def add_changelog_template(token: str, patch_version: int, cwd: str) -> None:
branch_name = changelog_branch_name(patch_version)
git_command("checkout", "-b", branch_name, cwd=cwd)
execute_command("python", "changelog.py", "--token", token, cwd=cwd)
git_command("add", "_posts", cwd=cwd)
git_command("commit", "-m", f"Changelog {patch_version}", cwd=cwd)
git_command("push", "origin", branch_name, cwd=cwd)
def pull_branch(branch):
output = execute_command('git checkout ' + branch)
if output.find('error:') > -1:
print_in_color("no branch exist for this name".upper(), 'red')
return
execute_command('git pull origin ' + branch)
print_in_color('succesfully pulled latest '.upper() + branch + ' IN REPO',
'green')
def _update_locally(self) -> None:
execute_command("cargo", "build", "--manifest-path",
"attributes-info/Cargo.toml", "--package",
"attributes-info")
execute_command(
"cargo",
"run",
"--manifest-path",
"attributes-info/Cargo.toml",
"--package",
"attributes-info",
"--bin",
"attributes-info",
)
def set_cap_source(cap_source, option):
""" Set the Caption Source. Option: 'Mic' (microphone) or
'Mix' (soundcard output). """
def get_numid_str(s):
""" extract the X value from numid=X,... """
back = None
result = re.search(r'numid=(\d+),', s)
if result:
back = result.group(1)
return back
if len(cap_source) == 0:
return
# else
id_str = get_numid_str(cap_source[0])
option_id_str = None
if id_str:
for e in cap_source:
result = re.search(r'Item #(\d+) '+"'"+option+"'", e)
if result:
option_id_str = result.group(1)
break
if id_str and option_id_str:
command = "amixer cset %s %s" % (cap_source[0], option_id_str)
sys.stdout.write( execute_command(command) )
def set_cap_switch(cap_switch, option):
""" set Caption Switch to 'on' or 'off' """
if len(cap_switch) == 0:
return
# else
command = "amixer cset %s %s" % (cap_switch[0], option)
sys.stdout.write( execute_command(command) )
def set_cap_switch(cap_switch, option):
""" set Caption Switch to 'on' or 'off' """
if len(cap_switch) == 0:
return
# else
command = "amixer cset %s %s" % (cap_switch[0], option)
sys.stdout.write(execute_command(command))
def set_cap_source(cap_source, option):
""" Set the Caption Source. Option: 'Mic' (microphone) or
'Mix' (soundcard output). """
def get_numid_str(s):
""" extract the X value from numid=X,... """
back = None
result = re.search(r'numid=(\d+),', s)
if result:
back = result.group(1)
return back
if len(cap_source) == 0:
return
# else
id_str = get_numid_str(cap_source[0])
option_id_str = None
if id_str:
for e in cap_source:
result = re.search(r'Item #(\d+) ' + "'" + option + "'", e)
if result:
option_id_str = result.group(1)
break
if id_str and option_id_str:
command = "amixer cset %s %s" % (cap_source[0], option_id_str)
sys.stdout.write(execute_command(command))
def unpushed_commit_message():
command_result = common.execute_command(
'git log --branches --not --remotes --pretty=format:%h:%aE:%s')
if command_result.status != 0:
return []
else:
return command_result.out.decode().split('\n')
def export(self):
# print(self.out_dir)
# print ("A7eeeh: ", os.pathsep.join(self.out_dir.split(os.pathsep)[:-1]))
cmd = "%s --no-adf --output %s %s" % (EXPORTER_SCRIPT, '/'.join(self.out_dir.split('/')[:-1]), self.accession)
# print(cmd)
out, err = execute_command(cmd)
if 'error' in err.lower():
print('EXPORT ERROR %s\n' % self.accession, out, err)
def gitlog(rev, rev2, options=''):
command = 'git log --first-parent ' + options + ' ' + rev + '..' + rev2
result = common.execute_command(command)
if result.status == 0:
return result.out.decode()
raise Exception('Error executing "%s"', command)
def git_command(*args,
print_stdout=True,
check=True,
cwd: Optional[str] = None) -> str:
return execute_command("git",
*args,
print_stdout=print_stdout,
check=check,
cwd=cwd)
def delete_these_branches(branches):
print_in_color("Started Deleting Operation", 'green')
for branch in branches:
output = execute_command('git branch -D ' + branch)
if "error" in output:
print_in_color(
output, 'red', "")
else:
print_in_color(
output, 'orange', "")
print_in_color("Completed Deleting Operation", 'green')
def run(self):
logging.debug("Start")
if self.force:
delete_command = "java -jar %s -o TRANKLUCATE -s %s -u %s -p %s '%s'" % (
SUBMISSION_TOOL_PATH, SUBMISSION_SERVER, SUBMISSION_USERNAME, SUBMISSION_PASSWORD, self.accession)
print(delete_command)
del_out, del_err = execute_command(delete_command)
print(del_out)
print(del_err)
self.convert()
command = "java -jar %s -o createupdate -s %s -u %s -p %s -d %s" % (
SUBMISSION_TOOL_PATH, SUBMISSION_SERVER, SUBMISSION_USERNAME, SUBMISSION_PASSWORD, self.page_tab_filename)
print(command)
out, err = execute_command(command)
print(out)
print(err)
logging.debug("end")
def run(self):
logging.debug("Start")
if self.force:
delete_command = "java -jar %s -o TRANKLUCATE -s %s -u %s -p %s '%s'" % (
SUBMISSION_TOOL_PATH, SUBMISSION_SERVER, SUBMISSION_USERNAME,
SUBMISSION_PASSWORD, self.accession)
print(delete_command)
del_out, del_err = execute_command(delete_command)
print(del_out)
print(del_err)
self.convert()
command = "java -jar %s -o createupdate -s %s -u %s -p %s -d %s" % (
SUBMISSION_TOOL_PATH, SUBMISSION_SERVER, SUBMISSION_USERNAME,
SUBMISSION_PASSWORD, self.page_tab_filename)
print(command)
out, err = execute_command(command)
print(out)
print(err)
logging.debug("end")
def commit_in_path(old_path=None, new_path=None):
git_command = 'git log --first-parent --pretty=format:%h:%aE:%s'
if old_path is not None and len(old_path) > 0:
git_command += ' ' + old_path
if new_path is not None and len(new_path) > 0:
git_command += '..' + new_path
command_result = common.execute_command(git_command)
if command_result.status != 0:
return []
else:
return command_result.out.decode().split('\n')
def run(self, ):
if self.force:
delete_command = "java -jar %s -o TRANKLUCATE -s %s -u %s -p %s '%s'" % (
SUBMISSION_TOOL_PATH, SUBMISSION_SERVER, SUBMISSION_USERNAME, SUBMISSION_PASSWORD, self.accession)
# print(delete_command)
del_out, del_err = execute_command(delete_command)
# print(del_out)
# print(del_err)
#
copied_files = self.convert_experiment_to_page_tab()
command = "java -jar %s -o createupdate -s %s -u %s -p %s -d %s" % (
SUBMISSION_TOOL_PATH, SUBMISSION_SERVER, SUBMISSION_USERNAME, SUBMISSION_PASSWORD, self.page_tab_filename)
# print(command)
# print("args: ",
# SUBMISSION_TOOL_PATH, SUBMISSION_SERVER, SUBMISSION_USERNAME, SUBMISSION_PASSWORD, self.page_tab_filename)
out, err = execute_command(command)
if 'error' in err.lower() or 'error' in out.lower():
print(self.accession)
print(out)
print(err)
print('=' * 50)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--token",
type=str,
required=True,
help="github token")
args = parser.parse_args()
repo = env("GITHUB_REPOSITORY")
nightly_branch = get_branch(repo, args.token, NIGHTLY_BRANCH)
if nightly_branch is not None:
print("Repo already has nightly branch")
return
git_command("checkout", "-b", NIGHTLY_BRANCH)
output = execute_command("rustc", "-V")
match_result = RUSTC_VERSION_RE.match(output)
date = match_result.group(1)
with open(CHECK_WORKFLOW_PATH) as f:
workflow_text = f.read()
result = re.search(WORKFLOW_RUSTC_VERSION_RE, workflow_text)
if result is None:
raise ValueError("Failed to find the current version of nightly rust")
new_workflow_text = re.sub(WORKFLOW_RUSTC_VERSION_RE,
f"\\g<1>{date}\\g<2>", workflow_text)
if new_workflow_text == workflow_text:
print("The latest nightly rustc version is already used")
return
with open(CHECK_WORKFLOW_PATH, "w") as f:
f.write(new_workflow_text)
if has_git_changes():
git_command("add", CHECK_WORKFLOW_PATH)
git_command("commit", "-m", ":arrow_up: nightly")
git_command("push", "origin", NIGHTLY_BRANCH)
pull_request = create_pull_request(repo, args.token, NIGHTLY_BRANCH,
":arrow_up: nightly")
add_assignee(repo, args.token, pull_request["number"],
DEFAULT_ASSIGNEE)
else:
print("Everything is up to date")
def is_alive(self):
if self.submitted:
out, err = execute_command('bjobs %s' % self.job_id)
# print(out, err)
status = [i for i in out.split('\n')[1].split(' ') if i != ''][2]
# print(status)
if status.lower() == 'done':
self.extract_output()
return False
if status.lower() == 'run' or status.lower() == 'pend':
return True
else:
self.extract_output()
raise Exception('Job %s exited with status %s' % (self.job_id, status))
else:
raise Exception('Job has not been submitted yet')
def _update_locally(self):
output = execute_command("rustc", "-V")
match_result = RUSTC_VERSION_RE.match(output)
date = match_result.group(1)
with open(CHECK_WORKFLOW_PATH) as f:
workflow_text = f.read()
result = re.search(WORKFLOW_RUSTC_VERSION_RE, workflow_text)
if result is None:
raise ValueError(
"Failed to find the current version of nightly rust")
new_workflow_text = re.sub(WORKFLOW_RUSTC_VERSION_RE,
f"\\g<1>{date}\\g<2>", workflow_text)
if new_workflow_text == workflow_text:
print("The latest nightly rustc version is already used")
return
with open(CHECK_WORKFLOW_PATH, "w") as f:
f.write(new_workflow_text)
def get_captures():
""" get the three Capture lines """
cap_source = cap_switch = cap_volume = []
output = execute_command("amixer contents")
li = output.split("numid=")
lines = []
for e in li:
e = e.rstrip("\n")
if len(e) == 0:
continue
lines.append(("numid=" + e).split("\n"))
for e in lines:
if "Capture Source" in e[0]:
cap_source = e
elif "Capture Switch" in e[0]:
cap_switch = e
elif "Capture Volume" in e[0]:
cap_volume = e
return (cap_source, cap_switch, cap_volume)
def get_captures():
""" get the three Capture lines """
cap_source = cap_switch = cap_volume = []
output = execute_command("amixer contents")
li = output.split("numid=")
lines = []
for e in li:
e = e.rstrip("\n")
if len(e) == 0:
continue
lines.append( ("numid=" + e).split("\n") )
for e in lines:
if "Capture Source" in e[0]:
cap_source = e
elif "Capture Switch" in e[0]:
cap_switch = e
elif "Capture Volume" in e[0]:
cap_volume = e
return (cap_source, cap_switch, cap_volume)
def delete_feature_branches(path, protected_branches):
os.chdir(converted_path(path))
output = execute_command('git branch')
branches = output.replace('*', '')
BRANCHES_TO_BE_SPARED = protected_branches
for branch in BRANCHES_TO_BE_SPARED:
branches = branches.replace(" "+branch+"\n", '')
BRANCHES_TO_BE_DELETED = list(filter(lambda item: len(item) != 0, map(
lambda item: item.strip(), branches.split('\n'))))
if(len(BRANCHES_TO_BE_DELETED) == 0):
print_in_color("No branch To Delete", 'green')
print_in_color("PROTECTED BRANCHES :: ", 'green', '')
print_in_color(BRANCHES_TO_BE_SPARED, 'orange')
else:
print_in_color(
"Are You Sure You Want To delete These Branches ? :: ", 'orange', '')
print_in_color(BRANCHES_TO_BE_DELETED, 'red')
print_in_color("Enter Y To Delete :: ", 'green', '')
answer = input()
if(answer.upper() == 'Y'):
delete_these_branches(BRANCHES_TO_BE_DELETED)
else:
print_in_color("CANCELLED THE OPERATION", 'red')
def codingstyle(files, enable_reformat, check_lgpl, check_commits_date):
source_patterns = common.get_option('codingstyle-hook.source-patterns', default='*.cpp *.cxx *.c').split()
header_patterns = common.get_option('codingstyle-hook.header-patterns', default='*.hpp *.hxx *.h').split()
misc_patterns = common.get_option('codingstyle-hook.misc-patterns', default='*.cmake *.txt *.xml *.json').split()
code_patterns = source_patterns + header_patterns
include_patterns = code_patterns + misc_patterns
sort_includes = common.get_option('codingstyle-hook.sort-includes', default="true", type='--bool') == "true"
global repoRoot
repoRoot = common.get_repo_root()
if repoRoot is None:
common.warn("Cannot find 'fw4spl' repository structure")
parent_repo = ""
else:
parent_repo = os.path.abspath(os.path.join(repoRoot, os.pardir))
fw4spl_configured_projects = common.get_option('codingstyle-hook.additional-projects', default=None)
fw4spl_projects = []
if fw4spl_configured_projects is None:
# no additional-projects specified in config file. Default is parent repository folder
fw4spl_projects.append(parent_repo)
else:
fw4spl_projects = fw4spl_configured_projects.split(";")
# adds current repository folder to the additional-projects specified in config file.
fw4spl_projects.append(repoRoot)
# normalize pathname
fw4spl_projects = list(map(os.path.normpath, fw4spl_projects))
# remove duplicates
fw4spl_projects = list(set(fw4spl_projects))
global UNCRUSTIFY_PATH
if common.g_uncrustify_path_arg is not None and len(common.g_uncrustify_path_arg) > 0:
UNCRUSTIFY_PATH = common.g_uncrustify_path_arg
else:
UNCRUSTIFY_PATH = common.get_option('codingstyle-hook.uncrustify-path', default=UNCRUSTIFY_PATH,
type='--path').strip()
common.note('Using uncrustify: ' + UNCRUSTIFY_PATH)
if common.execute_command(UNCRUSTIFY_PATH + ' -v -q').status != 0:
common.error('Failed to launch uncrustify.\n')
return []
checked = set()
reformatted_list = []
sortincludes.find_libraries_and_bundles(fw4spl_projects)
ret = False
count = 0
reformat_count = 0
for f in files:
if f in checked or not any(f.fnmatch(p) for p in include_patterns):
continue
content = f.contents
if not common.binary(content):
# Do this last because contents of the file will be modified by uncrustify
# Thus the variable content will no longer reflect the real content of the file
file_path = os.path.join(repoRoot, f.path)
if os.path.isfile(file_path):
res = format_file(file_path, enable_reformat, code_patterns, header_patterns, misc_patterns, check_lgpl,
sort_includes, f.status, check_commits_date)
count += 1
if res == FormatReturn.Modified:
reformatted_list.append(f.path)
reformat_count += 1
elif res == FormatReturn.Error:
# Error in reformatting
ret = True
checked.add(f)
common.note('%d file(s) checked, %d file(s) reformatted.' % (count, reformat_count))
return ret, reformatted_list
def format_file(source_file, enable_reformat, code_patterns, header_patterns, misc_patterns, check_lgpl, sort_includes,
status, check_commits_date):
# Invoke uncrustify for source code files
if any(fnmatch(source_file, p) for p in code_patterns):
common.trace('Launching uncrustify on : ' + source_file)
config_file = os.path.join(os.path.dirname(__file__), 'uncrustify.cfg')
ret = FormatReturn()
# Fix license year
if check_lgpl is True:
ret.add(fix_license_year(source_file, enable_reformat, status, check_commits_date))
# Sort headers
if sort_includes is True:
ret.add(sortincludes.sort_includes(source_file, enable_reformat))
if any(fnmatch(source_file, p) for p in header_patterns):
ret.add(fix_header_guard(source_file, enable_reformat))
# Uncrustify
command = UNCRUSTIFY_PATH + ' -c ' + config_file + ' -q %s ' + source_file
if enable_reformat is True:
# Check first
uncrustify = common.execute_command(command % '--check')
if uncrustify.status != 0:
uncrustify = common.execute_command(command % '--replace --no-backup --if-changed')
if uncrustify.status != 0:
common.error('Uncrustify failure on file: ' + source_file)
common.error(uncrustify.out.decode())
return FormatReturn.Error
ret.add(FormatReturn.Modified)
else:
uncrustify = common.execute_command(command % '--check')
if uncrustify.status != 0:
common.error('Uncrustify failure on file: ' + source_file)
return FormatReturn.Error
return ret.value
# Replace only YEAR, TAB, CRLF and CR for miscellaneous files
elif any(fnmatch(source_file, p) for p in misc_patterns):
common.trace('Parsing: ' + source_file + ' to replace CR, CRLF and TABs')
str_old_file = open(source_file, 'rb').read()
str_new_file = re.sub('\t', ' ', str_old_file.decode())
tmp_str = re.sub('\r\n', '\n', str_new_file)
str_new_file = re.sub('\r', '\n', tmp_str)
if str_old_file.decode() == str_new_file:
return FormatReturn.NotModified
# Something has been changed, write the new file
open(source_file, 'wb').write(str_new_file.encode())
return FormatReturn.Modified
def main():
args = extract_args()
dir_path = os.path.join(LOAD_DIR,
args.accession.split('-')[1], args.accession)
tmp_dir = os.path.join(MAGIC_DIR, args.accession)
skip_copy = args.skip_copy
skip_remove = args.skip_remove
if os.path.exists(tmp_dir):
print(execute_command('chmod 777 -R ' + tmp_dir))
print(execute_command('rm -rf ' + tmp_dir))
try:
os.mkdir(tmp_dir)
if skip_copy:
print('skipping copy')
execute_command('cp -r %s/*.txt %s' % (dir_path, tmp_dir))
else:
execute_command('cp -r %s/* %s' % (dir_path, tmp_dir))
# copy_tree(dir_path, tmp_dir)
for f in os.listdir(tmp_dir):
f = os.path.join(tmp_dir, f)
if os.path.isdir(f):
continue
f_name = os.path.split(f)[-1]
if f_name.endswith('.zip'):
print("extracting:: " + f_name + ' to ' + tmp_dir)
execute_command("Unzip %s -d %s" % (f, tmp_dir))
# zip_file = zipfile.ZipFile(f, 'r')
# zip_file.extractall(tmp_dir)
# zip_file.close()
converter = MAGETABConverter(args.accession, tmp_dir)
file_lists = converter.page_tab.export()
bst_usr = register_user(args.accession)
# truncate_dir(tmp_dir)
# move_dir(tmp_dir, args.accession, MAGIC_DIR, True)
files = ''
if file_lists:
files = ' -a ' + ','.join(file_lists)
submit = 'submit'
if args.asyn:
submit = 'submitAsync'
command = "java -jar {jar} {submit} -s {server} -u {user} -p {password} -i {page_tab} {files}". \
format(jar=BST_CLI_PATH, submit=submit, server=SUBMISSION_SERVER, user=SUBMISSION_USERNAME,
password=SUBMISSION_PASSWORD,
page_tab=os.path.join(converter.out_dir, args.accession + '.pagetab.tsv'),
files=files)
print(command)
out, err = execute_command(command)
print(out)
print(err)
update_owner(args.accession, bst_usr['id'])
# remove_ftp_dir(MAGIC_DIR + '/' + args.accession)
if not skip_remove:
execute_command('chmod 777 -R ' + tmp_dir)
execute_command('rm -rf ' + tmp_dir)
# remove_dir(magic_dir, tmp_dir)
except Exception as e:
print(e)
if not skip_remove:
execute_command('chmod 777 -R ' + tmp_dir)
execute_command('rm -rf ' + tmp_dir)
raise
def submit(self):
out, err = execute_command(self.cmd)
if out:
self.job_id = out.split('<')[1].split('>')[0]
self.submitted = True
def __init__(self, accession, out_dir, skip_remove=False):
self.accession = accession
self.out_dir = out_dir
if not os.path.exists(self.out_dir):
os.makedirs(self.out_dir)
self.adf_dict = {}
self.adf_dir = os.path.join(ARRAY_DIR,
accession.split('-')[1], accession)
self.page_tab_filename = os.path.join(self.out_dir,
self.accession + '.pagetab.tsv')
self.files = []
self.get_ftp_files()
self.copy_to_tmp()
self.adf_file_path = os.path.join(self.out_dir,
self.accession + '.adf.txt')
fix_encoding(self.adf_file_path)
self.adf_content = []
self.parse_adf()
# self.score = score_adf(self.adf_content)
release_date = datetime.datetime.now().date().isoformat()
if 'Public Release Date' in self.adf_dict.keys():
release_date = self.adf_dict['Public Release Date'][0]
elif 'ArrayExpressReleaseDate' in self.adf_dict.keys():
release_date = self.adf_dict['ArrayExpressReleaseDate'][0]
self.page_tab = PageTab(title=self.adf_dict['Array Design Name'][0],
accession=self.accession,
release_date=release_date,
out_dir=self.out_dir)
if not self.adf_dict.get('Provider', ['']):
self.adf_dict['Provider'] = ['']
section_fields = OrderedDict([
("Title", self.adf_dict['Array Design Name'][0]),
("Provider", self.adf_dict.get('Provider', [''])[0]),
("Description", self.adf_dict.get('Description', [''])[0]),
("Organism", self.adf_dict.get('Organism', [''])[0]),
("MIAME Compliant ADF",
'Yes' if self.adf_dict['score']['score'] else 'No'),
("Link", [
Field(name='Link',
value=self.accession,
extras=[["Type", "BioStudies Search"],
["Description", "Studies using this array"]])
])
])
table = None
if self.files:
table = [['Files', 'Type', 'Description']] + self.files
self.page_tab.sections.append(
Section(name="Array",
section_id='s-' + self.accession,
section_fields=section_fields,
table=table))
bst_usr = register_user(self.accession)
# truncate_dir(self.out_dir)
# move_dir(self.out_dir, self.accession, MAGIC_DIR, True)
self.page_tab.export()
command = "java -jar {jar} -s {server} -u {user} -p {password} -i {page_tab} {files}". \
format(jar=SUBMISSION_TOOL_PATH, server=SUBMISSION_SERVER, user=SUBMISSION_USERNAME,
password=SUBMISSION_PASSWORD,
page_tab=self.page_tab_filename,
files='')
update_owner(self.accession, bst_usr['id'])
print(command)
out, err = execute_command(command)
print(out)
print(err)
if not skip_remove:
execute_command('chmod 777 -R ' + self.out_dir)
execute_command('rm -rf ' + self.out_dir)
def main():
error_unload = {}
error_load = {}
unload_accs = os.listdir(os.path.join(STAGING_DIR, 'unload'))
load_accs = os.listdir(os.path.join(STAGING_DIR, 'load'))
unload_accs = [acc for acc in unload_accs if acc not in load_accs]
for acc in unload_accs:
print('unloading:', acc)
delete_command = "java -jar %s delete -s %s -u %s -p %s %s" % (
BST_CLI_PATH, SUBMISSION_SERVER, SUBMISSION_USERNAME,
SUBMISSION_PASSWORD, acc)
# print(delete_command)
# print(execute_command(delete_command))
out, err = execute_command(delete_command)
if out is None:
out = ''
if err is None:
err = ''
j_out = out + err
if 'error' in j_out.lower() or 'exception' in j_out.lower():
error_unload[acc] = j_out
continue
os.remove(os.path.join(STAGING_DIR, 'unload', acc))
# break
# os.remove(os.path.join(STAGING_DIR, 'unload', acc))
runner_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
'lsf', 'runner.py')
if load_accs:
# print('loading:', acc)
log_f_name = 'DUAL_' + datetime.datetime.utcnow().isoformat()
load_command = "export PYTHONPATH=\"${PYTHONPATH}:/nfs/biostudies/pyBiostudies\"; export " \
"LD_LIBRARY_PATH=/nfs/biostudies/instantclient_12_2:$LD_LIBRARY_PATH;source " \
"/nfs/biostudies/pyBiostudies/virtual_env/bin/activate;python %s -f -sync -acc %s -lg %s" % (
runner_path, ' '.join(load_accs), log_f_name)
print(load_command)
print(execute_command(load_command))
log_path = os.path.join(settings.LOG, log_f_name + ".csv")
if os.path.exists(log_path):
lg_file = open(log_path, 'r')
log = lg_file.read()
lg_file.close()
lines = log.split('\n')
new_lines = []
new_line = ''
for i in range(len(lines)):
if lines[i].startswith('E-'):
if new_line:
new_lines.append(new_line)
new_line = lines[i]
else:
new_line += lines[i]
for l in new_lines:
cells = l.split('\t')
acc = cells[0]
err = cells[-1]
if err.lower() != 'loaded':
error_load[acc] = err
email = ""
if error_unload:
email = "There's been error unloading the following from Biostudies:\n"
for k, v in error_unload.items():
email += '%s: %s\n' % (k, v)
email += '\n\n'
if error_load:
email = "There's been error loading the following into Biostudies:\n"
for k, v in error_load.items():
email += '%s: %s\n' % (k, v)
if email:
send_email(from_email="PyBiostudies<pybiostudies.ebi.ac.uk",
to_emails=['*****@*****.**'],
subject="Biiostudies Dual Load Error",
body=email)
for acc in load_accs:
if acc not in error_load.keys():
os.remove(os.path.join(STAGING_DIR, 'load', acc))
