Loading the NCBI36 Ensembl gives an OperationalError

[arahuja]

Anyone seen this before? `AttributeError: 'OperationalError' object has no attribute 'message'

INFO:root:Running sqlite query: "CREATE TABLE _datacache_metadata (version INT)"
INFO:root:Running sqlite query: "INSERT INTO _datacache_metadata VALUES (2)"

---------------------------------------------------------------------------
OperationalError                          Traceback (most recent call last)
/Users/arahuja/src/hammerlab/pyensembl/pyensembl/database.py in run_sql_query(self, sql, required, query_params)
    375         try:
--> 376             cursor = self.connection.execute(sql, query_params)
    377         except sqlite3.OperationalError as e:

OperationalError: no such column: transcript_biotype

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
<ipython-input-30-bcfa1b1c5957> in <module>()
      2 for patient_id in PATIENTS:
      3     primary_variants = PRIMARY_PATIENT_VARIANTS[patient_id]
----> 4     primary_effects = primary_variants.effects()
      5     recur_variants = RECUR_PATIENT_VARIANTS[patient_id]
      6     row = {'patient_id': patient_id,

/Users/arahuja/src/hammerlab/varcode/varcode/common.py in wrapped_fn(*args, **kwargs)
     43         key = (args, tuple(sorted(kwargs.items())))
     44         if key not in memoized_values:
---> 45             memoized_values[key] = fn(*args, **kwargs)
     46         return memoized_values[key]
     47 

/Users/arahuja/src/hammerlab/varcode/varcode/variant_collection.py in effects(self, raise_on_error)
     85         return EffectCollection([
     86             effect
---> 87             for variant in self
     88             for effect in variant.effects(raise_on_error=raise_on_error)
     89         ])

/Users/arahuja/src/hammerlab/varcode/varcode/variant_collection.py in <listcomp>(.0)
     86             effect
     87             for variant in self
---> 88             for effect in variant.effects(raise_on_error=raise_on_error)
     89         ])
     90 

/Users/arahuja/src/hammerlab/varcode/varcode/common.py in wrapped_fn(*args, **kwargs)
     43         key = (args, tuple(sorted(kwargs.items())))
     44         if key not in memoized_values:
---> 45             memoized_values[key] = fn(*args, **kwargs)
     46         return memoized_values[key]
     47 

/Users/arahuja/src/hammerlab/varcode/varcode/variant.py in effects(self, raise_on_error)
    362             return EffectCollection([Intergenic(self)])
    363 
--> 364         overlapping_transcripts = self.transcripts
    365 
    366         # group transcripts by their gene ID

/Users/arahuja/anaconda/envs/py34/lib/python3.4/site-packages/memoized_property-1.0.2-py3.4.egg/memoized_property.py in fget_memoized(self)
     38     def fget_memoized(self):
     39         if not hasattr(self, attr_name):
---> 40             setattr(self, attr_name, fget(self))
     41         return getattr(self, attr_name)
     42 

/Users/arahuja/src/hammerlab/varcode/varcode/variant.py in transcripts(self)
    283     def transcripts(self):
    284         return self.ensembl.transcripts_at_locus(
--> 285             self.contig, self.start, self.end)
    286 
    287     @memoized_property

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/ensembl_release.py in transcripts_at_locus(self, contig, position, end, strand)
    256         return [
    257             self.transcript_by_id(transcript_id)
--> 258             for transcript_id in transcript_ids
    259         ]
    260 

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/ensembl_release.py in <listcomp>(.0)
    256         return [
    257             self.transcript_by_id(transcript_id)
--> 258             for transcript_id in transcript_ids
    259         ]
    260 

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/common.py in wrapped_fn(*args, **kwargs)
     52         cache_key = _memoize_cache_key(args, kwargs)
     53         if cache_key not in cache:
---> 54             value = fn(*args, **kwargs)
     55             cache[cache_key] = value
     56             return value

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/ensembl_release.py in transcript_by_id(self, transcript_id)
    575             filter_value=transcript_id,
    576             feature="transcript",
--> 577             distinct=True)
    578         if not result:
    579             raise ValueError("Transcript not found: %s" % (transcript_id,))

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/common.py in wrapped_fn(*args, **kwargs)
     52         cache_key = _memoize_cache_key(args, kwargs)
     53         if cache_key not in cache:
---> 54             value = fn(*args, **kwargs)
     55             cache[cache_key] = value
     56             return value

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/database.py in query_one(self, select_column_names, filter_column, filter_value, feature, distinct, required)
    428             feature,
    429             distinct=distinct,
--> 430             required=required)
    431 
    432         if len(results) == 0:

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/common.py in wrapped_fn(*args, **kwargs)
     52         cache_key = _memoize_cache_key(args, kwargs)
     53         if cache_key not in cache:
---> 54             value = fn(*args, **kwargs)
     55             cache[cache_key] = value
     56             return value

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/database.py in query(self, select_column_names, filter_column, filter_value, feature, distinct, required)
    411         query_params = [filter_value]
    412         return self.run_sql_query(
--> 413             sql, required=required, query_params=query_params)
    414 
    415     @memoize

/Users/arahuja/src/hammerlab/pyensembl/pyensembl/database.py in run_sql_query(self, sql, required, query_params)
    378             logging.warn(
    379                 "Encountered error \"%s\" from query \"%s\" with parameters %s",
--> 380                 e.message, sql, query_params)
    381             raise
    382         results = cursor.fetchall()

AttributeError: 'OperationalError' object has no attribute 'message'

[tavinathanson]

I'm also getting this for release 54.