Merge branch 'master' into ssdm-13253-dataset-creation-from-v3

README.md

@@ -62,9 +62,10 @@ openbis.bundle.min.js
 
 ## Requirements
 
+- Software Requirements
 - IntelliJ IDEA CE
 
-## Step By Step:
+## Step By Step
 
 ```
 File -> New -> Project From Existing Sources
@@ -76,6 +77,50 @@ openBISDevelopementEnvironmentASStart
 openBISDevelopementEnvironmentDSSStart
 ```
 
+## Source Code Auto Formatting
+
+OpenBIS source code uses a particular style preset that guarantees all code is formatted uniformly.
+
+To make use of the preset go to File/Settings or IntelliJIDEA/Preferences depending on your OS.
+
+Then import the XML file under 'docs/codestyle/SIS_Conventions_IntelliJ_V3.xml'. See images below:
+
+!["IntelliJ Code Style Configuration 1"](./docs/readme/intellij-codestyle-config-1.png "IntelliJ Code Style Configuration 1")
+!["IntelliJ Code Style Configuration 2"](./docs/readme/intellij-codestyle-config-2.png "IntelliJ Code Style Configuration 2")
+!["IntelliJ Code Style Configuration 3"](./docs/readme/intellij-codestyle-config-3.png "IntelliJ Code Style Configuration 3")
+!["IntelliJ Code Style Configuration 4"](./docs/readme/intellij-codestyle-config-4.png "IntelliJ Code Style Configuration 4")
+
+## Commit Messages Formatting
+
+OpenBIS source code commit messages use a particular formatting.
+
+This formatting guarantees that there is a User Story behind it.
+
+To ensure commits follow the formatting 'Git Hooks' are provided.
+
+Just copy them from the root folder of this repo run the next command:
+````
+%/> cp ./docs/hooks/* ./.git/hooks/   
+%/> git add README.md
+%/> git commit -m "Test incorrectly formatted message"
+Aborting commit. Your commit message is missing an issue number ('SSDM-XXXXX:')
+````
+
+## Source Code Copyright Header
+
+OpenBIS source code is licensed under SIS copyright and licensed under 'Apache 2 License':
+````
+http://www.apache.org/licenses/LICENSE-2.0
+````
+To guarantee all new source files contain the appropriate license a preset is provided.
+
+To make use of the preset go to File/Settings or IntelliJIDEA/Preferences depending on your OS.
+
+Then import the XML file under 'docs/copyright/Copyright_IntelliJ.xml' under the copyright section as the image below indicate.
+!["IntelliJ Copyright Configuration 1"](./docs/readme/intellij-copyright-config-1.png "IntelliJ Copyright Configuration 1")
+Last, set the Copyright Profile under the Copyright section as the image below indicate:
+!["IntelliJ Copyright Configuration 2"](./docs/readme/intellij-copyright-config-2.png "IntelliJ Copyright Configuration 2")
+
 ## Typical Errors
 
 # IntelliJ can't find package com.sun.*, but I can compile the project using the command line!
@@ -83,22 +128,19 @@ openBISDevelopementEnvironmentDSSStart
 Turn off "File | Settings | Build, Execution, Deployment | Compiler | Java Compiler | Use --release
 option for cross-compilation".
 
-# IntelliJ can't find a particular method:
+# IntelliJ can't find a particular method
 
 Code compatiblity 1.8 is set by default to work well with our javadoc tools but it can be set to 17 on IntelliJ. See image below.
-
 !["IntelliJ Configuration 1"](./docs/readme/intellij-config-1.png "IntelliJ Configuration 1")
 
-# Test seem to run through Gradle and fail:
+# Test seem to run through Gradle and fail
 
 They need to be set to run using IntelliJ.
-
 !["IntelliJ Configuration 2"](./docs/readme/intellij-config-2.png "IntelliJ Configuration 2")
 
-# Test seem to run through intelliJ but throw a package not open error:
+# Test seem to run through intelliJ but throw a package not open error
 
 The project does not uses modules yet. Add '--add-opens' statements manually when launching the tests as shown below.
-
 !["IntelliJ Configuration 3"](./docs/readme/intellij-config-3.png "IntelliJ Configuration 3")
 
 ## Development of NG UI

api-openbis-python3-pybis/src/python/pybis/__init__.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 name = "pybis"
 __author__ = "ID SIS • ETH Zürich"
 __email__ = "openbis-support@id.ethz.ch"

api-openbis-python3-pybis/src/python/pybis/attachment.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 import base64
 import os
 

api-openbis-python3-pybis/src/python/pybis/attribute.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from pandas import DataFrame, Series
 from tabulate import tabulate
 from .definitions import (

api-openbis-python3-pybis/src/python/pybis/data_set.py

 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+
+
+
 """
 data_set.py
 

api-openbis-python3-pybis/src/python/pybis/dataset.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 import os
 from functools import partialmethod
 from pathlib import Path

api-openbis-python3-pybis/src/python/pybis/definitions.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 import copy
 
 

api-openbis-python3-pybis/src/python/pybis/entity_type.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from tabulate import tabulate
 from texttable import Texttable
 from pandas import DataFrame

api-openbis-python3-pybis/src/python/pybis/experiment.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from .property import PropertyHolder
 from .attribute import AttrHolder
 from .openbis_object import OpenBisObject

api-openbis-python3-pybis/src/python/pybis/group.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from .attribute import AttrHolder
 from .openbis_object import OpenBisObject
 from .utils import VERBOSE, extract_permid, extract_nested_permid, format_timestamp

api-openbis-python3-pybis/src/python/pybis/material.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from .attribute import AttrHolder
 from .openbis_object import OpenBisObject
 from .property import PropertyHolder

api-openbis-python3-pybis/src/python/pybis/openbis_object.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from .property import PropertyHolder
 from .attribute import AttrHolder
 from .utils import VERBOSE

api-openbis-python3-pybis/src/python/pybis/person.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from .attribute import AttrHolder
 from .openbis_object import OpenBisObject
 from .utils import VERBOSE

api-openbis-python3-pybis/src/python/pybis/project.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from .attribute import AttrHolder
 from .openbis_object import OpenBisObject
 from .utils import VERBOSE, is_identifier, is_permid

api-openbis-python3-pybis/src/python/pybis/property.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from tabulate import tabulate
 from texttable import Texttable
 from pybis.utils import (

api-openbis-python3-pybis/src/python/pybis/pybis.py

 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+
 """
 pybis.py
 

api-openbis-python3-pybis/src/python/pybis/role_assignment.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from .attribute import AttrHolder
 from .openbis_object import OpenBisObject
 from .utils import VERBOSE

api-openbis-python3-pybis/src/python/pybis/sample.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from .attribute import AttrHolder
 from .definitions import openbis_definitions
 from .openbis_object import OpenBisObject

api-openbis-python3-pybis/src/python/pybis/scripts/cli.py

-
-
+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 def main():
     print("called")

api-openbis-python3-pybis/src/python/pybis/semantic_annotation.py

+#   Copyright ETH 2018 - 2023 Zürich, Scientific IT Services
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+#   
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
 from tabulate import tabulate
 from .utils import VERBOSE