def get_file_links(accession, database):
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.FILE_LINKS_URL,
params={
"accession": accession,
"database": database
},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request accession {} and database {} thrown connection error"
.format(accession, database),
res.status_code,
payload=None)
file_links = []
if res.json():
for file_link in res.json():
file_links.append(file_link)
return file_links
def search(query,
sortfield=None,
order=None,
start=0,
size=20,
face_count=20):
params = {"start": start, "size": size, "faceCount": face_count}
if not query:
raise BadRequest("missing parameter query",
MISSING_PARAMETER,
payload=None)
else:
params.update(query=query)
if sortfield:
params.update(sortfield=sortfield)
if order:
params.update(order=order)
res = requests.get(constants.SEARCH_URL,
params=params,
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request query {} and sortfield {} and order {} thrown connection error"
.format(query, sortfield, order),
res.status_code,
payload=None)
return DataSetResult.get_object_from_json(res.json())
def batch(acc, database):
if not acc:
raise BadRequest("missing parameter acc",
MISSING_PARAMETER,
payload=None)
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.BATCH_URL,
params={
"accession": acc,
"database": database
},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request accession {} and database {} thrown connection error"
.format(acc, database),
res.status_code,
payload=None)
return BatchDataset.get_object_from_json(res.json())
def get_dataset_files(database, accession, position):
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
if not position:
raise BadRequest("missing parameter position",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.DATASET_URL + "/" + database + "/" +
accession + "/files",
params={"position": position},
headers=constants.HEADERS)
file_links = []
if res.json():
for file_link in res.json():
file_links.append(file_link)
return file_links
def get_dataset_details(database, accession):
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.DATASET_URL + "/" + database + "/" +
accession,
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request dataset accession {} and database {} thrown connection error"
.format(accession, database),
res.status_code,
payload=None)
dataset = Dataset.get_object_from_json(res.json())
return dataset
def get_similar(acc, database):
if not acc:
raise BadRequest("missing parameter acc",
MISSING_PARAMETER,
payload=None)
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.SIMILAR_URL,
params={
"acc": acc,
"database": database
},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request accession {} and database {} thrown connection error"
.format(acc, database),
res.status_code,
payload=None)
return res
def get_term_by_pattern(q="hom", size=10):
res = requests.get(constants.TERM_BY_PATTERN_URL, params={
"q": q,
"size": size
}, headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest("The request query {} and size {} thrown connection error".format(q, size), res.status_code, payload=None)
if res.status_code == 200 and res.json()["total_count"] ==0:
raise BadRequest("The request found nothing in server", DATA_NOT_FOUND, payload=None)
return res
def get_seo_schema(acc, domain):
if not acc:
raise BadRequest("missing parameter acc",
MISSING_PARAMETER,
payload=None)
if not domain:
raise BadRequest("missing parameter domain",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.SEO_SCHEMA_URL + "/" + domain + "/" + acc,
headers=constants.HEADERS)
return res
def get_seo_about():
res = requests.get(constants.SEO_ABOUT_URL, headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest("The request thrown connection error",
res.status_code,
payload=None)
return res
def get_db_name(lucene_name):
if not lucene_name:
raise BadRequest("missing parameter lucene_name", MISSING_PARAMETER, payload=None)
res = requests.get(constants.DB_NAME_URL, params={
"luceneName": lucene_name
}, headers=constants.HEADERS)
return res
def get_term_frequently_term_list(domain, field, size=20):
if not domain:
raise BadRequest("missing parameter domain", MISSING_PARAMETER, payload=None)
if not field:
raise BadRequest("missing parameter field", MISSING_PARAMETER, payload=None)
res = requests.get(constants.FREQUENTLY_TERM_URL, params={
"size": size,
"domain": domain,
"field": field
}, headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest("The request domain {} and field {} and size {} thrown connection error".format(domain, field, size), res.status_code, payload=None)
return res
def get_database_all():
res = requests.get(constants.DATABASE_ALL_URL,
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest("The request thrown connection error",
res.status_code,
payload=None)
return res
def get_lucene_name(db_name):
if not db_name:
raise BadRequest("missing parameter db_name", MISSING_PARAMETER, payload=None)
res = requests.get(constants.LUCENE_NAME_URL, params={
"dbName": db_name
}, headers=constants.HEADERS)
return res
def get_similar_by_pubmed(pubmed):
if not pubmed:
raise BadRequest("missing parameter pubmed",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.DATASET_URL + "/getSimilarByPubmed",
params={"pubmed": pubmed},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request pubmed {} thrown connection error".format(pubmed),
res.status_code,
payload=None)
return res
def get_synonyms_for_dataset(accession, database):
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.SYNONYMS_URL,
params={
"accession": accession,
"database": database
},
headers=constants.HEADERS)
return res
def get(acc, database):
if not acc:
raise BadRequest("missing parameter acc",
MISSING_PARAMETER,
payload=None)
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.GET_URL,
params={
"acc": acc,
"database": database
},
headers=constants.HEADERS)
return res.json()
def get_list(acc):
if not acc:
raise BadRequest("missing parameter acc",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.LIST_URL,
params={"acc": acc},
headers=constants.HEADERS)
return res
def get_enrichment_info(accession, database):
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.ENRICHMENT_INFO_URL,
params={
"accession": accession,
"database": database
},
headers=constants.HEADERS)
return res
def get_similar_datasets_by_biological_data(accession, database):
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.SIMILAR_DATASETS_BIOLOGY_URL,
params={
"accession": accession,
"database": database
},
headers=constants.HEADERS)
return res
def get_database_pic(database_name):
if not database_name:
raise BadRequest("missing parameter database_name",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.DATABASE_URL + "/" + database_name +
"/picture",
headers=constants.HEADERS)
return res
def latest(size=20):
res = requests.get(constants.LATEST_URL,
params={"size": size},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest("The request thrown connection error",
res.status_code,
payload=None)
return res
def get_statistics_organisms(size=20):
res = requests.get(constants.STATISTICS_URL + "/organisms",
params={"size": size},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request size {} thrown connection error".format(size),
res.status_code,
payload=None)
return res
def most_accessed(size=20):
res = requests.get(constants.MOST_ACCESSED_DATASETS,
params={"size": size},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest("The request thrown connection error",
res.status_code,
payload=None)
return res
def get_similar_by_pubmed(pubmed):
if not pubmed:
raise BadRequest("missing parameter pubmed",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.DATASET_URL + "/getSimilarByPubmed",
params={"pubmed": pubmed},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request pubmed {} thrown connection error".format(pubmed),
res.status_code,
payload=None)
datasets = []
for i in res.json():
dataset = Dataset.get_object_from_json(i)
datasets.append(dataset)
return datasets
def get_dataset_by_url(url):
if not url:
raise BadRequest("missing parameter url",
MISSING_PARAMETER,
payload=None)
res = requests.post(constants.DATASET_URL + "/getDatasetByUrl",
params={"url": url},
headers=constants.HEADERS)
return res
def get_dataset_files(domain, accession, position):
if not domain:
raise BadRequest("missing parameter domain",
MISSING_PARAMETER,
payload=None)
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
if not position:
raise BadRequest("missing parameter position",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.DATASET_URL + "/" + domain + "/" +
accession + "/files",
params={"position": position},
headers=constants.HEADERS)
return res
def get_seo_dataset(domain, acc):
if not acc:
raise BadRequest("missing parameter acc",
MISSING_PARAMETER,
payload=None)
if not domain:
raise BadRequest("missing parameter domain",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.SEO_DATASET_URL + "/" + domain + "/" +
acc,
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request accession {} and database {} thrown connection error",
res.status_code,
payload=None)
return res
def get_similarity_info(accession, database, threshold):
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
if not database:
raise BadRequest("missing parameter database",
MISSING_PARAMETER,
payload=None)
if not threshold:
raise BadRequest("missing parameter threshold",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.SIMILAR_INFO_URL,
params={
"accession": accession,
"database": database,
"threshold": threshold
},
headers=constants.HEADERS)
return res
def get_dataset_details(domain, accession, debug=False):
if not domain:
raise BadRequest("missing parameter domain",
MISSING_PARAMETER,
payload=None)
if not accession:
raise BadRequest("missing parameter accession",
MISSING_PARAMETER,
payload=None)
res = requests.get(constants.DATASET_URL + "/" + domain + "/" +
accession,
params={"debug": debug},
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest(
"The request dataset accession {} and database {} thrown connection error"
.format(accession, domain),
res.status_code,
payload=None)
return res.json()
def get_database_all():
res = requests.get(constants.DATABASE_ALL_URL,
headers=constants.HEADERS)
if res.status_code != 200:
raise BadRequest("The request thrown connection error",
res.status_code,
payload=None)
database_details = []
if res.json():
for database_detail_json in res.json():
database_detail = DatabaseDetail.get_object_from_json(
database_detail_json)
database_details.append(database_detail)
return database_details