Merge branch 'icat-schema' into develop

CHANGES.rst

@@ -8,6 +8,8 @@ Changelog
 New features
 ------------
 
++ `#73`_, `#106`_: Add support for the ICAT schema 5.0 extensions.
+
 + `#102`_, `#104`_: Make the obj argument to client.new() case
   insensitive.
 
@@ -28,6 +30,11 @@ New features
 Incompatible changes and deprecations
 -------------------------------------
 
++ The order and arrangement of data objects in the dump file created
+  by :ref:`icatdump` has been changed.  In some cases, older versions
+  of :ref:`icatingest` will fail to read dump files written by new
+  versions of :ref:`icatdump`.
+
 + As a consequence of switching to pathlib for filesystem paths some
   return values and variables are now :class:`pathlib.Path` objects
   rather then :class:`str`.  This affects:
@@ -74,6 +81,7 @@ Bug fixes and minor changes
 + Some (more) example scripts now require ICAT 4.4.0 or newer.
 
 .. _#66: https://github.com/icatproject/python-icat/issues/66
+.. _#73: https://github.com/icatproject/python-icat/issues/73
 .. _#74: https://github.com/icatproject/python-icat/issues/74
 .. _#75: https://github.com/icatproject/python-icat/pull/75
 .. _#77: https://github.com/icatproject/python-icat/issues/77
@@ -83,6 +91,7 @@ Bug fixes and minor changes
 .. _#103: https://github.com/icatproject/python-icat/pull/103
 .. _#104: https://github.com/icatproject/python-icat/pull/104
 .. _#105: https://github.com/icatproject/python-icat/pull/105
+.. _#106: https://github.com/icatproject/python-icat/pull/106
 
 
 0.21.0 (2022-01-28)

doc/examples/add-investigation-data.py

@@ -76,6 +76,18 @@ def makeparam(t, pdata):
 invsearch = "Investigation[name='%s']" % investigationdata['name']
 investigation = client.assertedSearch(invsearch)[0]
 
+instrumentname = data['instruments'][investigationdata['instrument']]['name']
+instrsearch = "Instrument[name='%s' %s]" % (instrumentname, facility_const)
+instrument = client.assertedSearch(instrsearch)[0]
+
+technique = None
+if "technique" in client.typemap:
+    t = data['instruments'][investigationdata['instrument']]['technique']
+    if t:
+        tn = data['techniques'][t]['name']
+        techsearch = "Technique [name='%s']" % tn
+        technique = client.assertedSearch(techsearch)[0]
+
 need_dataset_types = set()
 need_datafile_formats = set()
 for ds in investigationdata['datasets']:
@@ -146,5 +158,11 @@ def makeparam(t, pdata):
                                                          pdata))
             dataset.datafiles.append(datafile)
 
-    dataset.create()
+    if 'datasetInstruments' in dataset.InstMRel:
+        di = client.new("datasetInstrument", instrument=instrument)
+        dataset.datasetInstruments.append(di)
+    if 'datasetTechniques' in dataset.InstMRel and technique:
+        dt = client.new("datasetTechnique", technique=technique)
+        dataset.datasetTechniques.append(dt)
 
+    dataset.create()

doc/examples/create-investigation.py

@@ -10,6 +10,8 @@
 import yaml
 import icat
 import icat.config
+from icat.helper import parse_attr_string
+from icat.query import Query
 
 logging.basicConfig(level=logging.INFO)
 
@@ -116,6 +118,28 @@ def getUser(client, attrs):
         if 'instrument' in s.InstRel:
             s.instrument = instrument
         investigation.shifts.append(s)
+if 'investigationFacilityCycles' in investigation.InstMRel:
+    # ICAT 5.0 or newer
+    sd = investigation.startDate or investigation.endDate
+    ed = investigation.endDate or investigation.startDate
+    if sd and ed:
+        query = Query(client, "FacilityCycle", conditions={
+            "startDate": "<= '%s'" % parse_attr_string(ed, "Date"),
+            "endDate": "> '%s'" % parse_attr_string(sd, "Date"),
+        })
+        for fc in client.search(query):
+            ifc = client.new("investigationFacilityCycle", facilityCycle=fc)
+            investigation.investigationFacilityCycles.append(ifc)
+if 'fundingReferences' in investigation.InstMRel:
+    for fr in investigationdata['fundingReferences']:
+        funding_ref = client.new('fundingReference')
+        initobj(funding_ref, data['fundings'][fr])
+        try:
+            funding_ref.create()
+        except icat.ICATObjectExistsError:
+            funding_ref = client.searchMatching(funding_ref)
+        inv_fund = client.new('investigationFunding', funding=funding_ref)
+        investigation.fundingReferences.append(inv_fund)
 investigation.create()
 investigation.addInstrument(instrument)
 investigation.addKeywords(investigationdata['keywords'])