From 9014451e7289989d32a4f4ee7f706c3f927ece35 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Tue, 15 Mar 2022 10:37:31 +0100
Subject: [PATCH] sample: automatically add project if it is missing
---
pybis/src/python/CHANGELOG.md | 4 ++++
pybis/src/python/pybis/__init__.py | 2 +-
pybis/src/python/pybis/dataset.py | 5 ++++-
pybis/src/python/pybis/sample.py | 20 +++++++++++---------
pybis/src/python/setup.py | 2 +-
5 files changed, 21 insertions(+), 12 deletions(-)
diff --git a/pybis/src/python/CHANGELOG.md b/pybis/src/python/CHANGELOG.md
index a5f4e036737..08768a521de 100644
--- a/pybis/src/python/CHANGELOG.md
+++ b/pybis/src/python/CHANGELOG.md
@@ -1,3 +1,7 @@
+## Changes with pybis-1.31.6
+
+- automatically setting the project if only experiment was set
+
## Changes with pybis-1.31.5
- optimised error generation without assert
diff --git a/pybis/src/python/pybis/__init__.py b/pybis/src/python/pybis/__init__.py
index fd168de3f6c..48ae574245e 100644
--- a/pybis/src/python/pybis/__init__.py
+++ b/pybis/src/python/pybis/__init__.py
@@ -1,7 +1,7 @@
name = "pybis"
__author__ = "Swen Vermeul"
__email__ = "swen@ethz.ch"
-__version__ = "1.31.5"
+__version__ = "1.31.6"
from . import pybis
from .pybis import DataSet
diff --git a/pybis/src/python/pybis/dataset.py b/pybis/src/python/pybis/dataset.py
index 25b8c5581d5..df057ce229c 100644
--- a/pybis/src/python/pybis/dataset.py
+++ b/pybis/src/python/pybis/dataset.py
@@ -1060,7 +1060,10 @@ class DataSetUploadQueue:
resp = requests.post(upload_url, data=f, verify=verify_certificates)
resp.raise_for_status()
data = resp.json()
- assert filesize == int(data["size"])
+ if filesize != int(data["size"]):
+ raise ValueError(
+ f'size of file uploaded: {filesize} != data received: {int(data["size"])}'
+ )
# Tell the queue that we are done
self.upload_queue.task_done()
diff --git a/pybis/src/python/pybis/sample.py b/pybis/src/python/pybis/sample.py
index f0e8ee1514e..df1d7b0828e 100644
--- a/pybis/src/python/pybis/sample.py
+++ b/pybis/src/python/pybis/sample.py
@@ -21,15 +21,6 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
if data is not None:
self._set_data(data)
- # TODO: Why are we using getattr() and setattr() here? They are considerably slower.
- if project is not None:
- self.project = project
-
- if props is not None:
- for key in props:
- # self.p[key] = props[key]
- setattr(self.p, key, props[key])
-
if kwargs is not None:
for key in kwargs:
setattr(self, key, kwargs[key])
@@ -43,6 +34,17 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
except Exception:
pass
+ if project is None:
+ if self.experiment:
+ self.project = self.experiment.project
+ else:
+ self.project = project
+
+ if props is not None:
+ for key in props:
+ # self.p[key] = props[key]
+ setattr(self.p, key, props[key])
+
if getattr(self, "parents") is None:
self.a.__dict__["_parents"] = []
else:
diff --git a/pybis/src/python/setup.py b/pybis/src/python/setup.py
index 51ce66285fe..77513791c50 100644
--- a/pybis/src/python/setup.py
+++ b/pybis/src/python/setup.py
@@ -13,7 +13,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setup(
name="PyBIS",
- version="1.31.5",
+ version="1.31.6",
author="Swen Vermeul • ID SIS • ETH Zürich",
author_email="swen@ethz.ch",
description="openBIS connection and interaction, optimized for using with Jupyter",
--
GitLab