def _get_issues_collections(self, date_start, date_finish):
"""
Returns two collection of Issues for both of JIRAs.
"""
io.info('Getting issues...')
sk_issues = self._sk_helper.issues_by_worklog_date_range(
date_start, date_finish)
pub_issues = self._pub_helper.issues_by_worklog_date_range(
date_start, date_finish)
sk_collection = IssuesCollection(sk_issues)
pub_collection = PubIssuesCollection(pub_issues)
sk_issues = self._sk_helper.issues(pub_collection.sk_keys)
pub_issues = self._pub_helper.get_issues_by_sk_links(
sk_collection.links)
sk_collection.merge(sk_issues)
pub_collection.merge(pub_issues)
sk_collection = self._add_sk_worklogs(sk_collection, date_start,
date_finish)
pub_collection = self._add_pub_worklogs(pub_collection, date_start,
date_finish)
return sk_collection, pub_collection
def unsync_sk_issues(self, pub_map, sk_issues):
"""
Get all SK issues with different time
Print each step
:param pub_map:
:param sk_issues:
:return:
"""
unsync_sk_issues = {}
for sk_key, pub_issues in pub_map.items():
pub_time = sum(pub_issue.spent_time for pub_issue in pub_issues)
if sk_key is None:
io.print_time_diff_line(pub_issues, None, time_diff=pub_time, status="warning")
continue
sk_issue = sk_issues[sk_key]
time_diff = pub_time - sk_issue.spent_time
io.print_time_diff_line(pub_issues, sk_issue, time_diff)
if time_diff != 0:
unsync_sk_issues[sk_key] = sk_issue
return unsync_sk_issues
def find_start_stop_fragments(self) -> SeqFragmentCollection:
start_codons = config.START_CODONS
stop_codons = config.STOP_CODONS
start_stop_fragments = []
nucleotides = self.seq_record.seq
IO.print('Parsing start - stop codon sequences...')
for nuc_strand in [nucleotides, nucleotides.reverse_complement()]:
for frame in range(0, 2):
frame_codons = self.get_codons(nuc_strand, frame)
fragment = Seq('')
is_read_started = False
for index, codon in enumerate(frame_codons):
if codon in start_codons:
fragment += codon
is_read_started = True
elif is_read_started and codon not in stop_codons:
fragment += codon
elif is_read_started and codon in stop_codons:
fragment += codon
start_stop_fragments.append(fragment)
fragment = ''
is_read_started = False
IO.success('Done')
return SeqFragmentCollection(
self.seq_record,
self.__filter_out_shorter_than(
start_stop_fragments, config.MIN_START_STOP_FRAGMENT_LENGTH))
def wrapped(*args, **kwargs):
try:
return fn(*args, **kwargs)
except Exception as e:
if message is None:
io.error(str(e))
else:
io.error(message)
exit()
def __filter_out_shorter_than(fragments: List[Seq],
min_length: int) -> List[Seq]:
filtered = []
IO.print(
f'Filtering out sequences shorter than {min_length} symbols...')
for fragment in fragments:
if len(fragment) > min_length:
filtered.append(fragment)
IO.success('Done')
return filtered
def create_pub_issue(self, sk_issue):
"""
Migrate SK issue to PUB Jira
:param sk_issue:
:return:
"""
fields = self.convert_fields(sk_issue)
click.echo("\nPlease confirm migration:")
io.print_dict(fields, indent=1)
if not click.confirm('\nMigrate?', default=False):
return None
return self._pub_jira.create_issue(fields=fields)
def get_dicodon_freq_table(self, seq_fragment_collection: SeqFragmentCollection) -> FrequencyTable:
freq_table = dict.fromkeys(self.__possible_dicodons, 0)
fragments = seq_fragment_collection.get_fragments()
IO.print('Calculating dicodon frequencies...')
for frag in fragments:
frag_dicodons = SeqUtils.get_dicodons(frag)
for dicodon in self.__possible_dicodons:
freq_table[dicodon] += frag_dicodons.count(dicodon)
IO.success('Done')
total_items = self.__get_total_dicodons_in_fragments(fragments)
normalized_table = self.__normalize_freq_table(freq_table, total_items)
return FrequencyTable(normalized_table, seq_fragment_collection.get_seq_record())
def do(self, date_start):
"""
Find and sync differences between JIRAs
:type date_start: dt
:param date_start:
"""
date_start = date_start.replace(hour=0,
minute=0,
second=0,
microsecond=0)
date_finish = dt.today().replace(tzinfo=date_start.tzinfo,
hour=23,
minute=59,
second=59)
sk, pub = self._get_issues_collections(date_start, date_finish)
for date in date_range(date_start, date_finish):
io.echo_date(date)
sk_keys = sk.filter_by_worklog_date(date).keys
sk_keys += pub.filter_by_worklog_date(date).sk_keys
sk_keys = list(set(sk_keys))
worklogs_diff = []
for sk_key in sk_keys:
sk_issue = sk.get(sk_key)
sk_worklogs = sk_issue.worklogs.filter_by_date(
date) if sk_issue else WorklogsCollection()
pub_collection = pub.filter_by_sk_key(
sk_key).filter_by_worklog_date(date)
time_diff = pub_collection.total_worklogs_time(
date) - sk_worklogs.total_time
if time_diff != 0 and sk_issue:
worklogs_diff.append((sk_issue, pub_collection, date))
self._print_line(time_diff, sk_issue, pub_collection)
if worklogs_diff and self._confirm(worklogs_diff):
self._sync_time(worklogs_diff)
def main():
try:
sk_jira = config.JiraFactory.create_sk()
pub_jira = config.JiraFactory.create_pub()
except (configparser.NoSectionError, configparser.NoOptionError):
click.echo('Please, edit config file %s' % click.format_filename(config.AppConfig.get_file_path()))
return
started = IO.input_days_ago()
TimeSynchronizer(pub_jira, sk_jira).do_from(started)
def main():
try:
sk_jira = config.JiraFactory.create_sk()
pub_jira = config.JiraFactory.create_pub()
except (configparser.NoSectionError, configparser.NoOptionError):
click.echo('Please, edit config file %s' %
click.format_filename(config.AppConfig.get_file_path()))
return
started = io.input_days_ago(default=14)
IssueSync(pub_jira, sk_jira).do_many(started)
def _print_line(self, time_diff, sk_issue=None, pub_collection=None):
"""
Print time differences information.
"""
pub_issue = pub_collection.first() if pub_collection else None
pub_link = io.highlight_key(
issue=pub_issue) if pub_issue else 'Not found'
sk_link = io.highlight_key(issue=sk_issue) if sk_issue else 'Not found'
summary = sk_issue.summary if sk_issue else pub_collection.first(
).summary
hours = io.highlight_time(time_diff, prefix='[ ', suffix=' ]', ljust=5)
click.echo('%s -> %s\t%s %s' % (pub_link.rjust(54), sk_link.ljust(41),
hours, io.truncate_summary(summary)))
if pub_collection:
for issue in pub_collection.items[1:]:
click.echo('%s' % io.highlight_key(issue=issue))
def do(self, sk_key):
"""
Doing issue migration from SK jira to PUB by SK key
:param sk_key:
:return:
"""
try:
sk_issue = self._sk_jira.issue(sk_key)
except Exception:
raise Exception('Can\'t find the issue by key: %s' % sk_key)
pub_issues = self._pub_jira.search_issues(
"'External issue ID' ~ '%s'" % sk_issue.permalink())
if pub_issues:
click.echo('\nThis task has been already migrated to PUB: ')
for issue in pub_issues:
click.echo(
io.highlight_key(issue=issue) + '\t' +
issue.fields.summary)
if not click.confirm('\nContinue?', default=False):
return
click.echo('Beginning of migration %s' %
io.highlight_key(issue=sk_issue))
pub_issue = self.create_pub_issue(sk_issue)
if pub_issue is None:
return
click.echo('Issue was migrated: %s' %
io.highlight_key(issue=pub_issue))
click.echo('Beginning of migration attachments')
self.migrate_attachments(sk_issue, pub_issue)
return pub_issue
def do_from(self, started):
"""
Find and sync differences between JIRAs
:type started: dt
:param started:
"""
today = dt.today().replace(tzinfo=started.tzinfo)
for date in date_range(started, today):
date = date.replace(hour=0, minute=0, second=0, microsecond=0)
io.print_date_line(date)
started = date.astimezone(tz=timezone.utc)
finished = started + timedelta(days=1) - timedelta(seconds=1)
pub_issues, sk_issues = self.issues(started, finished)
uncync_issues = self.unsync_sk_issues(pub_issues, sk_issues)
if uncync_issues:
self.sync(uncync_issues, pub_issues)
def _sync_time(self, items):
"""
:type issue: IssuesCollection
"""
for issue, pub_collection, date in items:
self._sk_helper.remove_worklogs(
issue.data, issue.worklogs.filter_by_date(date))
if pub_collection is None:
continue
for pub_issue in pub_collection:
[
self._sk_helper.add_worklog(issue.data, worklog)
for worklog in pub_issue.worklogs.filter_by_date(date)
]
click.echo('Synchronized %s' % io.highlight_key(issue=issue))
def migrate_issues(self, started):
"""
Migrates issues from SK to PUB.
:param started:
:return:
"""
today = dt.today().replace(tzinfo=started.tzinfo)
days = int((today - started).days) + 1
sk_issues = self._sk_jira.search_issues(
'createdDate >= startOfDay(-%dd) and (assignee=currentUser() or worklogAuthor=currentUser())'
% days,
maxResults=100000)
pub_issues = self._pub_helper.get_issues_by_sk_links(
[sk_issue.permalink() for sk_issue in sk_issues])
exists_sk_links = [PubIssue(issue).sk_url for issue in pub_issues]
new_issues = [
issue for issue in sk_issues
if issue.permalink() not in exists_sk_links
]
if not new_issues:
click.echo('Nothing to do')
return
hidden_keys = config.AppConfig.read_hidden_keys()
new_issues = [
issue for issue in new_issues if issue.key not in hidden_keys
]
m_issues, s_issues, h_issues = io.edit_unsync_issues(new_issues)
h_keys = [h_issue.key for h_issue in h_issues]
config.AppConfig.write_hidden_keys(h_keys)
for issue in m_issues:
self.migrate(issue.key)
def convert_fields(self, sk_issue):
"""
Convert SK issue to PUB fileds
:param sk_issue:
:return:
"""
click.echo()
summary = sk_issue.key + ': ' + sk_issue.fields.summary
summary = click.prompt('Summary', default=summary, type=str)
estimate = io.input_jira_estimate('Original Estimate')
labels = ['auto_migration']
if sk_issue.fields.project.key == 'ULT':
labels += ['ultra']
return {
'project': {
'id': '10204', # Sheknows DT project
'name': 'SheknowsDT'
},
'issuetype':
self.convert_issue_type(sk_issue.fields.issuetype),
'summary':
summary,
'priority':
self.convert_priority(sk_issue.fields.priority),
'description':
sk_issue.fields.description
if sk_issue.fields.description else summary,
'timetracking': {
'originalEstimate': estimate
},
'labels':
labels,
config.Issue.EXTERNAL_ID_FIELD:
sk_issue.permalink()
}
def do_many(self, started):
"""
Doing issues migration from started
:param started:
:return:
"""
today = dt.today().replace(tzinfo=started.tzinfo)
days = int((today - started).days) + 1
sk_issues = self._sk_jira.search_issues(
'createdDate >= startOfDay(-%dd) and assignee=currentUser()' %
days)
unsync_issues = []
for sk_issue in sk_issues:
pub_issues = self._pub_jira.search_issues(
"'External issue ID' ~ '%s'" % sk_issue.permalink())
if pub_issues:
continue
unsync_issues.append(sk_issue)
if not unsync_issues:
click.echo('Nothing to do')
return
hidden_keys = config.AppConfig.read_hidden_keys()
unsync_issues = [
issue for issue in unsync_issues if issue.key not in hidden_keys
]
m_issues, s_issues, h_issues = io.edit_unsync_issues(unsync_issues)
h_keys = [h_issue.key for h_issue in h_issues]
config.AppConfig.write_hidden_keys(h_keys)
for issue in m_issues:
self.do(issue.key)
def jira_credential(url, section):
credentials = (url, None, None)
try:
pub_old = AppConfig.read_jira_config(section)
credentials = (pub_old.url, pub_old.username, pub_old.password)
except (configparser.NoSectionError, configparser.NoOptionError):
pass
while True:
try:
config = IO.input_jira_credentials(*credentials)
JiraFactory.create(config)
except Exception:
click.secho(click.style('Credentials are not valid', fg='red'))
if click.confirm('Try again?', default=True):
credentials = (config.url, config.username, config.password)
continue
return
click.secho(click.style('Credentials are valid', fg='green'))
AppConfig.write_jira_config(section, config)
return
def migrate(self, sk_key):
"""
Migrates issue from SK to PUB.
"""
try:
sk_issue = self._sk_jira.issue(sk_key)
except Exception:
io.error('Can\'t find the issue by key: %s' % sk_key)
return
pub_issues = self._pub_jira.search_issues(
"'External issue ID' ~ '%s'" % sk_issue.permalink())
if pub_issues:
click.echo('\nThis task has been already migrated to PUB: ')
for issue in pub_issues:
click.echo(
io.highlight_key(issue=issue) + '\t' +
io.truncate_summary(issue.fields.summary))
if not click.confirm('\nContinue?', default=False):
return
click.echo('Beginning of migration %s' %
io.highlight_key(issue=sk_issue))
pub_issue = self.create_pub_issue(sk_issue)
if pub_issue is None:
click.echo('Error has occurred')
return
click.echo('Issue was migrated: %s' %
io.highlight_key(issue=pub_issue))
self.migrate_attachments(sk_issue, pub_issue)
return pub_issue
paths.append(f'{project_root()}/dna-data/{filename}')
return paths
if __name__ == '__main__':
start_time = time()
freqCalculator = CodonFreqCalculator()
codon_freq_tables = []
dicodon_freq_tables = []
for file in get_file_paths():
seq_fragment_collection = (SeqUtils(file)).find_start_stop_fragments()
codon_freq_tables.append(
freqCalculator.get_codon_freq_table(seq_fragment_collection))
dicodon_freq_tables.append(
freqCalculator.get_dicodon_freq_table(seq_fragment_collection))
print('')
IO.print('Generating Phylip matrix for codon frequencies...')
codon_matrix = PhylipMatrix(codon_freq_tables)
codon_matrix.print()
IO.print('Generating Phylip matrix for dicodon frequencies...')
dicodon_matrix = PhylipMatrix(dicodon_freq_tables)
dicodon_matrix.print()
end_time = time()
print(f'\nAll done, took {round(end_time - start_time, 2)}s')
def insert_iv(self, data):
iv_sh = data['df_iv']
iv_sh_digit = data['df_iv_digit']
iv_info = data['iv_info_dict']
insertData = []
for col in iv_sh.columns:
if col != 'YYYYMM' and col != 'DATE' and col != 'DV':
for j in range(len(iv_sh[col])):
if datetime.datetime.strptime(
iv_sh['YYYYMM'][j] + '01', '%Y%m%d'
).date() == self.params['t1']:
if iv_info[col]['adf_test']:
adf_gb = '1'
else:
adf_gb = '0'
elem = (str(self.params['id_nm']),
str(self.params['seq']),
str(iv_sh['YYYYMM'][j]),
str(self.params['dv']),
str(col),
float(iv_sh[col][j]),
adf_gb,
iv_info[col]['dir'],
iv_info[col]['nts'],
iv_info[col]['thres'],
iv_info[col]['a'],
iv_info[col]['b'],
iv_info[col]['c'],
iv_info[col]['d'],
int(iv_sh_digit[col][j])
)
else:
elem = (str(self.params['id_nm']),
str(self.params['seq']),
str(iv_sh['YYYYMM'][j]),
str(self.params['dv']),
str(col),
float(iv_sh[col][j]),
None,
None,
None,
None,
None,
None,
None,
None,
int(iv_sh_digit[col][j])
)
insertData.append(elem)
conn = self.db.getConn()
cur = conn.cursor()
io = IO()
file = io.print_df(
'data_%s_%s_%s'%(
self.params['id_nm'], self.params['seq'], self.params['dv']
),
insertData
)
try:
warnings.filterwarnings('always', category=MySQLdb.Warning)
with warnings.catch_warnings(record=True) as w:
cur.execute(self.CONST.QR_DELETE_IND_VAR_INFO,
(self.params['id_nm'], self.params['seq'],
self.params['dv']))
cur.execute(self.CONST.QR_INSERT_IND_VAR_INFO, file)
# todo change to file
# if len(w) > 0: self.logger.warning(w[-1].message)
conn.commit()
io.remove_file(file)
except Exception as e:
conn.rollback()
conn.close()
io.remove_file(file)
raise Exception(e)
conn.close()
def __init__(self, filename: str):
self.seq_record = SeqIO.read(filename, config.SEQ_FILE_FORMAT)
IO.success('Loaded file ' + filename)
