def main():
Print('Merge finder starting')
with open(JSON, 'r') as f: # Read current table data
olddat = json.load(f)['aaData']
ids = {}
merged = []
for ali in olddat:
this = ali[3] # this = ali.id
current = ids.get(this) # I'm assuming/hoping this is O(1), i.e. independent of the size of the dict
if current is None: # No match for this id
ids[this] = ali[0] # ids[this] = ali.seq # this id corresponds to this seq
else: # found a match (i.e. a merge)
seq = ali[0]
if seq > current:
big = seq, current
else:
big = current, seq
Print(big[0], 'seems to have merged with', big[1])
merged.append(big)
if merged:
try:
email('Aliquot merge!', '\n'.join('{} seems to have merged with {}'.format(*merge) for merge in merged))
except Exception as e:
Print("alimerge email failed")
Print('Merge finder finished')
def main():
err = "Error: commands are 'add', 'drop', 'send', 'update', 'print', or 'spider'"
from sys import argv, exit
if len(argv) < 2:
print(err)
exit(-1)
get_all_reservations()
if argv[1] == 'send':
if len(argv[2:]) < 1: argv.append('')
send(' '.join(argv[2:]))
elif argv[1] == 'add':
backup()
db = read_db()
if len(argv[2:]) < 2:
Print("Error: {} add <name> <seq> [<seq>...]".format(argv[0]))
else:
Print("Add {} seqs".format(len(argv[3:])))
add_db(db, argv[2], [int(seq.replace(',','')) for seq in argv[3:]])
write_db(db)
elif argv[1] == 'drop':
backup()
db = read_db()
if len(argv[2:]) < 2:
Print("Error: {} add <name> <seq> [<seq>...]".format(argv[0]))
else:
Print("Drop {} seqs".format(len(argv[3:])))
drop_db(db, argv[2], [int(seq.replace(',','')) for seq in argv[3:]])
write_db(db)
elif argv[1] == 'print':
write_db(read_db())
with open(resfile, 'r') as f:
for line in f:
print(line, end='') # Line newline + print newline = extra whitespace
elif argv[1] == 'update':
update()
elif argv[1] == 'spider':
try:
with open(pid_file, 'r') as f:
last_pid = int(f.read())
except FileNotFoundError:
last_pid = None
last_pid = spider(last_pid)
with open(pid_file, 'w') as f:
f.write(str(last_pid) + '\n')
else:
print(err)
exit(-1)
if email_msg:
try:
email('Reservations script warnings', email_msg)
except Exception as e:
Print('Email failed:', e)
Print('Message:\n', email_msg)
def inner_main(special=None):
global error_msg
print("\n" + strftime(datefmt))
total = linecount(seqfile)
if special:
this = special
else:
this, start = current_update(per_hour)
reserves, updated = get_reservations(res_post_ids)
data, oldinfo = get_old_info(JSON, reserves, this, drop)
Print("Init complete, starting FDB queries")
count = 0
for old in oldinfo: # Loop over every sequence to be updated
if quitting:
data.append(old)
continue
ali = check(old, reserves=reserves, special=special)
if ali:
data.append(ali)
if not quitting:
count += 1
Print(count, "sequences complete:", old.seq)
sleep(1)
with open(template, "r") as f: # Read in webpage templates
html = f.read()
with open(template2, "r") as f:
stats = f.read()
# dato = {ali.seq: ali for ali in data}
# data = [dato[seq] for seq in set(dato.keys())]
# Now get all the stats (i.e. count all the instances of stuff)
sizes = Counter()
lens = Counter()
guides = Counter()
progs = Counter()
cofacts = Counter()
totsiz = 0
totlen = 0
avginc = 0
totprog = 0
txtdata = ""
for ali in sorted(data, key=lambda ali: ali.seq):
sizes[ali.size] += 1
totsiz += ali.size
lens[ali.index] += 1
totlen += ali.index
guides[ali.guide] += 1
avginc += ali.index / ali.size
progs[ali.progress] += 1
cofacts[ali.cofact] += 1
txtdata += str(ali)
if isinstance(ali.progress, int):
totprog += 1
# Create broken sequences HTML
if broken:
# horizontal table: create a list of tuples containing each column (i.e. each sequence)
entries = (
(
"""<a href="http://factordb.com/sequences.php?se=1&aq={}&action=last20">{}</a>""".format(
broken[seq][1], seq
),
str(broken[seq][0]),
)
for seq in sorted(broken)
)
row1, row2 = zip(*entries) # zip converts column data into row order
r1 = "".join("<td>{}</td>".format(datum) for datum in row1)
r2 = "".join("<td>{}</td>".format(datum) for datum in row2)
borken_html = '<table><tr><th scope="row">Sequence</th>{}</tr><tr><th scope="row">Index offset</th>{}</tr></table>'.format(
r1, r2
)
unborken_html = ""
else:
borken_html = ""
unborken_html = "none currently."
html = html.format(
updated, unborken_html, borken_html
) # Imbue the template with the reservation time and broken sequences
# Put stats table in json-able format
lentable = []
lencount = 0
sizetable = [[key, value] for key, value in sizes.items()]
cofactable = [[key, value] for key, value in cofacts.items()]
for leng, cnt in sorted(lens.items(), key=lambda tup: tup[0]):
lentable.append([leng, cnt, "{:2.2f}".format(lencount / (total - cnt) * 100)])
lencount += cnt
guidetable = [[key, value] for key, value in guides.items()]
progtable = [[key, value] for key, value in progs.items()]
stats = stats.format(totinc=totlen / totsiz, avginc=avginc / total, totprog=totprog, progcent=totprog / total)
# Write all the data and webpages
with open(FILE, "w") as f:
f.write(html)
with open(TXT, "w") as f:
f.write(txtdata)
with open(STATS, "w") as f:
f.write(stats)
with open(JSON, "w") as f:
f.write(json.dumps({"aaData": data}).replace("],", "],\n") + "\n")
with open(STATSON, "w") as f:
f.write(
json.dumps(
{
"aSizes": sizetable,
"aCofacts": cofactable,
"aGuides": guidetable,
"aProgress": progtable,
"aLens": lentable,
}
).replace("],", "],\n")
+ "\n"
)
# Cleanup
if not special:
start += count
if start >= total:
start = 0
if count != per_hour and start != 0:
error_msg += "Something went wrong. Only {} seqs were updated.\n".format(count)
Print("Next start is", start)
with open(statefile, "w") as conf: # Save how many sequences we updated
conf.write(str(start) + "\n")
if error_msg:
try:
email("Aliquot failure!", error_msg)
except Exception as e:
Print("Email failed:", e)
Print("Message:\n", error_msg)
Print("Written HTML and saved state.")
