def downepi(self, episode):
""" down a show """
pos = self.visible.posend
url, dest, cook = links.flvdown(episode, "")
if url:
try:
if (not ospath.isdir(dest.split('/')[0])):
osmkdir(dest.split('/')[0])
cmd = "wget -c " + url + " -O " + dest
proc = subpopen(cmd, shell=True, stderr=PIPE, stdout=PIPE)
while proc.poll() is None:
line = proc.stderr.readline()
resul = down.search(line[:-1])
if resul:
msg = resul.group(1) + ' ' + resul.group(2) + \
' ' + resul.group(3)
self.screen.addstr(pos[0], pos[1]+pos[2], msg)
self.screen.refresh()
subdown.downSub(episode, "")
except:
proc.kill()
self.error(episode.getBaseName() + ': down error')
else:
self.error(episode.getBaseName() + ': down finish')
episode.isOnDisk = True
self.display()
else:
self.error(episode.getBaseName() + ': url not found')
def CREATE_DIR(OUTDIR):
if not pathexists(pathjoin(OUTDIR)):
osmkdir(pathjoin(OUTDIR))
for DIR in ["IdListDIR", "IdListDIR/disease", "IdListDIR/query"]:
if not pathexists(pathjoin(OUTDIR, DIR)):
osmkdir(pathjoin(OUTDIR, DIR))
def saveConf(self):
""" save the config"""
if (not ospath.exists(ospath.expanduser('~') + "/.config/flvdown/")):
osmkdir(ospath.expanduser('~') + "/.config/flvdown/")
fileconf = open(ospath.expanduser('~') + \
"/.config/flvdown/flv.conf", "w", 0)
for key in self.conf.keys():
fileconf.write(key + '="' + self.conf[key] + '\"\n')
fileconf.write('order="')
for elt in self.list_site:
fileconf.write(elt + ', ')
fileconf.write('"\n')
fileconf.write('dict_bug=')
fileconf.write(repr(self.dict_bug))
fileconf.write('\n')
fileconf.close()
def createDir(self):
""" create directory if it doesn't exist """
if (not ospath.isdir(self.tvshow_)):
osmkdir(self.tvshow_)
f.write('export CSCOPE_DB="%s"\n' % OutCscopeDb )
f.write('export tagsfile="%s"\n' % OutCtagsTags)
f.write('export TAGS_HL="%s"\n' % OutVimTagsHl)
f.write('export VIMPROJSERVERNAME="%s"\n' % WorkDir )
if __name__ == "__main__":
from os import path as osp
from os import environ as ose
from os import makedirs as osmkdir
WorkDir = osp.abspath(osp.curdir)
VimTagsPathRoot = osp.join(ose['HOME'], '.vimtagsroot')
WorkDirFlat = "".join([ c if c.isalnum() else "_" for c in WorkDir ])
VimTagsPath = osp.join(VimTagsPathRoot, WorkDirFlat)
if not osp.isdir(VimTagsPath):
osmkdir(VimTagsPath)
OutFilesList = osp.join(VimTagsPath, 'files.list')
OutCscopeDb = osp.join(VimTagsPath, 'cscope.out')
OutCtagsTags = osp.join(VimTagsPath, 'tags')
OutVimTagsHl = osp.join(VimTagsPath, 'tags_hl.vim')
OutExportVar = osp.join(VimTagsPath, 'export_var_for_vim')
TagsIgnoreFile = osp.join(WorkDir, '.7tags.ignore')
TagsAddFile = osp.join(WorkDir, '.7tags.add')
ExtensionList = [ 'h', 'c', 'cc', 'cpp', 'hpp' ]
log("Tags artifact will be stored in %s" % VimTagsPath)
log(" + Generate files list")
def efetch_found_bioprojects(OUTDIR):
def printProgressBar (iteration, total, prefix = '', suffix = '', \
decimals = 1, length = 100, fill = '█'):
"""
Call in a loop to create terminal progress bar
@params:
iteration - Required : current iteration (Int)
total - Required : total iterations (Int)
prefix - Optional : prefix string (Str)
suffix - Optional : suffix string (Str)
decimals - Optional : positive number of decimals in percent \
complete (Int)
length - Optional : character length of bar (Int)
fill - Optional : bar fill character (Str)
"""
percent = ("{0:." + str(decimals) + "f}")\
.format(100 * (iteration / float(total)))
filledLength = int(length * iteration // total)
bar = fill * filledLength + '-' * (length - filledLength)
print('\r%s |%s| %s%% %s' % (prefix, bar, percent, suffix), end='\r')
# Print New Line on Complete
if iteration == total:
print()
"""
COLETAR INFORMAÇOES SOBRE BIOPROJECTS ECONTRADOS
"""
if pathexists(OUTDIR):
for DIR in ['Bioprojects', 'Bioprojects/xml']:
if not pathexists(pathjoin(OUTDIR, DIR)):
osmkdir(pathjoin(OUTDIR, DIR))
path_to_list = pathjoin(OUTDIR, 'IdListDIR/IdList_total.txt')
if isfile(path_to_list):
with open(path_to_list, 'r') as f:
IdList_total = list(filter(None, f.read().splitlines()))
else:
print('File '+f+' was not found. Run esearch_disease(OUTDIR) '\
'for making it.')
exit()
else:
print('Directory '+pathjoin(OUTDIR)+' is not accessible. Did you run'\
'esearch_disease() previously? If not, do it and try again.')
exit()
df2 = pd_DataFrame(index=range(0, len(IdList_total)), columns=range(0, 7))
df2.columns = [
"ID", "accession", "GEO", "title", "abstract", "disease", "COD"
]
df2["ID"] = IdList_total
print("\n\n") # ESSE PRINT SERVE PARA DISTANCIAR A BARRA DE PROCESSAMENTO
# QUE VEM LOGO ABAIXO DENTRO DO LOOPING
# prepare bar progress
l = len(IdList_total)
i = 0
printProgressBar(0, l, prefix='Download:', suffix='Complete', length=50)
RECALL = [] # if download fails, the ID is stored in RECALL
DIC_ID = {}
for ID in IdList_total:
try:
handle = Entrez.efetch(db="bioproject", id=ID)
except:
RECALL += [ID]
print('handle = Entrez.efetch(db="bioproject", id=' + ID +
')\tFAILED')
continue # avoid catastrophic event in case NCBI fails to give
# the informatio for one ID
try:
record = handle.read()
root = ET.fromstring(record)
DIC = root.find(".//ProjectID/ArchiveID").attrib
DIC_ID[DIC['accession']] = DIC_ID.get(DIC['accession'], DIC['id'])
outfile=pathjoin(OUTDIR,'Bioprojects/xml',DIC['accession']+\
'_'+DIC['id']+'.xml')
#print(outfile)
with open(outfile, "w", encoding="utf-8") as f:
print(record, file=f)
except:
RECALL += [ID]
print('FAILED to process ' + ID + ' during the first trial')
continue
printProgressBar(i + 1,
l,
prefix='Download:',
suffix='Complete',
length=50)
i += 1
# RECALL for failure IDs
if len(RECALL) > 0:
print("\n\nFailure to download IDs. STARTING RECALL.")
l = len(RECALL)
i = 0
printProgressBar(0,
l,
prefix='Download:',
suffix='Complete',
length=50)
RECALL2 = []
for ID in RECALL:
try:
handle = Entrez.efetch(db="bioproject", id=ID)
except:
RECALL2 += [ID]
print('handle = Entrez.efetch(db="bioproject", id='+ID+')'\
'\tFAILED in RECALL')
continue
try:
record = handle.read()
root = ET.fromstring(record)
DIC = root.find(".//ProjectID/ArchiveID").attrib
DIC_ID[DIC['accession']] = DIC_ID.get(DIC['accession'],
DIC['id'])
outfile=pathjoin(OUTDIR,'Bioprojects/xml',DIC['accession']+\
'_'+DIC['id']+'.xml')
#print(outfile)
with open(outfile, "w", encoding="utf-8") as f:
print(record, file=f)
except:
RECALL2 += [ID]
print('FAILED to process ' + ID + ' during the RECALL')
continue
printProgressBar(i + 1,
l,
prefix='RECALL:',
suffix='Complete',
length=50)
i += 1
if len(RECALL2) > 0:
outfile = pathjoin(OUTDIR, 'Bioprojects/', 'RECALL_failure.txt')
open(outfile, 'w').write(str(RECALL2))
print("It was not possible to get ID even during the RECALL\nYou"\
"can find the problematic IDs on file:\n"+outfile)
outfile = pathjoin(OUTDIR, 'Bioprojects/', 'dict_ID_ACC.txt')
open(outfile, 'w').write(str(DIC_ID))
