def test_dataset_init_invalid(self):
"""Test Dataset.init() with invalid data."""
pdv = Dataset()
# invalid data
for data in test_config["invalid_set_types"]:
with pytest.raises(AssertionError):
pdv.set(data)
def test_dataset_set_dv_up(self, import_dataset_min_dict):
"""Test Dataset.set() with format=`dv_up`.
Parameters
----------
import_dataset_min_dict : dict
Fixture, which returns a flat dataset dict().
"""
ds = Dataset()
data = import_dataset_min_dict
ds.set(data)
"""dataset"""
assert ds.license == 'CC0'
assert ds.termsOfUse == 'CC0 Waiver'
assert ds.termsOfAccess == 'Terms of Access'
"""citation"""
assert ds.citation_displayName == 'Citation Metadata'
assert ds.title == 'Replication Data for: Title'
def create_testdata(config_file: str, force: bool) -> None:
"""Create testdata defined in a config file.
Creates a pre-defined set of testdata on your
instance. By default, the function uses the
AUSSDA test data repository, which is so far not
publicly available. If `PRODUCTION` is `true`,
this function will not execute, as long as you
not add `--force` to the function call. This is
to protect from unwanted changes on a production
instance.
"""
# Init
if config.PRODUCTION and not force:
print(
"Create testdata on a PRODUCTION instance not allowed. Use --force to force it."
)
sys.exit()
pid_idx = []
users = read_json(config.USER_FILENAME)
workflow = read_json(os.path.join(ROOT_DIR, config_file))
# Dataverses
for dv_conf in workflow["dataverses"]:
dv_alias = None
if "create" in dv_conf:
api = NativeApi(
config.BASE_URL,
users[dv_conf["create"]["user-handle"]]["api-token"])
dv = Dataverse()
dv_filename = os.path.join(ROOT_DIR,
dv_conf["create"]["metadata-filename"])
dv.from_json(read_file(dv_filename))
if "update" in dv_conf["create"]:
for key, val in dv_conf["create"]["update"].items():
kwargs = {key: val}
dv.set(kwargs)
dv_alias = dv.get()["alias"]
resp = api.create_dataverse(dv_conf["create"]["parent"], dv.json())
if "publish" in dv_conf:
api = NativeApi(
config.BASE_URL,
users[dv_conf["publish"]["user-handle"]]["api-token"])
if not dv_alias and "alias" in dv_conf["publish"]:
dv_alias = dv_conf["publish"]["alias"]
resp = api.publish_dataverse(dv_alias)
# Datasets
for ds_conf in workflow["datasets"]:
pid = None
if "create" in ds_conf:
api = NativeApi(
config.BASE_URL,
users[ds_conf["create"]["user-handle"]]["api-token"])
ds = Dataset()
ds_filename = os.path.join(ROOT_DIR,
ds_conf["create"]["metadata-filename"])
ds.from_json(read_file(ds_filename))
if "update" in ds_conf["create"]:
for key, val in ds_conf["create"]["update"].items():
kwargs = {key: val}
ds.set(kwargs)
resp = api.create_dataset(dv_alias, ds.json())
pid = resp.json()["data"]["persistentId"]
pid_idx.append(pid)
if "publish" in ds_conf:
if not pid:
print("ERROR: PID missing!")
sys.exit()
api = NativeApi(
config.BASE_URL,
users[ds_conf["publish"]["user-handle"]]["api-token"])
resp = api.publish_dataset(pid, release_type="major")
# Datafiles
for dataset_id, ds_datafiles in workflow["datafiles"].items():
if int(dataset_id) == workflow["datasets"][int(dataset_id)]["id"]:
pid = pid_idx[int(dataset_id)]
else:
print("ERROR: Dataset ID not matching.")
sys.exit()
for df_conf in ds_datafiles:
if "upload" in df_conf:
api = NativeApi(
config.BASE_URL,
users[df_conf["upload"]["user-handle"]]["api-token"],
)
metadata = read_json(df_conf["upload"]["metadata-filename"])
df = Datafile()
df.set(metadata)
if "update" in df_conf["upload"]:
for key, val in df_conf["upload"]["update"].items():
kwargs = {key: val}
df.set(kwargs)
df.set({"pid": pid})
filename = df_conf["upload"]["filename"]
resp = api.upload_datafile(pid, filename, df.json())
if filename[-4:] == ".sav" or filename[-4:] == ".dta":
sleep(30)
else:
sleep(3)
if "publish-dataset" in df_conf:
api = NativeApi(
config.BASE_URL,
users[df_conf["publish-dataset"]["user-handle"]]["api-token"],
)
if df_conf["publish-dataset"]:
resp = api.publish_dataset(pid, release_type="major")
class DataverseData():
def __init__(self, REPO, validate=False):
self.ext = PARSABLE_EXTENSIONS
self.REPO = REPO
self.mapping_dsid2pid = {}
self.validate_df = validate
self.g = Github(GITHUB_TOKEN)
self.repo = self.g.get_repo(REPO)
self.urls_found = {}
self.ds_id = 0
self.DEBUG = True
def githubsearch(self, thisquery):
repositories = self.g.search_repositories(query=thisquery,
sort='updated')
return repositories
def search(self, thisquery):
search_api = SearchApi(BASE_URL, API_TOKEN)
return search_api.search(thisquery).json()['data']
def if_exist(self, thisquery):
self.exists = False
repoquery = "authorName:%s" % (thisquery)
try:
for item in self.search(repoquery)['items'][0]['authors']:
if item == thisquery:
self.exists = True
print(item)
except:
self.exists = False
if self.DEBUG:
print(self.exists)
return self.exists
def datasync(self):
native_api = NativeApi(BASE_URL, API_TOKEN)
self.ds_id = str(
int(self.make_dataset_id(self.REPO).hexdigest(),
16))[:6] ## turn the md5 string into a 6 digits integer
metadata = self.make_dataset_metadata(self.REPO)
print(metadata)
self.ds = Dataset()
self.ds.set(metadata)
self.ds.displayName = metadata['title']
self.ds.json = metadata
print(self.ds.get())
if self.DEBUG:
print("[datasync]")
print(self.ds)
print(self.ds_id)
print(self.ds.displayName)
self.create_dataset(native_api, self.ds, DV_ALIAS, self.ds_id,
BASE_URL)
if self.DEBUG:
print(metadata)
self.upload_files_to_dataverse(self.ds_id, self.urls_found)
return True
def extract_urls(self, content: str) -> list:
matches = re.findall(r"(http[^\s'\"\\]+)", content)
pattern = re.compile(r"([^/\w]+)$")
return [pattern.sub("", match) for match in matches]
def decode_github_content(self, content: str) -> str:
return base64.b64decode(content).decode("utf-8")
def make_dataset_id(self, repo_name):
return hashlib.md5(repo_name.encode("utf-8"))
def make_default_dataset(self, data, repo_name):
ds_id = self.make_dataset_id(repo_name)
data[ds_id] = {'metadata': make_dataset_metadata(repo_name)}
return data
def make_dataset_metadata(self, repo_name):
metadata = {}
repo = self.g.get_repo(repo_name)
metadata['termsOfAccess'] = ''
metadata[
'title'] = 'Automatic uploads from {} github repository'.format(
repo_name)
metadata[
'subtitle'] = 'Automatic uploads from {} github repository'.format(
repo_name)
metadata['author'] = [{
"authorName": repo_name,
"authorAffiliation": "CoronaWhy"
}]
metadata['dsDescription'] = [{'dsDescriptionValue': ''}]
metadata['dsDescription'] = [{
'dsDescriptionValue':
format(repo.get_topics())
}]
if len(metadata['dsDescription']) < 3:
metadata['dsDescription'] = [{'dsDescriptionValue': 'coronavirus'}]
metadata['subject'] = ['Medicine, Health and Life Sciences']
metadata['keyword'] = repo.get_topics()
metadata['datasetContact'] = [{
'datasetContactName':
'https://github.com/{}'.format(repo_name),
'datasetContactEmail':
'*****@*****.**'
}]
return metadata
def make_file_metadata(self, repo_name, file, url):
metadata = {}
metadata['description'] = file
metadata['filename'] = url
metadata['datafile_id'] = hashlib.md5(url.encode("utf-8"))
metadata['dataset_id'] = hashlib.md5(repo_name.encode("utf-8"))
return metadata
def create_dataset(self, api, ds, dv_alias, ds_id, base_url):
if self.DEBUG:
print("\n\n[create_dataset]")
print(ds.get())
# print(ds.to_json())
resp = ''
try:
resp = api.create_dataset(dv_alias, ds.json())
pid = resp.json()['data']['persistentId']
except:
# print(resp.content)
return resp, self.mapping_dsid2pid
self.mapping_dsid2pid[ds_id] = pid
time.sleep(1)
print('{0}/dataset.xhtml?persistentId={1}&version=DRAFT'.format(
base_url, pid))
return resp
# Implementation adapted from http://guides.dataverse.org/en/latest/api/native-api.html#id62
def upload_datafile(self, server, api_key, p_id, repo_name, filename,
repo_file, url, columns):
dataverse_server = server
api_key = api_key
persistentId = p_id
files = {'file': (url.split('/')[-1], open(filename, 'rb'))}
desc = "Data snapshot from %s" % url
cat = [repo_name.split('/')[1]]
for col in columns:
cat.append(col)
params = dict(description=desc,
directoryLabel=repo_file,
categories=cat)
params_as_json_string = json.dumps(params)
payload = dict(jsonData=params_as_json_string)
url_persistent_id = '%s/api/datasets/:persistentId/add?persistentId=%s&key=%s' % (
dataverse_server, persistentId, api_key)
print('-' * 40)
print('making request')
r = requests.post(url_persistent_id, data=payload, files=files)
print('-' * 40)
try:
print(r.json())
except:
print(r.content)
print(r.status_code)
return
def collect_urls(self):
contents = self.repo.get_contents("")
DEBUG = False
while contents:
file_content = contents.pop(0)
urlfullpath = "%s/%s/%s/%s" % (gitroot, self.REPO, gitblob,
file_content.path)
rawurl = "%s/%s/%s/%s" % (gituserroot, self.REPO, gitmaster,
file_content.path)
rawurl = rawurl.replace(' ', '%20')
if file_content.type == "dir":
contents.extend(self.repo.get_contents(file_content.path))
continue
if len(PARSABLE_EXTENSIONS) == 0 or file_content.name.split(
'.')[-1] in PARSABLE_EXTENSIONS:
if DEBUG:
print("%s -> %s" % (urlfullpath, rawurl))
self.urls_found[file_content.path] = rawurl
print('Found {} URLs'.format(len(self.urls_found)))
return self.urls_found
def upload_files_to_dataverse(self, ds_id, urls_found):
for file, url in urls_found.items():
columns = []
#for url in urls:
if file:
print(url)
try:
tmpfile = urllib.request.urlretrieve(
url
) # retrieve the csv in a temp file, if there is a problem with the URL it throws and we continue
except:
continue
try:
filename = 'file://{}'.format(tmpfile[0])
# TODO: try gzipped datasets as well
#if not re.findall(r'(gz$|np$|nt$)', filename):
# pd.read_csv(filename) # try reading it as csv, if fails continue
print("%s -> %s" % (filename, url))
if self.validate_df:
if re.search(r"(xls|xlsx)", url):
df = pd.read_excel(filename)
columns = list(df.columns)
elif re.search(r"json", url):
df = pd.read_excel(filename)
columns = list(df.columns)
else:
df = pd.read_csv(filename)
columns = list(df.columns)
if self.DEBUG:
print("Columns: %s" % df.columns)
metadata = self.make_file_metadata(REPO, file, url)
print('- uploading the following dataset {}'.format(url))
except:
continue
self.upload_datafile(BASE_URL, API_TOKEN, self.ds_id,
self.REPO, tmpfile[0], file, url, columns)
return