code stringlengths 3 6.57k |
|---|
context.bind.scalar(text("SELECT max(journalid) |
range(1, max_journalid + 1, BATCH_SIZE) |
text("UPDATE journal SET hidden = settings ~ 'h', friends_only = settings ~ 'f' WHERE (journalid BETWEEN :start AND :end) |
AND (hidden IS NULL OR friends_only IS NULL) |
text("UPDATE journal SET hidden = settings ~ 'h', friends_only = settings ~ 'f' WHERE (hidden IS NULL OR friends_only IS NULL) |
sa.BOOLEAN() |
sa.BOOLEAN() |
sa.BOOLEAN() |
sa.BOOLEAN() |
downgrade() |
sa.BOOLEAN() |
sa.BOOLEAN() |
sa.BOOLEAN() |
sa.BOOLEAN() |
op.get_context() |
context.autocommit_block() |
context.bind.scalar(text("SELECT max(charid) |
range(1, max_charid + 1, BATCH_SIZE) |
regexp_replace(settings, '[hf]', '', 'g') |
WHERE ((settings ~ 'h') |
OR (settings ~ 'f') |
AND (charid BETWEEN :start AND :end) |
regexp_replace(settings, '[hf]', '', 'g') |
WHERE ((settings ~ 'h') |
OR (settings ~ 'f') |
context.bind.scalar(text("SELECT max(journalid) |
range(1, max_journalid + 1, BATCH_SIZE) |
regexp_replace(settings, '[hf]', '', 'g') |
WHERE ((settings ~ 'h') |
OR (settings ~ 'f') |
AND (journalid BETWEEN :start AND :end) |
regexp_replace(settings, '[hf]', '', 'g') |
WHERE ((settings ~ 'h') |
OR (settings ~ 'f') |
AlleyoopUtrRates(Process) |
default("?") |
DataField("alignment:bam:slamdunk", label="Slamdunk results") |
FileField(label="Region of interest conversion rate plot") |
StringField(label="Species") |
StringField(label="Build") |
run(self, inputs, outputs) |
os.path.basename(inputs.slamdunk.output.bam.path) |
basename.endswith(".bam") |
TEE(retcode=None) |
self.error("Alleyoop utrrates analysis failed.") |
os.path.join("utrrates", f"{name}_mutationrates_utr.csv") |
os.path.join("utrrates", f"{name}_mutationrates.txt") |
os.rename(rates_file, rates_file_renamed) |
os.path.join("utrrates", f"{name}_mutationrates_utr.pdf") |
Database() |
ORMGroup(db.Entity) |
PrimaryKey(int, column='group_id') |
Optional(str, column='group_name') |
Optional(str, column='group_header') |
Optional(str, column='group_footer') |
Set(lambda: ORMFixtue.ORMContact, table='address_in_groups', column='id', reverse='groups', lazy=True) |
ORMContact(db.Entity) |
PrimaryKey(int, column='id') |
Optional(str, column='firstname') |
Optional(str, column='lastname') |
Optional(str, column='address') |
Optional(str, column='home') |
Optional(str, column='mobile') |
Optional(str, column='work') |
Optional(str, column='email') |
Optional(str, column='email2') |
Optional(str, column='email3') |
Optional(datetime, column='deprecated') |
Set(lambda: ORMFixtue.ORMGroup, table='address_in_groups', column='group_id', reverse='contacts', lazy = True) |
__init__(self, host, name, user, password) |
self.db.bind('mysql', host=host, database=name, user=user, password=password, conv=decoders) |
self.db.generate_mapping() |
convert_groups_to_model(self, groups) |
convert(group) |
Group(id=str(group.id) |
list(map(convert, groups) |
get_group_list(self) |
self.convert_groups_to_model(select(g for g in ORMFixtue.ORMGroup) |
convert_contacts_to_model(self, contacts) |
convert(contact) |
Contact(id=str(contact.id) |
list(map(convert, contacts) |
get_contact_list(self) |
self.convert_contacts_to_model(select(c for c in ORMFixtue.ORMContact if c.deprecated is None) |
get_orm_group(self, group) |
list(select(g for g in ORMFixtue.ORMGroup if g.id == group.id) |
get_contacts_in_group(self, group) |
self.get_orm_group(group) |
self.convert_contacts_to_model(orm_group.contacts) |
get_contacts_not_in_group(self, group) |
self.get_orm_group(group) |
select(c for c in ORMFixtue.ORMContact if c.deprecated is None and orm_group not in c.groups) |
get_contact_group_boundry(self) |
list(select(d for d in ORMFixtue.ORMBoundary) |
CarState(CarStateBase) |
__init__(self, CP) |
super() |
__init__(CP) |
CANDefine(DBC[CP.carFingerprint]["pt"]) |
update(self, cp, cp_cam) |
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