From 2b43395c0ed53059559c6d85ace41e74d1ae86b1 Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Mon, 24 Jul 2023 16:34:19 +0200
Subject: [PATCH] SSDM-13735: fixes to dataset upload, PyBIS-1.36.0
---
api-openbis-python3-pybis/src/python/CHANGELOG.md | 3 ++-
.../src/python/pybis/__init__.py | 2 +-
api-openbis-python3-pybis/src/python/pybis/dataset.py | 11 +++--------
api-openbis-python3-pybis/src/python/pybis/pybis.py | 9 ++++++++-
api-openbis-python3-pybis/src/python/setup.cfg | 2 +-
api-openbis-python3-pybis/src/python/setup.py | 3 +--
6 files changed, 16 insertions(+), 14 deletions(-)
diff --git a/api-openbis-python3-pybis/src/python/CHANGELOG.md b/api-openbis-python3-pybis/src/python/CHANGELOG.md
index ba02912c3e9..3e9f63a035a 100644
--- a/api-openbis-python3-pybis/src/python/CHANGELOG.md
+++ b/api-openbis-python3-pybis/src/python/CHANGELOG.md
@@ -1,6 +1,7 @@
## Changes with pybis-1.36.0
-- Added dependency to requests-toolbelt
+- Reverted breaking changes to dataset upload functionality
+- Performance improvements to get_sample and get_samples methods
## Changes with pybis-1.35.11
diff --git a/api-openbis-python3-pybis/src/python/pybis/__init__.py b/api-openbis-python3-pybis/src/python/pybis/__init__.py
index 82c03f6cb41..8a25c785035 100644
--- a/api-openbis-python3-pybis/src/python/pybis/__init__.py
+++ b/api-openbis-python3-pybis/src/python/pybis/__init__.py
@@ -15,7 +15,7 @@
name = "pybis"
__author__ = "ID SIS • ETH Zürich"
__email__ = "openbis-support@id.ethz.ch"
-__version__ = "1.36.0rc1"
+__version__ = "1.36.0"
from . import pybis
from .pybis import DataSet
diff --git a/api-openbis-python3-pybis/src/python/pybis/dataset.py b/api-openbis-python3-pybis/src/python/pybis/dataset.py
index e845406e9af..9ba2f319b59 100644
--- a/api-openbis-python3-pybis/src/python/pybis/dataset.py
+++ b/api-openbis-python3-pybis/src/python/pybis/dataset.py
@@ -29,7 +29,6 @@ from urllib.parse import urljoin, quote
import requests
from pandas import DataFrame
from requests import Session
-from requests_toolbelt.multipart.encoder import MultipartEncoder
from tabulate import tabulate
from .definitions import (
@@ -1246,13 +1245,9 @@ class DataSetUploadQueue:
file_size = os.path.getsize(filename)
if self.multipart is True:
- with open(filename, "rb") as f:
- m = MultipartEncoder(
- fields={filename: (filename, f, 'application/octet-stream')})
- headers = {'Content-Type': m.content_type}
- r = requests.post(upload_url, data=m, headers=headers,
- verify=verify_certificates)
- r.raise_for_status()
+ file = {filename: open(filename, "rb")}
+ resp = requests.post(upload_url, files=file, verify=verify_certificates)
+ resp.raise_for_status()
else:
# upload the file to our DSS session workspace
with open(filename, "rb") as f:
diff --git a/api-openbis-python3-pybis/src/python/pybis/pybis.py b/api-openbis-python3-pybis/src/python/pybis/pybis.py
index a0b8674fe58..12e50318f81 100644
--- a/api-openbis-python3-pybis/src/python/pybis/pybis.py
+++ b/api-openbis-python3-pybis/src/python/pybis/pybis.py
@@ -2380,6 +2380,7 @@ class Openbis:
attrs=None,
props=None,
where=None,
+ raw_response=False,
**properties,
):
"""Returns a DataFrame of all samples for a given space/project/experiment (or any combination).
@@ -2512,6 +2513,8 @@ class Openbis:
resp = self._post_request(self.as_v3, request)
parse_jackson(resp)
+ if raw_response:
+ return resp
response = resp["objects"]
@@ -4663,7 +4666,8 @@ class Openbis:
)
def get_sample(
- self, sample_ident, only_data=False, withAttachments=False, props=None, withDataSetIds=False, **kvals
+ self, sample_ident, only_data=False, withAttachments=False, props=None,
+ withDataSetIds=False, raw_response=False, **kvals
):
"""Retrieve metadata for the sample.
Get metadata for the sample and any directly connected parents of the sample to allow access
@@ -4729,6 +4733,9 @@ class Openbis:
data=resp[sample_ident],
)
else:
+ if raw_response:
+ parse_jackson(resp)
+ return resp
return self._sample_list_for_response(
response=list(resp.values()), props=props, parsed=False
)
diff --git a/api-openbis-python3-pybis/src/python/setup.cfg b/api-openbis-python3-pybis/src/python/setup.cfg
index 4b809868084..ae2a809cf65 100644
--- a/api-openbis-python3-pybis/src/python/setup.cfg
+++ b/api-openbis-python3-pybis/src/python/setup.cfg
@@ -1,6 +1,6 @@
[metadata]
name = PyBIS
-version = 1.36.0rc1
+version = 1.36.0
author = ID SIS • ETH Zürich
author_email = openbis-support@id.ethz.ch
license = Apache Software License Version 2.0
diff --git a/api-openbis-python3-pybis/src/python/setup.py b/api-openbis-python3-pybis/src/python/setup.py
index dbd0fada902..0efb031a3d7 100644
--- a/api-openbis-python3-pybis/src/python/setup.py
+++ b/api-openbis-python3-pybis/src/python/setup.py
@@ -26,7 +26,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setup(
name="PyBIS",
- version="1.36.0rc1",
+ version="1.36.0",
author="ID SIS • ETH Zürich",
author_email="openbis-support@id.ethz.ch",
description="openBIS connection and interaction, optimized for using with Jupyter",
@@ -38,7 +38,6 @@ setup(
install_requires=[
"pytest",
"requests",
- "requests_toolbelt",
"urllib3",
"pandas",
"texttable",
--
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