def make_dbnote():
st = state.State()
r = st.get_active()
name = r['name']
ready = True if r['ready'] == 1 else False
path = r['path']
molcount = r['molcount']
confcount = r['confcount']
basename = os.path.split(path)[1]
info = f'{basename} ({name}): ' \
f'{molcount:,} mols, {confcount:,} confs, ready={ready}'
count = st.get_queue_count()
if ready and count == 0:
link = '<a href="/changedb_page">Change Database</a>'
else:
link = '<span style="color: #ccc;">Change Database</span>'
s = f"""
<table width="100%">
<tr>
<td>{info}</td>
<td align="right" style="font-size:80%;">{link}</td>
</tr>
</table>
""".lstrip()
return s
def poll(app):
d = misc.read_config()
while True:
st = state.State()
for r in st.get_queue():
# wait for active db to be ready
while True:
active_db = st.get_active()
if active_db['ready'] == 1:
break
time.sleep(d['POLLING_INTERVAL'])
dbname = active_db['name']
oid = r['oid']
ext = r['ext']
hitsize = r['hitsize']
st.update_repo(oid, status=1, dbname=dbname)
client = d['FASTROCS_CLIENT']
host = d['FASTROCS_HOST']
query = f'instance/{oid}/query.{ext}'
hitlist = f'instance/{oid}/hitlist.sdf'
command = f'{client} {host} {query} {hitlist} {hitsize}'
print(f'[LOG:COMMAND] {command}', flush=True)
proc = misc.run_proc(command)
for line in misc.read_output(proc):
print(line, flush=True)
proc.wait()
if r['reportable']:
# Correct SDF for ROCS_REPORT
misc.fix_sdf(hitlist)
rocs_report = d['ROCS_REPORT']
report_pdf = f'instance/{oid}/report.pdf'
command = f"{rocs_report} -in {hitlist} -refmol {query} -out {report_pdf}"
print(f'[LOG:COMMAND] {command}', flush=True)
proc = misc.run_proc(command)
for line in misc.read_output(proc):
print(line, flush=True)
proc.wait()
timestamp2 = time.time()
st.update_repo(oid, timestamp2=timestamp2, status=2)
time.sleep(d['POLLING_INTERVAL'])
def upload(self, file, hitsize, remote_addr):
oid = uuid.uuid4().hex
filename = secure_filename(file.filename)
ext = oechem.OEGetFileExtension(filename)
os.makedirs(f'instance/{oid}', exist_ok=True)
opath = f'instance/{oid}/query.{ext}'
file.save(opath)
if ext != 'sq' and not misc.check_mol(opath):
os.unlink(opath)
return
st = state.State()
print('hitsize:', hitsize) #@@
st.repo_new(oid, filename, hitsize, remote_addr)
def changedb(self, dbname):
st = state.State()
if 0 < st.get_queue_count():
return
active_db = st.get_active()
count = active_db['count']
pid = active_db['pid']
st.set_active(dbname)
st.update_active_db(count=count+1)
if 0 < pid:
print('[LOG] killing', pid, flush=True)
kill = misc.run_proc(f'kill -9 {pid}')
kill.wait()
time.sleep(2) # for safety releasing network port etc.
self.fastrocs_server_proc = mp.Process(target=fastrocs_server.run, args=(self,))
self.fastrocs_server_proc.start()
def __init__(self):
Flask.__init__(self, __name__)
self.config.from_mapping(misc.read_config())
os.makedirs('instance', exist_ok=True)
self.instance_path = os.path.abspath(self.config['INSTANCE_PATH'])
st = state.State()
st.initialize(self.config['DATABASES'])
name = self.config['DEFAULT_DB']
st.set_active(name)
st.update_active_db(count=1)
self.fastrocs_server_proc = mp.Process(target=fastrocs_server.run, args=(self,))
self.fastrocs_server_proc.start()
self.polling_proc = mp.Process(target=polling.poll, args=(self,))
self.polling_proc.start()
def download(self, klass, oid):
st = state.State()
r = st.get_one(oid)
ext = r['ext']
basename = r['basename']
if klass == 'query':
iname = f'{oid}/query.{ext}'
oname = f'{basename}.{ext}'
elif klass == 'result':
iname = f'{oid}/hitlist.sdf'
oname = f'{basename}_hitlist.sdf'
else:
iname = f'{oid}/report.pdf'
oname = f'{basename}_report.pdf'
if klass == 'query':
return send_from_directory(self.instance_path, iname, as_attachment=True, \
attachment_filename=oname)
elif klass == 'result':
return send_from_directory(self.instance_path, iname, as_attachment=True, \
attachment_filename=oname)
else:
return send_from_directory(self.instance_path, iname, attachment_filename=oname)
def run(app):
FASTROCS_SERVER = misc.read_config()['FASTROCS_SERVER']
st = state.State()
active_db = st.get_active()
name = active_db['name']
path = active_db['path']
command = f'{FASTROCS_SERVER} {path}'
print(f'[LOG:COMMAND] {command}', flush=True)
proc = misc.run_proc(command)
st.update_active_db(pid=proc.pid)
for line in misc.read_output(proc):
print(line, flush=True)
if line.startswith('Total:') and line.endswith(
'conformers processed.'):
confcount = int(line.split()[1])
st.update_db(name, confcount=confcount)
if line.endswith('seconds to load database'):
loadtime = float(line.split()[0])
st.update_active_db(loadtime=loadtime, ready=1)
def background_thread():
st = state.State()
since = time.time() - app.config['MAX_DAYS'] * 60 * 60 * 24
fp_old = ''
while True:
fp = st.get_footprint(since)
if fp != fp_old:
print(f'[LOG] list updated {fp}', flush=True)
table = messaging.make_table(app.config)
db_status = messaging.make_dbnote()
args = dict(table=table, db_status=db_status)
socketio.emit('listings_changed',
args,
broadcast=True,
namespace='/listings')
else:
socketio.sleep(app.config['POLLING_INTERVAL'])
fp_old = fp
def make_table(config):
st = state.State()
now = time.time()
since = now - config['MAX_DAYS'] * 60 * 60 * 24
s = """
<table>
<tr>
<td></td>
<td><b>Query</b></td>
<td><b>Hitsize</b></td>
<td><b>Hitlist</b></td>
<td><b>ROCS Report</b></td>
<td><b>DB</b></td>
<td><b>From</b></td>
<td><b>Timestamp</b></td>
<td><b>OID</b></td>
</tr>
""".lstrip()
for r in st.get_list(since):
oid = r['oid']
basename = r['basename']
ext = r['ext']
reportable = r['reportable']
timestamp1 = r['timestamp1']
timestamp2 = r['timestamp2']
hitsize = r['hitsize']
dbname = r['dbname']
rstatus = r['status']
ip = r['ip']
timestamp1 = misc.iso_time(timestamp1, millisec=True)
rstatus_mark = ['⊹', '✷', '✓'][rstatus]
if rstatus == 1:
query_link = f'<a class="bred" href="/download/query/{oid}">{basename}.{ext}</a>'
else:
query_link = f'<a href="/download/query/{oid}">{basename}.{ext}</a>'
result_link = ''
report_link = ''
tr_begin = '<tr>'
if rstatus == 1:
tr_begin = '<tr class="bred">'
if rstatus == 2:
result_link = f'<a href="/download/result/{oid}">Hits</a>'
if reportable == 1 and rstatus == 2:
report_link = f'<a href="/download/report/{oid}" target="_blank">PDF</a>'
s += f"""
{tr_begin}
<td>{rstatus_mark}</td>
<td>{query_link}</td>
<td align="right">{hitsize}</td>
<td>{result_link}</td>
<td>{report_link}</td>
<td>{dbname}</td>
<td>{ip}</td>
<td>{timestamp1}</td>
<td><span style="font-family:monospace; font-size:80%;">{oid}</span></td>
</tr>
""".lstrip()
s += """
</table>
""".lstrip()
return s