 @@
 {
-    "rdf.source" : "lazy_pickle",
+    "rdf.source" : "zodb",
     "rdf.store_conf" : "$HERE/.owm/worm.db"
 }
 

Diff for: tests/data_integrity_test.conf

@@ -1,7 +1,7 @@
 {
     "connectomecsv" : "OpenWormData/aux_data/connectome.csv",
     "neuronscsv" : "OpenWormData/aux_data/neurons.csv",
-    "rdf.source" : "lazy_pickle",
+    "rdf.source" : "zodb",
     "rdf.store_conf" : ".owm/worm.db",
     "rdf.upload_block_statement_count" : 50
 }