def voiceRecord():
rate = 44100
duration = 5
targetAudio = recorder.rec(int(duration * rate),
samplerate=rate,
channels=2)
recorder.wait()
write(audioName, rate, targetAudio)
encodedAudioString = encodeBase64(audioName)
# audioAnalyse()
log = "[ Date: " + getDateAndTime("date") \
+ ", Time: " + getDateAndTime("time") \
+ ", ID: " + stringGenerator(9) \
+ ", EncodedAudioString: " + asString(encodedAudioString, "double") \
+ " ]"
logTitle = "audio_analyse_" + getDateAndTime(
"date") + "_" + getDateAndTime("time") + ".log"
return createLogFile("audio_analyse_logs", logTitle, log)
def Logging():
log = "[ Date: " + getDateAndTime("date") \
+ ", Time: " + getDateAndTime("time") \
+ ", IPAddress: " + getHostIPaddress() \
+ ", ID: " + stringGenerator(9) + " ]"
return storeData("record.log", log)
def PostWord():
datas = request.json
data = datas[0]
# get word
targetWord = str(data["word"])
# get voice
voice = data["currentVoice"]
if voice == "0":
DefaultTTS(data)
else:
TTS(targetWord)
space = " "
# save log
log = "[\n" + space + "Date: " + asString(getDateAndTime("date"), "double") \
+ ", \n" + space + "Time: " + asString(getDateAndTime("time"), "double") \
+ ", \n" + space + "IPAddress: " + getHostIPaddress() \
+ ", \n" + space + "ID: " + asString(stringGenerator(9), "double") \
+ ", \n" + space + "ServerHost: " + asString(request.host, "double") \
+ ", \n" + space + "RequestedAPI: " + asString(request.path, "double") \
+ ", \n" + space + "RequestMethod: " + asString(request.method, "double") \
+ ", \n" + space + "Origin: " + asString(request.origin, "double") \
+ ", \n" + space + "TargetMessage: " + asString(targetWord, "double") \
+ ", \n" + space + "Voice: " + asString(voice, "double") \
+ "\n]"
resp = jsonify(success=True)
StoreHistory(targetWord)
return str(resp.status_code) + ": " + storeData("api_request.log", log)
def OnFinishRegister(self):
self.new_register.Enable(True)
# self.finish_register.Enable(False)
self.cap.release()
self.bmp.SetBitmap(wx.Bitmap(self.pic_index))
if self.flag_registed == True:
dir = PATH_FACE + '{}_{}_{}_{}'.format(str(self.id), self.unit,
self.name, self.gender)
for file in os.listdir(dir):
os.remove(dir + '/' + file)
print('已删除已录入人脸的图片', dir + '/' + file)
os.rmdir(dir)
print('已删除已录入人脸的姓名文件夹', dir)
self.initData()
return
if self.pic_num > 0:
# face_descriptor = prepare_one_facebank(conf,
# learner.model,
# mtcnn,
# PATH_FACE + '{}_{}_{}_{}'.format(str(self.id), self.unit, self.name, self.gender))
# insert to database
self.insertRow([self.id, self.unit, self.name, self.gender], 1)
self.infoText.AppendText('[{}]数据已保存：{}\r\n'.format(
getDateAndTime(hms=1), self.name))
self.OnUpdateRegister()
else:
os.rmdir(dir)
print('已删除空文件夹', dir)
self.initData()
def OnUpdateRegister(self):
self.initDatabase(update=1)
self.targets, self.names = prepare_facebank(conf, learner.model, mtcnn,
True)
for i in range(len(self.targets)):
id_, unit, name, gender = self.names[i + 1].split('_')
self.insertRow([id_, unit, name, gender], 1)
print('人脸数据更新成功')
self.infoText.AppendText('[%s]' % getDateAndTime(hms=1) +
'人脸数据库已更新\r\n')
self.loadDataBase(1)
def initInfoText(self):
# 少了这两句infoText背景颜色设置失败，莫名奇怪
resultText = wx.StaticText(parent=self, pos=(10, 20), size=(90, 60))
resultText.SetBackgroundColour('red')
self.info = '\r\n' + '[%s]' % getDateAndTime(hms=1) + '初始化成功\r\n'
# 第二个参数水平混动条
self.infoText = wx.TextCtrl(parent=self,
size=(320, 500),
style=(wx.TE_MULTILINE | wx.HSCROLL
| wx.TE_READONLY))
# 前景色，也就是字体颜色
self.infoText.SetForegroundColour('ORANGE')
self.infoText.SetLabel(self.info)
# API:https://www.cnblogs.com/wangjian8888/p/6028777.html
# 没有这样的重载函数造成'par is not a key word',只好Set
font = wx.Font()
font.SetPointSize(12)
font.SetWeight(wx.BOLD)
font.SetUnderlined(True)
self.infoText.SetFont(font)
self.infoText.SetBackgroundColour('TURQUOISE')
def StoreHistory(word):
now = datetime.datetime.now()
hr = ""
min = ""
if len(str(now.minute)) == 1:
min = "0" + str(now.minute)
else:
min = str(now.minute)
if len(str(now.hour)) == 1:
hr = "0" + str(now.hour)
else:
hr = str(now.hour)
historyData = '{' \
+ '"message": ' + '"' + word + '"' \
+ ', "date": ' + asString(getDateAndTime("date"), "double") \
+ ', "time": ' + '"' + str(hr) + ":" + str(min) + '"' \
+ '},'
sh = open("history.log", "a")
sh.write(historyData)
sh.close()
def main(arguments):
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-l',
'--launch_directory',
action=readable_dir,
default="")
parser.add_argument(
'-f',
'--ftp',
action=readable_dir,
default="/ebi/ftp/pub/databases/metabolights/compounds/",
help="FTP directory")
args = parser.parse_args(arguments)
global destinationDirectory
global ftp
workingDirectory = args.launch_directory
ftp = args.ftp
if (workingDirectory == ""):
workingDirectory = os.getcwd()
# log file configuration
st = utils.getDateAndTime()
randomInt = str(randint(1, 1000))
logDirectory = workingDirectory + "/logs/exporter_" + st
if not os.path.exists(logDirectory):
os.makedirs(logDirectory)
logging.basicConfig(filename=logDirectory + "/log_" + randomInt + ".log",
level=logging.DEBUG)
utils.init(logging)
logging.info("-----------------------------------------------")
logging.info('# Run started -' + utils.getDateAndTime())
metabolightsFlagsJSONFile = ftp + "ml_flags.json"
with open(metabolightsFlagsJSONFile) as flags_file:
metabolightsFlagsData = json.load(flags_file)
query = ""
for metabolite in metabolightsFlagsData:
has_species = int(
str(metabolightsFlagsData[metabolite]["flags"]
["hasSpecies"]).lower() == "true")
has_pathways = int(
str(metabolightsFlagsData[metabolite]["flags"]
["hasPathways"]).lower() == "true")
has_reactions = int(
str(metabolightsFlagsData[metabolite]["flags"]
["hasReactions"]).lower() == "true")
has_nmr = int(
str(metabolightsFlagsData[metabolite]["flags"]["hasNMR"]).lower()
== "true")
has_ms = int(
str(metabolightsFlagsData[metabolite]["flags"]["hasMS"]).lower() ==
"true")
has_literature = int(
str(metabolightsFlagsData[metabolite]["flags"]
["hasLiterature"]).lower() == "true")
query += "update mmimtbldev.isatab.ref_metabolite set has_species = " + str(
has_species) + ", has_pathways = " + str(
has_pathways) + ", has_reactions = " + str(
has_reactions
) + ", has_nmr= " + str(has_nmr) + ", has_ms= " + str(
has_ms) + ", has_literature= " + str(
has_literature) + " where acc = '" + metabolite.strip(
) + "';" + "\n"
file = open(workingDirectory + "/query.txt", "w")
file.write(query)
def OnChangeTimeClicked(self, event):
# cur_hour = datetime.datetime.now().hour
# print(cur_hour)
# if cur_hour>=8 or cur_hour<6:
# wx.MessageBox(message='''您错过了今天的签到时间，请明天再来\n
# 每天的签到时间是:6:00~7:59''', caption='警告')
# return
# pass
pw = wx.GetPasswordFromUser('请输入管理密码',
caption="修改",
default_value="",
parent=self.bmp)
if pw == '':
print('取消修改')
elif pw != PASSWORD:
wx.MessageBox(message='密码错误，退出修改', caption='警告')
else:
# 输入修改时间，如果输入为空，则取消修改，如果输入格式错误，则重新修改
flag = 1
time_type = ['签到时间', '签退时间']
index = -1
while flag and index == -1:
# 选择时间
choice_time_type = wx.SingleChoiceDialog(
parent=self.bmp,
message='请选择您要修改的时间',
caption='修改',
choices=time_type,
)
if choice_time_type.ShowModal() == wx.ID_CANCEL:
print('取消修改')
flag = 0
break
else:
index = choice_time_type.GetSelection()
# break
# 输入时间
# TODO 确认是否更新今日签到记录
while flag and index != -1:
change_time = wx.GetTextFromUser(
message='请输入修改的时间(格式HH:MM:SS)',
caption='修改{}'.format(time_type[index]),
default_value=self.puncard_time[index],
parent=self.bmp)
if change_time.strip(
) == '' or change_time == self.puncard_time[index]:
self.infoText.AppendText('[{}]取消修改(上一次为：{})\r\n'.format(
getDateAndTime(hms=1), self.puncard_time[index]))
print('取消修改')
index = -1
break
else:
try:
# 判断时间大小
changed = datetime.datetime.strptime(
change_time, '%H:%M:%S')
original = datetime.datetime.strptime(
self.puncard_time[1 - index], '%H:%M:%S')
if changed > original if index else changed < original:
self.puncard_time[index] = change_time
np.save(conf.data_path / 'time.npy',
self.puncard_time)
self.infoText.AppendText('[{}]{}已修改：{}\r\n'.format(
getDateAndTime(hms=1), time_type[index],
self.puncard_time[index]))
print('修改成功%s' % self.puncard_time[index])
index = -1
break
else:
print('修改错误：签到时间需早于签退时间')
wx.MessageBox(message='签到时间需早于签退时间，请重新输入',
caption='警告')
except ValueError:
print('格式错误(格式为HH:MM:SS)')
wx.MessageBox(message='格式错误(格式为HH:MM:SS)',
caption='警告')
def punchcard_cap(self, event):
self.cap = cv2.VideoCapture(0)
# cap是否初始化成功
flag_print_info = [1, 1]
flag_repeat = 0
while self.cap.isOpened() and not self.start_punchcard.IsEnabled():
flag, im_rd = self.cap.read()
# 检测人脸
try:
image = Image.fromarray(im_rd[..., ::-1]) # bgr to rgb
bboxes, faces = mtcnn.align_multi(image, 2, conf.min_face_size)
bboxes = bboxes[:, :
-1] # shape:[10,4],only keep 10 highest possibiity faces
bboxes = bboxes.astype(int)
bboxes = bboxes + [-1, -1, 1, 1] # personal choice
results, score = learner.infer(conf, faces, self.targets, True)
# print(results[0])
except:
continue
# cv2.putText(im_rd, getDateAndTime(), (10, 50), cv2.FONT_HERSHEY_SIMPLEX, 0.7, (0, 255, 0), 2,
# cv2.LINE_AA)
# img_height, img_width = im_rd.shape[:2]
# image_ = cv2.cvtColor(im_rd, cv2.COLOR_BGR2RGB)
# pic = wx.Bitmap.FromBuffer(img_width, img_height, image_)
# self.bmp.SetBitmap(pic)
# print('请对准摄像头')
# # 取占比最大的脸
biggest_face = bboxes[0]
if results[0] == -1:
cv2.rectangle(im_rd, (biggest_face[0], biggest_face[1]),
(biggest_face[2], biggest_face[3]), (0, 0, 255),
2)
cv2.putText(im_rd, 'Unknown',
(biggest_face[0], biggest_face[1]),
cv2.FONT_HERSHEY_SIMPLEX, 0.7, (0, 255, 0), 2,
cv2.LINE_AA)
cv2.putText(im_rd, getDateAndTime(), (10, 50),
cv2.FONT_HERSHEY_SIMPLEX, 0.7, (255, 255, 255), 2,
cv2.LINE_AA)
img_height, img_width = im_rd.shape[:2]
image_ = cv2.cvtColor(im_rd, cv2.COLOR_BGR2RGB)
pic = wx.Bitmap.FromBuffer(img_width, img_height, image_)
# 显示图片在panel上
self.bmp.SetBitmap(pic)
else:
for j, logcat_id in enumerate(self.logcat_id):
# 名字一样且当日日期一样，判定为签退
# print(logcat_id==self.knew_id[results[0]])
# print(getDateAndTime(ymd=True) == self.logcat_datetime_in[j][0:self.logcat_datetime_in[j].index(' ')])
same_id = logcat_id == self.knew_id[results[0]]
same_day = getDateAndTime(
ymd=1) == self.logcat_datetime_in[j][
0:self.logcat_datetime_in[j].index(' ')]
if same_id and same_day:
delta_seconds = (datetime.datetime.now() -
datetime.datetime.strptime(
self.logcat_datetime_in[j],
'%Y-%m-%d %H:%M:%S')).seconds
if delta_seconds > 3 * 3:
# 间隔一段时间才能签退
after_check_out_time = int(
getDateAndTime(hms=1).replace(':', '')) >= int(
self.puncard_time[1].replace(':', ''))
self.updateRow([
getDateAndTime(),
'否' if after_check_out_time else '是',
self.logcat_datetime_in[j],
self.knew_name[results[0]]
], 1)
if flag_print_info[1]:
self.infoText.AppendText(
'[{}]已签退：{}\r\n'.format(
getDateAndTime(hms=1),
self.knew_name[results[0]]))
flag_print_info[1] = 0
else:
if flag_print_info[0]:
self.infoText.AppendText(
'[{}]重复签到：{}\r\n'.format(
getDateAndTime(hms=1),
self.knew_name[results[0]]))
flag_print_info[0] = 0
flag_repeat = 1
# color = (0, 255, 0) if self.logcat_late[j] == '否' else (0, 0, 255)
if not flag_repeat:
# 判断此刻的时间是否在签到时间之前
before_check_in_time = int(
getDateAndTime(hms=1).replace(':', '')) <= int(
self.puncard_time[0].replace(':', ''))
self.infoText.AppendText('[{}]{}: {}\r\n'.format(
getDateAndTime(hms=1),
'已签到' if before_check_in_time else '迟到了',
self.knew_name[results[0]]))
self.insertRow([
self.knew_id[results[0]], self.knew_unit[results[0]],
self.knew_name[results[0]],
getDateAndTime(), '否' if before_check_in_time else '是',
'-', '-'
], 2)
# color = (0, 255, 0) if condition else (0, 0, 255)
# flag_print_info = 0
# rectangle()绘制矩形框
# utText(): 图像，文字内容， 坐标 ，字体，大小，颜色，字体厚度
cv2.rectangle(im_rd, (biggest_face[0], biggest_face[1]),
(biggest_face[2], biggest_face[3]), (0, 0, 255),
2)
cv2.putText(im_rd, 'No. %d' % self.knew_id[results[0]],
(biggest_face[0], biggest_face[1]),
cv2.FONT_HERSHEY_SIMPLEX, 0.7, (0, 255, 0), 2,
cv2.LINE_AA)
cv2.putText(im_rd, getDateAndTime(), (10, 50),
cv2.FONT_HERSHEY_SIMPLEX, 0.7, (255, 255, 255), 2,
cv2.LINE_AA)
img_height, img_width = im_rd.shape[:2]
image_ = cv2.cvtColor(im_rd, cv2.COLOR_BGR2RGB)
pic = wx.Bitmap.FromBuffer(img_width, img_height, image_)
# 显示图片在panel上
self.bmp.SetBitmap(pic)
self.loadDataBase(2)
self.cap.release()
self.bmp.SetBitmap(wx.Bitmap(self.pic_index))
_thread.exit()
def register_cap(self, event):
self.cap = cv2.VideoCapture(0)
# cap是否初始化成功
while self.cap.isOpened():
# cap.read()
# 返回两个值：
# 一个布尔值true/false，用来判断读取视频是否成功/是否到视频末尾
# 图像对象，图像的三维矩阵
flag, im_rd = self.cap.read()
# 每帧数据延时1ms，延时为0读取的是静态帧
cv2.waitKey(1)
if flag:
# 检测人脸
detect = 0
try:
image = Image.fromarray(im_rd[..., ::-1]) # bgr to rgb
bboxes, faces = mtcnn.align_multi(image, 1,
conf.min_face_size)
bboxes = bboxes[:, :
-1] # shape:[10,4],only keep 10 highest possibiity faces
bboxes = bboxes.astype(int)
bboxes = bboxes + [-1, -1, 1, 1] # personal choice
# # 取占比最大的脸
biggest_face = bboxes[0]
# 绘制矩形框
cv2.rectangle(im_rd, (biggest_face[0], biggest_face[1]),
(biggest_face[2], biggest_face[3]),
(0, 0, 255), 3)
cv2.putText(im_rd, getDateAndTime(), (10, 50),
cv2.FONT_HERSHEY_SIMPLEX, 0.7, (0, 255, 0), 2,
cv2.LINE_AA)
img_height, img_width = im_rd.shape[:2]
image_ = cv2.cvtColor(im_rd, cv2.COLOR_BGR2RGB)
pic = wx.Bitmap.FromBuffer(img_width, img_height, image_)
# 显示图片在panel上
self.bmp.SetBitmap(pic)
detect = 1
except:
print('检测错误')
# 识别
if detect:
# try:
results, score = learner.infer(conf, faces, self.targets,
True)
print('识别结果:{}({})'.format(self.knew_name, results[0]))
if results[0] != -1:
self.infoText.AppendText('[{}]人脸已注册：{}\r\n'.format(
getDateAndTime(hms=1), self.knew_name[results[0]]))
self.flag_registed = True
self.OnFinishRegister()
_thread.exit()
cv2.imencode(
'.jpg',
np.array(faces[0])[..., ::-1])[1].tofile(
PATH_FACE +
'{}_{}_{}_{}'.format(str(self.id), self.unit,
self.name, self.gender) +
'/{}.jpg'.format(self.pic_num))
# cv2.imwrite(PATH_FACE + self.name+'/{}.jpg'.format(self.pic_num), np.array(faces[0])[..., ::-1])
self.pic_num += 1
print(
'写入本地：',
PATH_FACE + self.name + '/{}.jpg'.format(self.pic_num))
self.infoText.AppendText('[{}]数据已采集：{}{}张图像\r\n'.format(
getDateAndTime(hms=1), self.name, self.pic_num))
cv2.waitKey(5)
# except:
# print('请对准摄像头')
if self.new_register.IsEnabled():
_thread.exit()
if self.pic_num == 5:
self.OnFinishRegister()
_thread.exit()
def main(arguments):
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-l', '--launch_directory', action=readable_dir, default = "" )
parser.add_argument('-w', '--destination', action=readable_dir, help="Output directory", default="/nfs/www-prod/web_hx2/cm/metabolights/prod/reference/")
parser.add_argument('-c', '--compound', help="- MetaboLights Compound Identifier", default="all")
parser.add_argument('-s', '--stars', help="- Compounds import level", default="0")
parser.add_argument('-f', '--ftp', action=readable_dir, default="/ebi/ftp/pub/databases/metabolights/compounds/", help="FTP directory")
parser.add_argument('-p', '--process', action=readable_dir, default="false", help="Use parallel threads")
args = parser.parse_args(arguments)
global workingDirectory
global destinationDirectory
global requestedCompound
global ftp
global importLevel
batch = 10
workingDirectory = args.launch_directory
destinationDirectory = args.destination
requestedCompound = args.compound.replace('"','')
ftp = args.ftp
importLevel = args.stars
parallelProcessing = args.process
if(workingDirectory == ""):
workingDirectory = os.getcwd();
# log file configuration
st = utils.getDateAndTime();
randomInt = str(randint(1, 1000))
logDirectory = workingDirectory + "/logs/" + st
if not os.path.exists(logDirectory):
os.makedirs(logDirectory)
logging.basicConfig(filename= logDirectory + "/log_" +randomInt +".log",level=logging.DEBUG)
utils.init(logging)
logging.info("-----------------------------------------------")
logging.info('# Run started -' + utils.getDateAndTime())
logging.info('Reading MetaboLights Study - Compound Mapping file')
global mlSCMappingFile
mlSCMappingFile = ftp + "mapping.json"
logging.info('Reading Reactome data')
global reactomeJSONFile
reactomeJSONFile = ftp + "reactome.json"
with open(reactomeJSONFile) as reactome_file:
global reactomeData
reactomeData = json.load(reactome_file)
with open(mlSCMappingFile) as mapping_file:
global mlMapping
mlMapping = json.load(mapping_file)
if (requestedCompound != "all") :
# metabolightsFlagsJSONFile = ftp + "ml_flags.json"
# with open(metabolightsFlagsJSONFile) as flags_file:
# metabolightsFlagsData = json.load(flags_file)
# for metabolite in metabolightsFlagsData:
# print metabolite
# logging.info("-----------------------------------------------")
# logging.info("Fetching compound: " + metabolite)
# if metabolightsFlagsData[metabolite]['rating'] <= int(importLevel):
utils.fetchCompound(requestedCompound.strip(), workingDirectory, destinationDirectory, reactomeData, mlMapping)
else:
requestCompoundsList = utils.fetchMetaboLightsCompoundsList()
for compound in requestCompoundsList:
logging.info("-----------------------------------------------")
logging.info("Fetching compound: " + compound)
try:
utils.fetchCompound(compound.strip(), workingDirectory, destinationDirectory, reactomeData, mlMapping)
except:
logging.info("Error: " + compound)
pass
def main(arguments):
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-l',
'--launch_directory',
action=readable_dir,
default="")
parser.add_argument(
'-w',
'--destination',
action=readable_dir,
help="Output directory",
default="/nfs/www-prod/web_hx2/cm/metabolights/prod/reference/")
parser.add_argument(
'-f',
'--ftp',
action=readable_dir,
default="/ebi/ftp/pub/databases/metabolights/compounds/",
help="FTP directory")
args = parser.parse_args(arguments)
global workingDirectory
global destinationDirectory
global ftp
global globalReport
workingDirectory = args.launch_directory
destinationDirectory = args.destination
ftp = args.ftp
if (workingDirectory == ""):
workingDirectory = os.getcwd()
# log file configuration
st = utils.getDateAndTime()
randomInt = str(randint(1, 1000))
logDirectory = workingDirectory + "/logs/exporter_" + st
if not os.path.exists(logDirectory):
os.makedirs(logDirectory)
logging.basicConfig(filename=logDirectory + "/log_" + randomInt + ".log",
level=logging.DEBUG)
utils.init(logging)
logging.info("-----------------------------------------------")
logging.info('# Run started -' + utils.getDateAndTime())
fieldnames = [
"MetabolightsId", "InChIKey", "HasPathways", "KEGGPathways",
"WikiPathways", "ReactomePathways"
]
rows = []
requestCompoundsList = utils.fetchMetaboLightsCompoundsList()
i = 0
for compound in requestCompoundsList:
i = i + 1
print str(i) + "-" + str(len(requestCompoundsList))
compoundURL = "http://www.ebi.ac.uk/metabolights/webservice/beta/compound/" + compound
response = urllib2.urlopen(compoundURL)
compoundData = json.loads(response.read())
row = {}
chebiString = compound.replace("MTBLC", "CHEBI:")
row["MetabolightsId"] = compound
row["InChIKey"] = compoundData['inchiKey']
row["HasPathways"] = int(
compoundData["flags"]["hasPathways"] == 'true')
row["KEGGPathways"] = ""
row["WikiPathways"] = ""
row["ReactomePathways"] = ""
try:
if (compoundData["flags"]["hasPathways"]):
for resource in compoundData["pathways"]:
if resource == "WikiPathways":
for species in compoundData["pathways"][resource]:
for pathway in compoundData["pathways"][resource][
species]:
if row[resource] != "":
row[resource] = row[
resource] + "," + pathway["id"]
else:
row[resource] = pathway["id"]
elif resource == "ReactomePathways":
for species in compoundData["pathways"][resource]:
for pathway in compoundData["pathways"][resource][
species]:
if row[resource] != "":
row[resource] = row[
resource] + "," + pathway["reactomeId"]
else:
row[resource] = pathway["reactomeId"]
else:
for pathway in compoundData["pathways"][
"KEGGPathways"]:
if row[resource] != "":
row[resource] = row[resource] + "," + pathway[
"KO_PATHWAY"]
else:
row[resource] = pathway["KO_PATHWAY"]
except:
logging.error(compound)
rows.append(row)
with open('data/metabolites_inchikey.tsv', 'w') as csvfile:
writer = csv.DictWriter(csvfile, delimiter='\t', fieldnames=fieldnames)
writer.writeheader()
for row in rows:
writer.writerow(row)
def main(arguments):
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-l',
'--launch_directory',
action=readable_dir,
default="")
parser.add_argument(
'-w',
'--destination',
action=readable_dir,
help="Output directory",
default="/nfs/www-prod/web_hx2/cm/metabolights/prod/reference/")
parser.add_argument(
'-f',
'--ftp',
action=readable_dir,
default="/ebi/ftp/pub/databases/metabolights/compounds/",
help="FTP directory")
args = parser.parse_args(arguments)
global workingDirectory
global destinationDirectory
global ftp
global globalReport
workingDirectory = args.launch_directory
destinationDirectory = args.destination
ftp = args.ftp
if (workingDirectory == ""):
workingDirectory = os.getcwd()
# log file configuration
st = utils.getDateAndTime()
randomInt = str(randint(1, 1000))
logDirectory = workingDirectory + "/logs/exporter_" + st
if not os.path.exists(logDirectory):
os.makedirs(logDirectory)
logging.basicConfig(filename=logDirectory + "/log_" + randomInt + ".log",
level=logging.DEBUG)
utils.init(logging)
logging.info("-----------------------------------------------")
logging.info('# Run started -' + utils.getDateAndTime())
requestCompoundsList = utils.fetchMetaboLightsCompoundsList()
for compound in requestCompoundsList:
logging.info("-----------------------------------------------")
try:
logging.info("Exporting: " + compound)
tempCompoundReport = {
"rating": 5,
"flags": {
"hasInchiKey": False,
"hasLiterature": False,
"hasReactions": False,
"hasNMR": False,
"hasSpecies": False,
"hasMS": False,
"hasPathways": False,
"has3d": False
}
}
filePath = destinationDirectory + compound + "/" + compound + "_data.json"
tempCompoundReport = checkIfFileEmptyOrNotExist(
filePath, tempCompoundReport)
if tempCompoundReport["rating"] != 0:
tempCompoundReport = setFlags(filePath, tempCompoundReport)
else:
logging.warning("WARNING: Missing data - " + compound)
globalReport[compound] = tempCompoundReport
except:
logging.warning("Error: " + compound)
pass
utils.writeDataToFile(ftp + "ml_flags.json", globalReport)