def repo_items():
"""
get list of items in a repository.
param required: repo_id: id of repository
"""
# repo_id = request.args.get('repo_id')
# repo_name = request.args.get('repo_name')
client = custom_seafileapi.connect(server,
token=session['seafile_token'],
verify_ssl=False)
list_repos = client.repos.list_repos(type="mine")
if len(list_repos) < 1:
return "You dont have any repository"
data = []
repo_name = ''
for repo in list_repos:
repo_item = client.repos.get_repo(repo.id)
#return array of SeafDir objects
items = repo.get_items(recursive=0, type='d')
for item in items:
if item.name == 'FTICR_DATA':
data.append(item)
repo_name = repo.name
return render_template('seafile_client/repo_items.html',
data=data,
repo_name=repo_name)
def list_repositories():
"""
get list of all repositories in seafile server
"""
client = custom_seafileapi.connect(server,
token=session['seafile_token'],
verify_ssl=False)
list_repos = client.repos.list_repos(type="mine")
if len(list_repos) < 1:
return "You dont have any repository"
return render_template('seafile_client/list_repositories.html',
data=list_repos)
def login():
"""
Login page
param required: username: user email
param required: password
return login token from seafile server
"""
if 'seafile_token' in session and session['seafile_token'] != '':
return redirect(url_for('seafile_client.dir_items'))
if request.method == 'POST':
email = request.form.get('email')
_password = request.form.get('password')
request_token_url = server + "/api2/auth-token/"
_data = {"username": email, "password": _password}
_headers = {
"Accept-Encoding": "gzip",
"Accept-Language": "fr-FR,fr;q=0.9,en-US;q=0.8,en;q=0.7"
}
response = requests.post(url=request_token_url,
data=_data,
headers=_headers,
verify=False)
if response.status_code == 200:
content = json.loads(response.text)
session["seafile_token"] = content['token']
session["current_user"] = email
# get client username
client = custom_seafileapi.connect(server,
token=session['seafile_token'],
verify_ssl=False)
client_prof = client.get_user_profile()
session["username"] = client_prof['name']
# get user profile here
# create user temp folder
tmp_folder_path = os.path.join(seafile_client.root_path,
'static/tmp',
session['current_user'])
if not os.path.exists(tmp_folder_path):
os.makedirs(tmp_folder_path)
return redirect(url_for('seafile_client.dir_items'))
else:
flash(message="Login Fail", category="error")
return render_template('seafile_client/login.html')
def download_mscf_file(repo_id, file_full_path, parent_dir):
"""
Download mscf file to a temporary local directory
"""
# create temp local dir path
tmp_folder_path = os.path.join(seafile_client.root_path, 'static/tmp',
session['current_user'])
if not os.path.exists(tmp_folder_path):
os.makedirs(tmp_folder_path)
# if file doesnt exist in seafile server, file_full_path is None, then we create a default mscf file in temp local dir
if file_full_path == '':
tmp_file_path = os.path.join(tmp_folder_path, 'new.mscf')
default_conf_file = os.path.join(seafile_client.root_path, "static",
"files", "process2D.default.mscf")
with open(tmp_file_path, "w") as f:
with open(default_conf_file, 'r') as data:
f.write(data.read())
# else, mscf file exists in seafile server
else:
# connect to seafile server
client = custom_seafileapi.connect(server,
token=session['seafile_token'],
verify_ssl=False)
# get repo
repo = client.repos.get_repo(repo_id)
# check if temp local folder existed or not. if not, creat temp local folder
# get mscf file
file = repo.get_file(file_full_path, parent_dir)
# get mscf file download link
download_file_link = file._get_download_link()
# return download_file_link
# in dev: fix bug can not connect to host:
# urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='seafile.fticr-ms.eu', port=443)
download_path = urlparse(download_file_link).path
re_download_file_link = server + download_path
file_name = file.name
tmp_file_path = os.path.join(tmp_folder_path, file_name)
file_content = requests.get(url=re_download_file_link,
stream=True,
verify=False)
# write mscf file into local file
with open(tmp_file_path, "wb") as f:
for chunk in file_content.iter_lines():
f.write(chunk)
f.write(("\n").encode())
return tmp_file_path
def dir_items():
"""
get list of .d downstream directories in a FTICR_DATA directory
"""
# return session['seafile_token']
client = custom_seafileapi.connect(server,
token=session['seafile_token'],
verify_ssl=False)
list_repos = client.repos.list_repos(type="mine",
nameContains='My Library')
if len(list_repos) != 1:
return "You dont have any repository named'My Library'"
my_library_repo = list_repos[0]
repo_id = my_library_repo.id
dir_name = 'FTICR_DATA'
# # create FTICR_DATA dir object. It is a upstream directory of My Library, so parent_dir is '/' and we no need to declare in object
# FTICR_DATA_dir = SeafDir(repo=my_library_repo, name=dir_name, type='dir')
# # load dir items
# FTICR_DATA_dir.load_entries(recursive=1, type='d')
directories = my_library_repo.get_items(type="d", recursive=True)
data = []
# for item in FTICR_DATA_dir.entries:
for item in directories:
# if item['name'].endswith('.d'):
if item.name.endswith('.d'):
# sub_dir = SeafDir(repo=my_library_repo, name=item['name'], type='dir', parent_dir=item['parent_dir'])
# check if in .d folder has ser file or not
try:
# check if sub directory of FTICR_DATA has ser file or not
# re = my_library_repo.get_file(path=sub_dir.full_path+'ser', parent_dir=sub_dir.full_path)
re = my_library_repo.get_file(path=item.full_path + 'ser',
parent_dir=item.full_path)
# if 'FTICR_DATA' in sub_dir.full_path:
# data.append(sub_dir)
data.append(item)
except:
# return render_template("errors/general_error.html", message="There is not a project in which has a ser file.")
pass
return render_template('seafile_client/dir_items.html',
data=data,
dir_name=dir_name,
repo_id=repo_id)
def sub_dir():
repo_id = request.args.get('repo_id')
dir_name = request.args.get('dir_name')
parent_dir = request.args.get('parent_dir')
dir_fullpath = request.args.get('dir_fullpath')
# connect to seafile server
client = custom_seafileapi.connect(server,
token=session['seafile_token'],
verify_ssl=False)
# get repository data
repo = client.repos.get_repo(repo_id)
dir = SeafDir(repo=repo, name=dir_name, type='dir', parent_dir=parent_dir)
dir.load_entries(recursive=1, type='f')
data = []
for item in dir.entries:
if item['name'].endswith(
'.mscf') and item['parent_dir'] in dir_fullpath:
mscf_file = SeafFile(repo=repo,
name=item['name'],
type='file',
parent_dir=item['parent_dir'])
if dir_name in mscf_file.full_path:
data.append(mscf_file)
# for go back button or go back link in edit_mscf page
# session['prev_url'] = request.referrer
# return session['prev_url']
return render_template('seafile_client/sub_dir.html',
data=data,
dir_name=dir_name,
repo_id=repo_id,
dir_fullpath=dir_fullpath,
job_email=session['current_user'],
job_username=session['username'])
def load_corresponse_files(repo_id, parent_dir):
"""
Get .method, ExciteSweep and scan.xml files in a directory
"""
# create temporary local folder to contain method file. Method local file should be in same folder with mscf file
tmp_folder_path = os.path.join(seafile_client.root_path, 'static/tmp',
session['current_user'], parent_dir)
if not os.path.exists(tmp_folder_path):
os.makedirs(tmp_folder_path)
# check if .method file has already existed in temp local folder
met = glob.glob(os.path.join(tmp_folder_path, "*", ".method"))
exc = glob.glob(os.path.join(tmp_folder_path, "*", "ExciteSweep"))
scanxml = glob.glob(os.path.join(tmp_folder_path, "*", "scan.xml"))
corresponse_files = {}
if len(met) > 1 or len(exc) > 1 or len(scanxml) > 1:
# if there are more than 1 file, raise exeption
return render_template(
"errors/general_error.html",
message=
"You have more than 1 apexAcquisition.method or ExciteSweep or scan.xml file in the %s folder, using the first one"
% parent_dir)
elif len(met) == 1 and len(exc) == 1 and len(scanxml) == 1:
corresponse_files["method"] = met
corresponse_files["excitesweep"] = exc
corresponse_files["scanxml"] = scanxml
# if there is just one file, return file path
return corresponse_files
else:
# if there is not a file, then we load it from seafile server
client = custom_seafileapi.connect(server,
token=session['seafile_token'],
verify_ssl=False)
repo = client.repos.get_repo(repo_id)
method_files = repo.get_items(type='f', recursive=1)
data = []
# check number of method files in seafile server
for file in method_files:
if parent_dir in file.full_path:
# return (file.full_path, parent_dir, file.path + '\n')
if (file.name.endswith('.method') or file.name == 'ExciteSweep'
or file.name == 'scan.xml'
) and file.type == 'file' and (parent_dir
in file.full_path):
data.append(file)
# return data
# if len(data) > 3:
# return render_template("errors/400.html", message="You have more than 1 apexAcquisition.method or ExciteSweep or scan.xml file in the %s folder, using the first one"%parent_dir)
# if len(data) < 3:
# return render_template("errors/400.html", message="You don't have any apexAcquisition.method or ExciteSweep or scan.xml file in the %s folder"%parent_dir)
# else:
for item in data:
download_file_link = item._get_download_link()
# in dev: fix bug can not connect to host:
# urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='seafile.fticr-ms.eu', port=443)
download_path = urlparse(download_file_link).path
re_download_file_link = server + download_path
file_name = item.name
tmp_file_path = os.path.join(tmp_folder_path, file_name)
file_content = requests.get(url=re_download_file_link,
stream=True,
verify=False)
with open(tmp_file_path, "wb") as f:
for chunk in file_content.iter_lines():
f.write(chunk)
f.write(("\n").encode())
corresponse_files[item.name] = tmp_file_path
# return path of temporary method file in local folder
return corresponse_files