def search_gene_names(request, key=None):
'''
get: render a form for user to search_gene_names the sequence id for a fasta sequence from a genome.
post: redirect to a page which will show the id.
key: used to pass a message (via the cache)
'''
message = ''
if request.method == 'POST': # If the form has been submitted...
form = SearchGeneNamesForm(request.POST) # A form bound to the POST data
if form.is_valid(): # All validation rules pass
logging.debug(form.cleaned_data)
search_type, query_string = form.cleaned_data['search_type'], form.cleaned_data['query_string']
pairs = roundup_db.findGeneNameGenomePairsLike(
webconfig.CURRENT_RELEASE, substring=query_string,
searchType=search_type)
# store result in cache, so can do a redirect/get.
key = makeUniqueId()
roundup_util.cacheSet(key, {'search_type': search_type, 'query_string': query_string, 'pairs': pairs})
# redirect the post to a get. http://en.wikipedia.org/wiki/Post/Redirect/Get
return django.shortcuts.redirect(django.core.urlresolvers.reverse(search_gene_names_result, kwargs={'key': key}))
else:
if key and roundup_util.cacheHasKey(key):
# a message for the search page can be passed via the cache.
kw = roundup_util.cacheGet(key)
message = kw['message']
form = SearchGeneNamesForm(kw) # A bound form
else:
form = SearchGeneNamesForm() # An unbound form
example = "{'search_type': 'contains', 'query_string': 'ata'}" # javascript
return django.shortcuts.render(request, 'search_gene_names.html', {'message': message, 'form': form, 'nav_id': 'search_gene_names', 'form_doc_id': 'search_gene_names',
'form_action': django.core.urlresolvers.reverse(search_gene_names), 'form_example': example})
def lookup_result(request, key):
if roundup_util.cacheHasKey(key):
kw = roundup_util.cacheGet(key)
page = '<h2>Lookup a Sequence Id for a FASTA Sequence Result</h2>\n<h3>Query</h3>Genome: <pre>{}</pre>'.format(GENOME_TO_NAME[kw['genome']])
page += 'FASTA Sequence: <pre>{}</pre>'.format(kw['fasta'])
page += u'<h3>Result</h3>Sequence Id: {}'.format(kw['seqId'])
return django.shortcuts.render(request, 'regular.html', {'html': page, 'nav_id': 'contact'})
else:
raise django.http.Http404
def orth_query(request, queryId):
'''
run an orthology query to create a "result".
GET: return a page which will get the result of the query. either gets result from the cache or runs the query and stores the result in the cache.
'''
logging.debug('orth_query queryId={}'.format(queryId))
if not roundup_util.cacheHasKey(queryId):
raise django.http.Http404
orthQuery = roundup_util.cacheGet(queryId)
querySize = len(orthQuery['limit_genomes']) + len(orthQuery['genomes'])
resultId = getResultId(queryId)
resultPath = orthresult.getResultFilename(resultId)
logging.debug(u'orth_query():\northQuery={}\nresultId={}\nqueryId={}\nresultPath={}'.format(orthQuery, resultId, queryId, resultPath))
if USE_CACHE and roundup_util.cacheHasKey(resultId) and orthresult.resultExists(resultId):
logging.debug('cache hit.')
return django.shortcuts.redirect(django.core.urlresolvers.reverse(orth_result, kwargs={'resultId': resultId}))
elif not webconfig.NO_LSF and lsf.isJobNameOn(resultId, retry=True, delay=0.2):
logging.debug('cache miss. job is already running. go to waiting page.')
return django.shortcuts.redirect(django.core.urlresolvers.reverse(orth_wait, kwargs={'resultId': resultId}))
elif webconfig.NO_LSF or querySize <= SYNC_QUERY_LIMIT:
logging.debug('cache miss. run job sync.')
# wait for query to run and store query
roundup_util.do_orthology_query(cache_key=resultId,
cache_file=resultPath,
query_kws=orthQuery)
return django.shortcuts.redirect(
django.core.urlresolvers.reverse(orth_result,
kwargs={'resultId': resultId}))
else:
logging.debug('cache miss. run job async.')
# run on lsf and have result page poll for job completion
roundup_util.bsub_orthology_query(cache_key=resultId,
cache_file=resultPath,
query_kws=orthQuery,
job_name=resultId)
return django.shortcuts.redirect(
django.core.urlresolvers.reverse(orth_wait,
kwargs={'resultId': resultId}))
def search_gene_names_result(request, key):
'''
search_type: e.g. starts with, contains, etc.
query: the substring to search for
'''
if roundup_util.cacheHasKey(key):
kw = roundup_util.cacheGet(key)
pairs = kw['pairs']
page = '<h2>Gene Names Search Result</h2>\n'
page += u'<p>Gene names that "{}" the query string "{}":</p>\n'.format(displayName(kw['search_type']), django.utils.html.escape(kw['query_string']))
page += u'<div>{} matching combination{} of gene name and genome found. Try another <a href="{}">search</a>.</div>'.format(len(pairs), '' if len(pairs) == 1 else 's', django.core.urlresolvers.reverse(search_gene_names))
page += "<table>\n"
page += "<tr><td>Gene Name</td><td>Genome</td></tr>\n"
for geneName, genome in pairs:
page += u'<tr><td>{}</td><td>{}: {}</td></tr>\n'.format(geneName, genome, GENOME_TO_NAME[genome])
page += "</table>\n"
return django.shortcuts.render(request, 'regular.html', {'html': page, 'nav_id': 'search_gene_names'})
else:
raise django.http.Http404
