def entries_file():
# TODO: speed up this method
collection = request.args.get('collection')
databank_name = request.args.get('databank')
comment_text = request.args.get('comment')
# listing determines what is shown per entry(pdb ids, databank names, comments, file names, etc.)
listing = request.args.get('listing')
_log.info("request for entries file %s %s %s %s" %(collection, databank_name, comment_text, listing))
if not listing:
return ''
listing = listing.lower()
entries = []
name="0"
if databank_name and collection:
entries = get_entries_from_collection(databank_name, collection)
name = "%s%s" %(databank_name, collection)
elif databank_name and comment_text:
entries = get_entries_with_comment(databank_name, comment_text)
name = "%s%s" %(databank_name, remove_tags(comment_text))
elif comment_text:
entries = get_all_entries_with_comment(comment_text)
name = remove_tags(comment_text)
text = ''
if listing == 'comments':
d = {}
for entry in entries:
if 'comment' in entry:
c = entry ['comment']
if c not in d:
d [c] = ''
d [c] += '%s,%s\n' %(entry['databank_name'], entry['pdbid'])
for comment in d:
text += comment + ":\n" + d [comment]
else:
for entry in entries:
if listing == 'pdbids':
text += entry ['pdbid'] + '\n'
elif listing == 'entries':
text += '%s,%s\n' %(entry['databank_name'], entry ['pdbid'])
elif listing == 'files' and 'filepath' in entry:
text += '%s,%s,%s\n' %(entry['databank_name'], entry ['pdbid'], entry ['filepath'])
response = Response(text, mimetype='text/plain')
response.headers["Content-Disposition"] = "attachment; filename=%s" %('%s_%s' %(name, listing))
return response
def entries_file():
# TODO: speed up this method
collection = request.args.get('collection')
databank_name = request.args.get('databank')
comment_text = request.args.get('comment')
# listing determines what is shown per entry(pdb ids, databank names,
# comments, file names, etc.)
listing = request.args.get('listing')
_log.info("request for entries file %s %s %s %s" % (
collection, databank_name, comment_text, listing))
if not listing:
return ''
listing = listing.lower()
entries = []
name = "0"
if databank_name and collection:
entries = get_entries_from_collection(databank_name, collection)
name = "%s%s" % (databank_name, collection)
elif databank_name and comment_text:
entries = get_entries_with_comment(databank_name, comment_text)
name = "%s%s" % (databank_name, remove_tags(comment_text))
elif comment_text:
entries = get_all_entries_with_comment(comment_text)
name = remove_tags(comment_text)
text = ''
if listing == 'comments':
d = {}
for entry in entries:
if 'comment' in entry:
c = entry['comment']
if c not in d:
d[c] = ''
d[c] += '%s,%s\n' % (entry['databank_name'], entry['pdb_id'])
for comment in d:
text += comment + ":\n" + d[comment]
else:
for entry in entries:
if listing == 'pdb_ids':
text += entry['pdb_id'] + '\n'
elif listing == 'entries':
text += '%s,%s\n' % (entry['databank_name'], entry['pdb_id'])
elif listing == 'files' and 'filepath' in entry:
text += '%s,%s,%s\n' % (entry['databank_name'],
entry['pdb_id'],
entry['filepath'])
response = Response(text, mimetype='text/plain')
header_val = "attachment; filename=%s_%s" % (name, listing)
response.headers["Content-Disposition"] = header_val
return response
def entries():
collection = request.args.get('collection')
databank_name = request.args.get('databank')
comment_text = request.args.get('comment')
_log.info("request for entries %s %s %s" %
(collection, databank_name, comment_text))
title = 'No entries selected'
entries = []
files = []
comments = {}
if databank_name and collection:
start_time = time()
entries = get_entries_from_collection(databank_name, collection)
end_time = time()
title = "%s %s" % (databank_name, collection)
elif databank_name and comment_text:
start_time = time()
entries = get_entries_with_comment(databank_name, comment_text)
end_time = time()
title = comment_text
elif comment_text:
start_time = time()
entries = get_all_entries_with_comment(comment_text)
end_time = time()
title = comment_text
databank = storage.find_one('databanks', {'name': databank_name})
for entry in entries:
if databank and 'filepath' in entry:
f = {
'name': os.path.basename(entry['filepath']),
'url': get_file_link(databank, entry['pdbid'])
}
files.append(f)
elif 'comment' in entry:
if entry['comment'] not in comments:
comments[entry['comment']] = []
comments[entry['comment']].append(
'%s,%s' % (entry['databank_name'], entry['pdbid']))
comment_tree = comments_to_tree(comments)
return render_template('entries/EntriesPage.html',
db_tree=db_tree,
nav_disabled='entries',
collection=collection,
databank_name=databank_name,
comment=comment_text,
title=title,
entries=entries,
files=files,
comment_tree=comment_tree)
def entries(databank_name, collection):
"""
Request all entries in a given databank and collection.
:param databank_name: Name of the whynot databank.
:param collection: Name of the collection within the databank. Either PRESENT, VALID, OBSOLETE, MISSING, ANNOTATED or UNANNOTATED.
:return: a text string with all pdb ids of entries that match the selection.
"""
# TODO: SPEED THIS UP
text = ""
for entry in get_entries_from_collection(databank_name, collection):
text += entry['pdbid'] + '\n'
return Response(text, mimetype='text/plain')
def entries (databank_name, collection):
"""
Request all entries in a given databank and collection.
:param databank_name: Name of the whynot databank.
:param collection: Name of the collection within the databank. Either PRESENT, VALID, OBSOLETE, MISSING, ANNOTATED or UNANNOTATED.
:return: a text string with all pdb ids of entries that match the selection.
"""
# TODO: SPEED THIS UP
text = ""
for entry in get_entries_from_collection (databank_name, collection):
text += entry ['pdbid'] + '\n'
return Response (text, mimetype='text/plain')
def entries():
collection = request.args.get('collection')
databank_name = request.args.get('databank')
comment_text = request.args.get('comment')
_log.info("request for entries %s %s %s" %(collection, databank_name, comment_text))
title = 'No entries selected'
entries = []
files = []
comments = {}
if databank_name and collection:
start_time = time()
entries = get_entries_from_collection(databank_name, collection)
end_time = time()
title = "%s %s" %(databank_name, collection)
elif databank_name and comment_text:
start_time = time()
entries = get_entries_with_comment(databank_name, comment_text)
end_time = time()
title = comment_text
elif comment_text:
start_time = time()
entries = get_all_entries_with_comment(comment_text)
end_time = time()
title = comment_text
databank = storage.find_one('databanks', {'name': databank_name})
for entry in entries:
if databank and 'filepath' in entry:
f = {'name': os.path.basename(entry ['filepath']),
'url': get_file_link(databank, entry ['pdbid'])}
files.append(f)
elif 'comment' in entry:
if entry ['comment'] not in comments:
comments [entry ['comment']] = []
comments [entry ['comment']].append('%s,%s' %(entry ['databank_name'], entry ['pdbid']))
comment_tree = comments_to_tree(comments)
return render_template('entries/EntriesPage.html', db_tree=db_tree, nav_disabled='entries',
collection=collection, databank_name=databank_name, comment=comment_text,
title=title, entries=entries, files=files, comment_tree=comment_tree)
def resources(tolist):
_log.info("request for resources " + tolist)
if '_' not in tolist: # syntax error
return '', 400
# TODO: speed up this method
last = tolist.rfind('_')
databank_name = tolist [:last]
collection = tolist [last + 1:]
text = ''
for entry in get_entries_from_collection(databank_name, collection):
text += entry ['pdbid'] + '\n'
response = Response(text, mimetype='text/plain')
response.headers["Content-Disposition"] = "attachment; filename=%s" % tolist
return response
def resources(tolist):
_log.info("request for resources " + tolist)
if '_' not in tolist:
return '', 400
# TODO: speed up this method
last = tolist.rfind('_')
databank_name = tolist[:last]
collection = tolist[last + 1:]
text = ''
for entry in get_entries_from_collection(databank_name, collection):
text += entry['pdb_id'] + '\n'
response = Response(text, mimetype='text/plain')
header_val = "attachment; filename=%s" % tolist
response.headers["Content-Disposition"] = header_val
return response