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Working on #4 #7

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38ebbca
Closes #5
necrolyte2 Jan 15, 2016
5a9cf42
Addresses #4
necrolyte2 Jan 15, 2016
0548fa8
moved template code into template instead of in views where it should…
necrolyte2 Jan 15, 2016
96a248e
Implemented ability do download fasta file. #4
necrolyte2 Jan 15, 2016
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2 changes: 2 additions & 0 deletions biosql_pyramid/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,5 +10,7 @@ def main(global_config, **settings):
#config.add_route('home', '/')
config.add_route('summary', '/')
config.add_route('bioentry_details', 'bioentry_details')
config.add_route('genbank_upload', 'genbank_upload')
config.add_route('download_file', 'download_file')
config.scan()
return config.make_wsgi_app()
8 changes: 5 additions & 3 deletions biosql_pyramid/static/javascript/summary.js
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Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,13 @@ $(document).ready(function() {
this.disable();
},
onComplete: function(file, response) {
console.info(response);
if (response.indexOf('Success') == -1) {
alert(response);
}
//button.text('Upload');
button.removeClass("ui-state-disabled");
this.enable();
}
location.reload();
},
});

/* Hover and click logic for buttons:
Expand Down
65 changes: 40 additions & 25 deletions biosql_pyramid/templates/bioentry_details.mako
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Original file line number Diff line number Diff line change
@@ -1,25 +1,40 @@
<table id="hor-minimalist-a">
% for key, val in annotations:
<tr>
<td><b>${key}</b></td>
% if isinstance(val, list):
<td>
<table>
% for v in val:
<tr>
<td>${v[0]}</td>
</tr>
% endfor
</table>
</td>
% else:
<td>${val}</td>
% endif
</tr>
% endfor
</table>
<pre>
% for seqcol in sequence:
${seqcol}
% endfor
</pre>
<script src="${request.static_url('biosql_pyramid:static/javascript/jquery/jquery-1.3.2.min.js')}"></script>
<div id='bioentry-${id}'>
<div style='float: right'>
<button id="download-fasta-${id}">Download Fasta</button>
</div>
<div>
<table id="hor-minimalist-a">
% for key, val in info:
<tr>
<td><b>${key}</b></td>
% if isinstance(val, list):
<td>
<table>
% for v in val:
<tr>
<td>${v[0]}</td>
</tr>
% endfor
</table>
</td>
% else:
<td>${val}</td>
% endif
</tr>
% endfor
</table>
<pre>
% for seqcol in sequence:
${seqcol}
% endfor
</pre>
</div>
</div>
<script type='text/javascript'>
// Provide download fasta interaction
$( ":button" ).click(function() {
accession = this.id.split('-')[2];
window.location.href = 'download_file?accession=' + accession + '&format=fasta'
});
</script>
12 changes: 10 additions & 2 deletions biosql_pyramid/templates/summary.mako
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Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,19 @@
<body>
<h1>BioEntry Records</h1>
<div id="bioentry_records">
% for record in records:
${record | n}
% for dbid, record in records:
<h3>
<a href="bioentry_details?bioentry_key=${dbid}">${record.id} ${record.description}</a>
</h3>
<div>
</div>
% endfor
</div>
<br/>
<a href="#" id="button1" class="fg-button ui-state-default fg-button-icon-left ui-corner-all"><span class="ui-icon ui-icon-newwin"></span>GenBank Upload</a>
</body>
</html>

<!-- <a href="#" id="button_download_${id}" class="fg-button ui-state-default fg-button-icon-left ui-corner-all">
<span class="ui-icon ui-icon-newwin"></span>GenBank Upload</a>
--!>
85 changes: 52 additions & 33 deletions biosql_pyramid/views.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,14 @@
import collections
import json
from StringIO import StringIO

from pyramid.view import view_config
from pyramid.response import Response, FileIter
import pyramid.httpexceptions as httpexceptions
from mako.template import Template

from BioSQL import BioSeqDatabase
from Bio import SeqIO

dbpath = 'biosql.sqlite3'
dbname = 'local_db'
Expand All @@ -25,26 +30,8 @@ def __init__(self, request):
self.request = request

def __call__(self):
return {'records': self._get_records('')}

def _get_records(self, biodb_name):
"""Retrieve BioSQL records in the database.
"""
bioentries = self._get_bioentries(biodb_name)
records = []
for bioentry in bioentries:
key = bioentry[0]
entry = bioentry[1]
b_tmpl = Template(bioentry_template)
retrieve_url = "bioentry_details?bioentry_key=%s" % key
records.append(
b_tmpl.render(
id=entry.id,
description=entry.description,
retrieve_url=retrieve_url
)
)
return records
#return {'records': self._get_records('')}
return {'records': self._get_bioentries('')}

def _get_bioentries(self, biodb_name, start=0, limit=10):
"""Retreive bioentries associated with the database.
Expand All @@ -63,32 +50,64 @@ def bioentry_details(request):
bioentry_key = request.params.get('bioentry_key', '')
biodb = _get_db()
bioentry = biodb.get_Seq_by_primary_id(bioentry_key)
annotations = _build_annotations(bioentry)
annotations.sort()
info = _build_info(bioentry.annotations) + _build_info(bioentry.features[0].qualifiers)
info.sort()
seqstr = str(bioentry.seq)
seqstr = [
seqstr[pos:pos+80] for pos in range(0, len(seqstr), 80)
]
return {'annotations': annotations, 'sequence': seqstr}
return {'id': bioentry.id, 'info': info, 'sequence': seqstr}

def _build_annotations(bioentry):
@view_config(route_name='download_file')
def download_file(request):
biodb = _get_db()
bioentry_id = request.params.get('accession')
outformat = request.params.get('format', 'fasta')
if not bioentry_id:
raise httpexceptions.HTTPBadRequest('No Accession given')
try:
bioentry = biodb.get_Seq_by_ver(bioentry_id)
except Exception as e:
raise httpexceptions.HTTPNotFound('No entry found for %s' % bioentry_id)
try:
out = bioentry.format(outformat)
except ValueError as e:
raise httpexceptions.HTTPBadRequest('%s is not a supported format' % outformat)
output = StringIO(bioentry.format(outformat))
response = request.response
response.content_type = 'text/plain'
response.content_disposition = 'attachment; filename="%s.%s"' % (bioentry_id, outformat)
response.app_iter = FileIter(output)
return response

def _build_info(info_dict):
'''
build a simple (key, value) list from dictionary but for all values that are
iterable, " ,".join(value) them
'''
ann = {}
for key, value in bioentry.annotations.items():
info = {}
for key, value in info_dict.items():
if key.lower() == 'references':
strval = [(ref.title, ref.authors) for ref in value]
elif isinstance(value, list):
strval = ", ".join(map(str, value))
else:
strval = str(value)
ann[key] = strval
return ann.items()
info[key] = strval
return info.items()

@view_config(route_name='genbank_upload')
def genbank_upload(request):
# XXX hack for os.linesep not being present; where did it go?
# os.linesep = "\n"
biodb = _get_db()
handle = request.POST['upload_file'].file
try:
biodb.load(SeqIO.parse(handle, "genbank"))
biodb.adaptor.commit()
except Exception as e: # I would catch the IntegrityError, however, would have to somehow dynamically detect db driver and import that exception
# columns identifier, biodatabase_id are not unique
raise httpexceptions.HTTPClientError("Failed Saving record to database. Likely duplicate record")

bioentry_template = """
<h3><a href="${retrieve_url}">${id} ${description}</a></h3>
<div>
</div>
"""
handle.close()
return Response('Success', content_type='text/javascript')