Merge branch 'develop'

icatproject · Oct 31, 2023 · 54ac77c · 54ac77c
2 parents 184a759 + ced13e0
commit 54ac77c
Show file tree

Hide file tree

Showing 52 changed files with 1,727 additions and 1,032 deletions.
diff --git a/.rtd-require b/.rtd-require
@@ -4,5 +4,6 @@ packaging
 setuptools
 setuptools_scm
 suds
+jinja2<3.1
 sphinx>=2,<3
 sphinx-rtd-theme>=0.5,<1
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -2,6 +2,54 @@ Changelog
 =========
 
 
+1.2.0 (2023-10-31)
+~~~~~~~~~~~~~~~~~~
+
+New features
+------------
+
++ `#125`_, `#140`_: Add support to link datasets with samples in
+  :mod:`icat.ingest`.
+
++ `#122`_, `#133`_: Allow referencing related objects by reference key
+  in object references in XML ICAT data file format.
+
+Incompatible changes
+--------------------
+
++ `#138`_, `#139`_: Fix the input that :mod:`icat.ingest` generates on
+  the fly to be valid according to the ICAT data file schema.  This
+  also affects the input that the module accepts: the order of
+  subelements of `data` need to be changed such that
+  `datasetTechnique` comes before `datasetInstrument`.
+
+  Note that :mod:`icat.ingest` has been declared experimental for now.
+
+Bug fixes and minor changes
+---------------------------
+
++ `#131`_, `#135`_: Fix :meth:`icat.ids.IDSClient.getApiVersion` to
+  yield correct results for ids.server 2.0.0 and newer.
+
++ `#132`_, `#136`_: Fix a spurious :exc:`AttributeError` on cleanup
+  after connecting to an invalid url.
+
++ `#130`_, `#137`_: Review test suite.
+
+.. _#122: https://github.com/icatproject/python-icat/issues/122
+.. _#125: https://github.com/icatproject/python-icat/issues/125
+.. _#130: https://github.com/icatproject/python-icat/issues/130
+.. _#131: https://github.com/icatproject/python-icat/issues/131
+.. _#132: https://github.com/icatproject/python-icat/issues/132
+.. _#133: https://github.com/icatproject/python-icat/pull/133
+.. _#135: https://github.com/icatproject/python-icat/pull/135
+.. _#136: https://github.com/icatproject/python-icat/pull/136
+.. _#137: https://github.com/icatproject/python-icat/pull/137
+.. _#138: https://github.com/icatproject/python-icat/issues/138
+.. _#139: https://github.com/icatproject/python-icat/pull/139
+.. _#140: https://github.com/icatproject/python-icat/pull/140
+
+
 1.1.0 (2023-06-30)
 ~~~~~~~~~~~~~~~~~~
 

diff --git a/CITATION.cff b/CITATION.cff
@@ -3,7 +3,6 @@
 
 cff-version: 1.2.0
 title: python-icat – Python interface to ICAT and IDS
-message: Please cite this software using these metadata.
 type: software
 authors:
   - given-names: Rolf
@@ -13,22 +12,21 @@ authors:
       Helmholtz-Zentrum Berlin für Materialien und
       Energie
     orcid: 'https://orcid.org/0000-0002-1266-3819'
-  - name: "The ICAT project"
-    website: https://icatproject.org/
+  - name: The ICAT project
+    website: 'https://icatproject.org/'
 repository-code: 'https://github.com/icatproject/python-icat'
-repository-artifact: 'https://pypi.org/project/python-icat/'
+repository-artifact: 'https://github.com/icatproject/python-icat/releases/latest'
 abstract: >-
-  The ICAT server is a metadata catalogue to support
-  Large Facility experimental data, linking all
-  aspects of the research chain from proposal through
-  to publication. It provides SOAP and RESTful web
-  service interfaces to an underlying database.
+  The ICAT server is a metadata catalogue to support Large
+  Facility experimental data, linking all aspects of the
+  research chain from proposal through to publication. It
+  provides SOAP and RESTful web service interfaces to an
+  underlying database.
 
-  python-icat is a Python package that provides a
-  collection of modules for writing programs that
-  access an ICAT service using the SOAP interface. It
-  is based on Suds and extends it with ICAT specific
-  features.
+  python-icat is a Python package that provides a collection
+  of modules for writing programs that access an ICAT
+  service using the SOAP interface. It is based on Suds and
+  extends it with ICAT specific features.
 keywords:
   - python
   - metadata

diff --git a/doc/examples/icatdump-4.10.xml b/doc/examples/icatdump-4.10.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <icatdata>
 <head>
-  <date>2022-12-21T15:08:20+00:00</date>
+  <date>2023-10-16T14:48:15+00:00</date>
   <service>https://icat.example.com:8181/ICATService/ICAT?wsdl</service>
   <apiversion>4.10.0</apiversion>
   <generator>icatdump (python-icat 1.0.0)</generator>
@@ -431,226 +431,231 @@
     <grouping ref="Grouping_name-ingest"/>
   </rule>
   <rule id="Rule_00000066">
+    <crudFlags>CRU</crudFlags>
+    <what>Sample</what>
+    <grouping ref="Grouping_name-ingest"/>
+  </rule>
+  <rule id="Rule_00000067">
     <crudFlags>R</crudFlags>
     <what>Shift</what>
     <grouping ref="Grouping_name-ingest"/>
   </rule>
-  <rule id="Rule_00000067">
+  <rule id="Rule_00000068">
     <crudFlags>R</crudFlags>
     <what>DataCollection</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000068">
+  <rule id="Rule_00000069">
     <crudFlags>R</crudFlags>
     <what>DataCollectionDatafile</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000069">
+  <rule id="Rule_00000070">
     <crudFlags>R</crudFlags>
     <what>DataCollectionDataset</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000070">
+  <rule id="Rule_00000071">
     <crudFlags>R</crudFlags>
     <what>DataCollectionParameter</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000071">
+  <rule id="Rule_00000072">
     <crudFlags>R</crudFlags>
     <what>Datafile</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000072">
+  <rule id="Rule_00000073">
     <crudFlags>R</crudFlags>
     <what>DatafileParameter</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000073">
+  <rule id="Rule_00000074">
     <crudFlags>R</crudFlags>
     <what>Dataset</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000074">
+  <rule id="Rule_00000075">
     <crudFlags>R</crudFlags>
     <what>DatasetParameter</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000075">
+  <rule id="Rule_00000076">
     <crudFlags>R</crudFlags>
     <what>Grouping</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000076">
+  <rule id="Rule_00000077">
     <crudFlags>R</crudFlags>
     <what>InstrumentScientist</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000077">
+  <rule id="Rule_00000078">
     <crudFlags>R</crudFlags>
     <what>Investigation</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000078">
+  <rule id="Rule_00000079">
     <crudFlags>R</crudFlags>
     <what>InvestigationGroup</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000079">
+  <rule id="Rule_00000080">
     <crudFlags>R</crudFlags>
     <what>InvestigationInstrument</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000080">
+  <rule id="Rule_00000081">
     <crudFlags>R</crudFlags>
     <what>InvestigationParameter</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000081">
+  <rule id="Rule_00000082">
     <crudFlags>R</crudFlags>
     <what>InvestigationUser</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000082">
+  <rule id="Rule_00000083">
     <crudFlags>R</crudFlags>
     <what>Job</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000083">
+  <rule id="Rule_00000084">
     <crudFlags>R</crudFlags>
     <what>Keyword</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000084">
+  <rule id="Rule_00000085">
     <crudFlags>R</crudFlags>
     <what>PublicStep</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000085">
+  <rule id="Rule_00000086">
     <crudFlags>R</crudFlags>
     <what>Publication</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000086">
+  <rule id="Rule_00000087">
     <crudFlags>R</crudFlags>
     <what>RelatedDatafile</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000087">
+  <rule id="Rule_00000088">
     <crudFlags>R</crudFlags>
     <what>Rule</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000088">
+  <rule id="Rule_00000089">
     <crudFlags>R</crudFlags>
     <what>Sample</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000089">
+  <rule id="Rule_00000090">
     <crudFlags>R</crudFlags>
     <what>SampleParameter</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000090">
+  <rule id="Rule_00000091">
     <crudFlags>R</crudFlags>
     <what>Shift</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000091">
+  <rule id="Rule_00000092">
     <crudFlags>R</crudFlags>
     <what>Study</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000092">
+  <rule id="Rule_00000093">
     <crudFlags>R</crudFlags>
     <what>StudyInvestigation</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000093">
+  <rule id="Rule_00000094">
     <crudFlags>R</crudFlags>
     <what>UserGroup</what>
     <grouping ref="Grouping_name-rall"/>
   </rule>
-  <rule id="Rule_00000094">
+  <rule id="Rule_00000095">
     <crudFlags>RU</crudFlags>
     <what>Sample</what>
     <grouping ref="Grouping_name-scientific=5Fstaff"/>
   </rule>
-  <rule id="Rule_00000095">
+  <rule id="Rule_00000096">
     <crudFlags>UD</crudFlags>
     <what>SampleType</what>
     <grouping ref="Grouping_name-scientific=5Fstaff"/>
   </rule>
-  <rule id="Rule_00000096">
+  <rule id="Rule_00000097">
     <crudFlags>CRUD</crudFlags>
     <what>FacilityCycle</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000097">
+  <rule id="Rule_00000098">
     <crudFlags>CRUD</crudFlags>
     <what>Grouping</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000098">
+  <rule id="Rule_00000099">
     <crudFlags>CRUD</crudFlags>
     <what>InstrumentScientist</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000099">
+  <rule id="Rule_00000100">
     <crudFlags>CRUD</crudFlags>
     <what>Investigation</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000100">
+  <rule id="Rule_00000101">
     <crudFlags>CRUD</crudFlags>
     <what>InvestigationGroup</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000101">
+  <rule id="Rule_00000102">
     <crudFlags>CRUD</crudFlags>
     <what>InvestigationInstrument</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000102">
+  <rule id="Rule_00000103">
     <crudFlags>CRUD</crudFlags>
     <what>InvestigationParameter</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000103">
+  <rule id="Rule_00000104">
     <crudFlags>CRUD</crudFlags>
     <what>InvestigationUser</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000104">
+  <rule id="Rule_00000105">
     <crudFlags>CRUD</crudFlags>
     <what>Keyword</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000105">
+  <rule id="Rule_00000106">
     <crudFlags>CRUD</crudFlags>
     <what>Publication</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000106">
+  <rule id="Rule_00000107">
     <crudFlags>CRUD</crudFlags>
     <what>Shift</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000107">
+  <rule id="Rule_00000108">
     <crudFlags>CRUD</crudFlags>
     <what>Study</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000108">
+  <rule id="Rule_00000109">
     <crudFlags>CRUD</crudFlags>
     <what>StudyInvestigation</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000109">
+  <rule id="Rule_00000110">
     <crudFlags>CRUD</crudFlags>
     <what>User</what>
     <grouping ref="Grouping_name-useroffice"/>
   </rule>
-  <rule id="Rule_00000110">
+  <rule id="Rule_00000111">
     <crudFlags>CRUD</crudFlags>
     <what>UserGroup</what>
     <grouping ref="Grouping_name-useroffice"/>