def databanks(name=None):
if name is None:
databanks = list(storage.db.databanks.find({}))
else:
databanks = [storage.db.databanks.find_one({'name': name})]
db_tree = get_databank_hierarchy()
return render_template('databank.html', db_tree=db_tree,
nav_disabled='databanks', databanks=databanks)
def search(pdb_id):
_log.info("request for pdb_id " + pdb_id)
# On old browsers, the pdb id might end up in the url parameters:
urlparam = request.args.get('pdb_id', '')
if len(urlparam) == 4:
pdb_id = urlparam
db_tree = get_databank_hierarchy()
results = search_results_for(pdb_id)
db_order = names_from_hierarchy(db_tree)
return render_template('search_results.html', db_tree=db_tree,
db_order=db_order, pdb_id=pdb_id, results=results)
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:
entries = list(get_entries_from_collection(databank_name, collection))
title = "%s %s" % (databank_name, collection)
elif databank_name and comment_text:
entries = list(get_entries_with_comment(databank_name, comment_text))
title = comment_text
elif comment_text:
entries = list(get_all_entries_with_comment(comment_text))
title = comment_text
databank = storage.db.databanks.find_one({'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['pdb_id'])}
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['pdb_id']))
comment_tree = comments_to_tree(comments)
db_tree = get_databank_hierarchy()
return render_template('entries.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 docs():
from whynot.api.routes import annotations, entries
p = re.compile(r"\@bp\.route\s*\(\'([\w\/\<\>]*)\'\)")
fs = [annotations, entries]
docs = {}
for f in fs:
src = inspect.getsourcelines(f)
m = p.search(src[0][0])
if not m: # pragma: no cover
_log.debug("Unable to document function '{}'".format(f))
continue
url = m.group(1)
docstring = inspect.getdoc(f)
docs[url] = docstring
db_tree = get_databank_hierarchy()
return render_template('docs.html', docs=docs, db_tree=db_tree)
bp = Blueprint('dashboard', __name__)
date_format = '%d/%m/%Y %H:%M'
from storage import storage
def names_from_hierarchy(d):
names = []
for key in sorted(d.keys()):
names.append(key)
names.extend(names_from_hierarchy(d [key]))
return names
db_tree = get_databank_hierarchy()
db_order = names_from_hierarchy(db_tree)
@bp.route('/')
def index():
return render_template('home/HomePage.html', db_tree=db_tree)
@bp.route('/search/pdbid/<pdbid>/')
def search(pdbid):
_log.info("request for pdbid " + pdbid)
# On old browsers, the pdb id might end up in the url parameters:
urlparam = request.args.get('pdbid', '')
if len(urlparam) == 4:
pdbid = urlparam
def comment():
db_tree = get_databank_hierarchy()
return render_template('comments.html', db_tree=db_tree,
nav_disabled='comments')
def about():
db_tree = get_databank_hierarchy()
return render_template('about.html', db_tree=db_tree, nav_disabled='about')
def index():
db_tree = get_databank_hierarchy()
return render_template('index.html', db_tree=db_tree)
def statistics():
db_tree = get_databank_hierarchy()
return render_template('stats.html', nav_disabled='statistics',
db_tree=db_tree)
date_format = '%d/%m/%Y %H:%M'
from storage import storage
def names_from_hierarchy(d):
names = []
for key in sorted(d.keys()):
names.append(key)
names.extend(names_from_hierarchy(d[key]))
return names
db_tree = get_databank_hierarchy()
db_order = names_from_hierarchy(db_tree)
@bp.route('/')
def index():
return render_template('home/HomePage.html', db_tree=db_tree)
@bp.route('/search/pdbid/<pdbid>/')
def search(pdbid):
_log.info("request for pdbid " + pdbid)
# On old browsers, the pdb id might end up in the url parameters:
urlparam = request.args.get('pdbid', '')
if len(urlparam) == 4: