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ChangeLog
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2012-03-12 Luca Lianas <luca@tensa-zangetsu>
* bl/vl/app/kb_query/map_vid.py: added rules for mapping
DataCollectionItem objects.
* bl/vl/app/importer/data_collection.py: updated importer, now
existing DataCollection are allowed, if a label of a know
DataCollection is passed as input the DataCollection will be used,
if an unknown one is passed the importer creates a new
DataCollection.
* bl/vl/kb/drivers/omero/objects_collections.py
(DataCollectionItem): DataCollectionItem class updated with vid
and dataCollectionItemUK fields.
* models/collection.ome.xml: added fields vid and
dataCollectionItemUK to object ome.model.vl.DataCollectionItem.
2012-02-13 Luca Lianas <luca@tensa-zangetsu>
* bl/vl/kb/drivers/omero/proxy_core.py
(ProxyCore.update_table_rows): added new method that makes
possible to update multiple table rows at the same time.
* bl/vl/kb/drivers/omero/proxy.py (Proxy): added new methods that
make possible to mark multiple EHR record as valid\invalid.
2012-02-06 <[email protected]>
* bl/vl/kb/drivers/omero/snp_markers_set.py (SNPMarkersSet):
defined appropriate constants for max markers set len and genome
len.
2012-02-03 <zag@manzanillo>
* bl/vl/kb/drivers/omero/snp_markers_set.py
(SNPMarkersSet.has_add_marker_info): added
(SNPMarkersSet.get_add_marker_info_fields): added
(SNPMarkersSet.has_add_marker_info): added
(SNPMarkersSet.define_range_selector): added
* bl/vl/genotype/io.py (read_ssc): updated to the new
SNPMarkersSet interface.
2012-01-24 <[email protected]>
* bl/vl/kb/drivers/omero/utils.py (ome_hash): changed to hash
objects by their oldest ancestor's class.
2012-01-23 <zag@manzanillo>
* bl/vl/kb/drivers/omero/snp_markers_set.py
(SNPMarkersSet.load_alignments): Now we use the new, hopefully
faster, mset-based convention for alignment storing/retrieval.
2012-01-23 <[email protected]>
* bl/vl/individual/pedigree.py (up_propagate_front): fixed problem
where it might add individuals not included in the selected ones
-- simleo & lianas.
2012-01-19 <[email protected]>
* bl/vl/kb/drivers/omero/wrapper.py (OmeroWrapper): added
__update_constraints__. This is called by kb object setters and
provides a hook for updating properties (in particular, unique
keys) depending on other attributes -- simleo & lianas
* bl/vl/kb/drivers/omero/demographic.py (Demographic): fixed UK
components -- simleo & lianas
2012-01-11 <[email protected]>
* bl/vl/individual/pedigree.py (down_propagate_front): fixed a bug
where the children dict was being looked up by individual id
instead of individual.
2011-12-21 Luca Lianas <luca@tensa-zangetsu>
* bl/vl/kb/drivers/omero/wrapper.py: the __getattr__ of the kb
objects will now resolve encapsulated objects reading them
directly from the cache or from Omero.
2011-11-22 Luca Lianas <luca@tensa-zangetsu>
* bl/vl/kb/drivers/omero/proxy.py: added a method for retrieving
all vessels related to an individual.
2011-11-22 <[email protected]>
* bl/vl/kb/drivers/omero/proxy.py: added a method for getting a
container object by label.
2011-11-04 <zag@manzanillo>
* bl/vl/genotype/algo.py (hwe_probabilites): bugfx: Added handling
of the n_a ==0 corner case.
2011-11-02 <zag@manzanillo>
* bl/vl/kb/drivers/omero/admin.py (Admin): Added basic admin support.
* bl/vl/kb/drivers/omero/proxy.py (Proxy.create_markers): Added
ref_rs_genome, dbsnp_build
2011-11-01 <zag@manzanillo>
* bl/vl/kb/drivers/omero/proxy.py (Proxy.__init__): Added group
support. It can be set at initialization and run time with a new
change_group method.
2011-10-31 <zag@manzanillo>
* galaxy/tools/VL/importer/data_sample.xml: It could happen that
physicalLocation is None.
* bl/vl/kb/drivers/omero/genotyping.py
(GenotypingAdapter.get_snp_markers_by_source): added a new
markers list query method.
2011-10-28 <zag@manzanillo>
* bl/vl/app/kb_query/map_vid.py
(MapVIDApp.resolve_mapping_individual): Changed
behavior: it will skip records that cannot map.
2011-10-28 <[email protected]>
* bl/vl/app/importer/marker_definition.py (Recorder.record):
manufacturer's label is now treated as the unique marker row
attribute.
* bl/vl/app/kb_query/map_vid.py
(MapVIDApp.resolve_mapping_marker): changed back to expect chip
manufacturer's labels instead of rs_labels for mapping to VIDs.
2011-10-25 <[email protected]>
* bl/vl/app/importer/marker_definition.py (Recorder.record): added
check for known markers; changed to save manufacturer's SNP label
when there is no rs label and original mask when it can't be
converted to top.
2011-10-15 <zag@manzanillo>
* bl/vl/kb/drivers/omero/proxy_core.py (ProxyCore.reload_object):
Added support for deep reload. Untested.
* bl/vl/app/importer/data_sample.py
(Recorder.do_consistency_checks): Added a missing safety check.
2011-10-03 <zag@manzanillo>
* models/actions.ome.xml: Added GenotypingProgram as a clean way
to automatize the attaching of a SnpMarkersSet to GenotypeDataSample.
2011-10-02 <zag@manzanillo>
* bl/vl/kb/drivers/omero/proxy.py (Proxy.update_snp_positions):
Now we use slice here too.
2011-10-01 <zag@manzanillo>
* bl/vl/kb/drivers/omero/proxy_core.py (ProxyCore.get_table_rows):
Now we use slice and we allow for column selection.
2011-09-28 <zag@manzanillo>
* examples/import_taqman_results.py: new name for define_taq_markers.
2011-09-27 <zag@manzanillo>
* bl/vl/utils/snp.py (approx_equal_masks): Added.
* bl/vl/kb/drivers/omero/proxy_core.py
(ProxyCore.find_all_by_query): Now it is possible to pass None as
params.
* bl/vl/kb/drivers/omero/modeling.py
(ModelingAdapter.get_objects): removed redundant 'select' from
query.
2011-09-26 <zag@manzanillo>
* bl/vl/genotype/io.py (PedWriter): Added a plink compliant ped
writer.
* bl/vl/kb/drivers/omero/wrapper.py (MetaWrapper.make_getter):
changed so that it will return a None when the ome_obj field is
None. It could be used to trigger a reload, if the field is not
optional. For the time being, this is left as an exercise for the
caller.
2011-09-24 <zag@manzanillo>
* bl/vl/kb/drivers/omero/genotyping.py
(GenotypingAdapter.SNP_ALIGNMENT_COLS): added Pseudo-autosomal
region of x (XY), assigned code 25, moved MT to 26.
* bl/vl/individual/pedigree.py: Now the genotyping status of
individuals is passed as an aux dict and not as an attribute to
the individual object.
2011-09-23 <zag@manzanillo>
* bl/vl/kb/drivers/omero/data_samples.py (SNPMarkersSet): Added
support to bring markers set markers in memory.
* bl/vl/kb/drivers/omero/proxy.py
(Proxy.add_snp_marker_definitions): Changed the op_vid parameter
to be either an Action or a string. Added some sort of documentation.
(Proxy.create_snp_markers_set): Added new syntactic sugar.
(Proxy.create_markers): Added new syntactic sugar
2011-09-20 <zag@manzanillo>
* bl/vl/app/importer/data_sample.py (make_parser_data_sample):
Added support to be able to directly import DataSample that
directly link to individuals.
2011-09-18 <zag@manzanillo>
* .ropeproject/config.py: Added ropemacs support.
2011-09-21 <[email protected]>
* bl/vl/app/snp_reannotator/convert_sam.py
(SnpHitProcessor.process): fixed starting position for segment
extractor output.
2011-09-20 <[email protected]>
* bl/vl/app/snp_reannotator/convert_sam.py: added an output format
for Galaxy's genome segment extractor.
2011-09-19 <[email protected]>
* bl/vl/app/snp_reannotator/convert_sam.py (SnpHitProcessor):
changed to use numeric values for chromosomes and 'None' instead
of '*' for a null value.
2011-09-14 <[email protected]>
* bl/vl/app/snp_reannotator/markers_to_fastq.py: renamed from
masks_to_fastq.py; quality string char set to '~', the maximum for
all fastq subformats.
2011-09-12 <[email protected]>
* bl/vl/app/snp_reannotator/convert_dbsnp.py: changed to output a
VL marker definition file. Added an option for trimming the mask
down to a maximum given size.
2011-09-07 Luca Lianas <luca@tensa-zangetsu>
* bl/vl/kb/drivers/omero/data_samples.py (DataSample): lastUpdate property removed
* models/data_sample.ome.xml: lastUpdate property removed
* models/vessel.ome.xml: lastUpdate property added to Vessel model (and to all children classes by inheritance).
* bl/vl/kb/drivers/omero/vessels.py (Vessel): lastUpdate property added to Vessel class.
* bl/vl/kb/drivers/omero/data_samples.py (DataSample): lastUpdate property added to DataSample class.
* models/data_sample.ome.xml: added lastUpdate property to DataSample model (and to all children classes by inheritance).
2011-09-05 Luca Lianas <luca@tensa-zangetsu>
* bl/vl/kb/drivers/omero/objects_collections.py (VLCollection): lastUpdate field added
* models/collection.ome.xml: added lastUpdate property to VLCollection model (and to all children classes by inheritance). This field has to be used to track all the changes.
2011-08-15 <zag@manzanillo>
* bl/vl/kb/drivers/omero/ehr.py (EHR.__init__): Now we can handle
multiple records for the same archetype for the same individual.
2011-08-12 <zag@manzanillo>
* bl/vl/app/importer/data_sample.py (Recorder.process_chunk):
added an hack to deal with data reloads. It is really a quick hack.
* bl/vl/kb/drivers/omero/data_samples.py
(IlluminaBeadChipAssayType): Missing HUMAN1M_DUO constant.
2011-08-11 <zag@manzanillo>
* bl/vl/kb/drivers/omero/objects_collections.py (ContainerStatus):
updated to new enum.
* models/collection.ome.xml: added 'USED' to ContainerStatus.
* bl/vl/kb/drivers/omero/data_samples.py
(IlluminaBeadChipAssayType): updated to new enum.
* models/data_sample.ome.xml: changed IlluminaBeadChipAssayType to
more reasonable string values.
* tests/bl/vl/kb/test_enums.py: added.
* bl/vl/app/importer/titer_plate.py (Recorder.process_chunk): oops
in the handling of barcodes.
* tools/build_dependency.py (dump_dna_samples): bug fix. it was
using a sample_label == label, which is not very useful.
2011-08-10 <zag@manzanillo>
* bl/vl/app/importer/device.py (Recorder.do_consistency_checks):
bug fix. It was rejecting devices with no barcode (it is legal,
after all)
* tools/build_dependency.py: another quick and dirty importer for
Ilenia style csv. This one should be less lenient on ambiguos
records. It makes extract_individuals.py and extract_samples.py
obsolete.
2011-08-09 <zag@manzanillo>
* bl/vl/kb/drivers/omero/genotyping.py
(GenotypingAdapter.SNP_SET_COLS): Removed the field 'label'. This
field, the label of the marker in the specific technological
context (e.g., affy SNP_A_xxx codes, it redundant, since the
marker is identified by the marker_vid, and it is dangerous, since
it can generate confusion.
2011-08-08 <zag@manzanillo>
* tests/bl/vl/kb/drivers/omero/test_table.py (TestProxyCore):
added a test for the new get_table_rows selector type cases.
* bl/vl/kb/drivers/omero/proxy_core.py (ProxyCore.get_table_rows):
selector can now be either a selection or a list of selections. In
the latter case, it is interpreted as an 'or' condition between
the list elements.
* bl/vl/kb/drivers/omero/genotyping.py (Marker): Added. It is only
a placeholder for the time being.
* bl/vl/kb/drivers/omero/proxy.py (Proxy.get_snp_markers): we may
want markers as standard objects, afterall...
2011-08-05 <zag@manzanillo>
* galaxy/lib/galaxy/webapps/vlweb/vl_app.py (UniverseApplication):
Now we can gather omero specific variables from the application
configuration file
(UniverseApplication.__init__): Added conf variable 'vl_loglevel'
2011-08-05 <[email protected]>
* bl/vl/utils/snp.py: generalized to support SNPs with more than
two possible alleles.
2011-08-04 <[email protected]>
* bl/vl/app/import modules now have a galaxy front-end.
* bl/vl/utils/snp.py (_identify_strand): simpler implementation
that works with sequences containing non-ACGT letters (basically,
anything that's not explicitly defined as unambiguous is
ambiguous). After skipping indels, this version correctly
identifies all illumina 'TopGenomicSeq' masks as TOP (see
tests/bl/vl/utils/check_strand_vs_ann.py).
2011-08-03 <zag@manzanillo>
* bl/vl/app/importer/diagnosis.py: Changed to new style.
* bl/vl/app/importer/data_collection.py: Changed to new style.
* bl/vl/app/importer/data_object.py: Changed to new style.
* bl/vl/app/importer/data_sample.py: Changed to new style.
2011-08-03 <[email protected]>
* bl/vl/app/check_rs.py: changed to convert all masks to TOP
before doing anything with them.
* bl/vl/utils/snp.py: rewrote to work without side effects on a
split mask (this is emphasized by the fact that a split mask is
now a tuple). Added join_mask.
2011-08-03 <zag@manzanillo>
* bl/vl/app/importer/data_sample.py: Major rewrite. Now it has, at
least in spirit, a code structure similar to the one of
biosample.py and the rest.
* models/actions.ome.xml: Specialized Device some more, now we
have Chip (derived from Device) and Scanner (derived from
HardwareDevice). We have SoftwareProgram too (derived from Device)
* bl/vl/app/importer/biosample.py: now it can be used to import
PlateWells. Removed plate_well.py.
2011-08-02 <[email protected]>
* bl/vl/app/check_rs.py: does not read the full annotation table
into memory anymore.
(SnpAnnReader): changed to use bl.vl.utils.snp.split_mask to split
masks and to return a (label, rs_label, split_mask) tuple.
* bl/vl/utils/snp.py: code cleanup; convert_to_top now supports
split masks.
2011-08-01 <zag@manzanillo>
* galaxy/tools/VL/tools/map_vid.xml: Added.
* galaxy/tools/VL/importer/biosample.xml: Added
* galaxy: Renamed galaxy_ui to galaxy. Restructured to be easily
installed in a standard galaxy deployment.
* galaxi_ui: Added. This should provide galaxy based interfaces to
galaxy. It requires a (minimally) hacked version of galaxy.
* bl/vl/app/importer/main.py: Added. This should simplify
supporting galaxy_ui
2011-07-31 <zag@manzanillo>
* tools/create_tables: Changed name from create_snp_tables, added
support for ehr tables.
* bl/vl/kb/drivers/omero/objects_collections.py (ContainerStatus):
Added.
(Container): Added field 'status'.
* bl/vl/kb/drivers/omero/demographic.py (InformedConsent): added.
(Demographic): added.
2011-07-29 <[email protected]>
* tools/check_rs.py: moved DbSnpReader to bl/core. Changed to
compute a "consensus" sequence for multiple matches.
2011-07-29 <zag@manzanillo>
* bl/vl/app/importer/study.py: Added a study module. It is
probably an overkill, but it was needed.
* tools/importer: Now supports importing study and
biosample. Explicit blood and dna samples have been removed.
* bl/vl/app/importer/biosample.py (do_register): Added a biosample
module. It makes blood_sample and dna_sample obsolete.
2011-07-28 <[email protected]>
* tools/check_rs.py (SnpAnnReader): changed to compile mask
pattern only once.
2011-07-28 <zag@manzanillo>
* bl/vl/kb/drivers/omero/genotyping.py
(GenotypingAdapter.SNP_SET_COLS): Added a 'label' column to keep
track of the label of the marker in the specific technological
context (i.e., label given by the producer)
2011-07-27 <[email protected]>
* tools/check_rs.py: changed to use a shelf to store the dbSNP
index. Output sequences are now stored together with the rs
labels, allowing for a single read of the dbSNP files.
2011-07-26 <[email protected]>
* tools/check_rs.py (DbSnpReader): header parser made more robust.
2011-07-25 <[email protected]>
* tools/check_rs.py: changed to output dbSNP sequences.
2011-07-22 <zag@manzanillo>
* docs/index.rst: Started documentation restructuring. Mostly
moving things around.
2011-07-18 <zag@manzanillo>
* models/collection.ome.xml: Added ContainerStatus as an enum.
added it as a required parameter in Container. The idea is to be
able to track titerplate preparation phases.
* bl/vl/app/importer/marker_alignment.py: Back to use marker_vid
to identify markers. It is the only solution with a reasonable hope
to scale.
2011-07-16 <[email protected]>
* tools/check_rs.py: added an option for specifying a custom cut
size; fixed auto-calculation of the cut size (we want min flank
size from the annotation, not max); added checks for over-short
flanks.
2011-07-06 <zag@manzanillo>
* bl/vl/kb/drivers/omero/proxy.py (Proxy.add_ehr_record): Added
interface to eav.py
* tests/bl/vl/kb/test_eav.py: Added.
* bl/vl/kb/drivers/omero/eav.py: Added.
2011-07-06 <[email protected]>
* bl/vl/app/kb_query/markers.py (Markers): fixed dump_mapping.
* bl/vl/app/importer/marker_definition.py
(Recorder.save_snp_marker_definitions.ns): fixed a bug where
context was also saved as 'release'.
2011-06-04 <zag@manzanillo>
* bl/vl/kb/drivers/omero/utils.py: created.
2011-05-26 <zag@manzanillo>
* models/sample/dna_sample.ome.xml: Removed all the nanodrop
details, they should be provided as a DataResult produced by a
NanoDrop device.
2011-05-24 <zag@manzanillo>
* tests/bl/vl/individual/kb/test_ikb.py
(TestIKB.create_individual_sample_chain): disabled since it was
using get_root.
* tests/bl/vl/sample/kb/test_skb_extended.py
(TestSKBExtended.check_object): disabled. It will not work, since
we have dropped proxy_indexed.
* bl/vl/sample/kb/drivers/omero/sample.py (DataSample): patched to
map label to name. This is a bug in the DataSample model.
* bl/vl/sample/kb/drivers/omero/wrapper.py (OmeroWrapper.unload):
Added support for omero object unloading. It is an experiment.
2011-05-23 <zag@manzanillo>
* bl/vl/sample/kb/drivers/omero/samples_container.py
(DataCollection.__setup__): label disabled.
* bl/vl/app/importer/data_collection.py (Recorder.__init__):
disabled data_collection.label as a temporary measure before we
sync the server on the new models.
2011-05-21 <zag@manzanillo>
* bl/vl/app/importer/data_sample.py
(import_data_sample_implementation): added a default-contrast-qc
flag.
2011-05-18 <zag@manzanillo>
* bl/vl/app/importer/data_collection.py (Recorder): moved
default_study handling to core.
* bl/vl/sample/kb/drivers/omero/dependency_tree.py
(DependencyTree): Added as a more general (albeit slower)
replacement to proxy_index indexing functions.
2011-05-17 <zag@manzanillo>
* bl/vl/sample/kb/drivers/omero/proxy_core.py
(ProxyCore.find_all_by_query): Now we have a factory controlled
object wrapping. It is a hack, it should converge to the general
proxy class.
* bl/vl/individual/pedigree.py (import_pedigree): people can have
children with more than one partner...
(import_pedigree): oops, forgot to properly mark
founder-non-founder families.
2011-05-13 <zag@manzanillo>
* tests/bl/vl/sample/kb/skb_object_creator.py (SKBObjectCreator.create_data_collection):
Changed to the new DataCollection model.
* examples/load_data.py, examples/call_gt.py (App.preload):
Changed to the new DataCollection model.
* bl/vl/sample/kb/drivers/omero/samples_container.py (DataCollection):
Changed to the new DataCollection model.
* models/sample/data_collection.ome.xml: added a label field.
* bl/vl/app/exporter/markers_set.py (do_register): can dump
markers set definitions.
2011-05-12 <zag@manzanillo>
* bl/vl/app/exporter/marker_definition.py (do_register): can dump
marker definitions.
* tools/exporter (main): Added an exporter utility.
2011-05-11 <zag@manzanillo>
* bl/vl/app/importer/markers_set.py: Added new tool.
* bl/vl/app/importer/marker_definition.py (Recorder): Added new tool.
* tools/create_snp_tables: Added new tool.
2011-05-08 <zag@manzanillo>
* bl/vl/sample/kb/drivers/omero/data_object.py
(DataObject.__init__): added support for proxy propagation. This
should be fixed in a systematic way.
2011-05-05 <zag@manzanillo>
* bl/vl/app/importer/plate_well.py (Recorder): Added prefetching support.
2011-05-03 <zag@manzanillo>
* bl/vl/app/importer/individual.py (Recorder.record): clean up.
* bl/vl/individual/kb/drivers/omero/proxy.py (Proxy.get_enrolled): Added.
2011-04-30 <zag@manzanillo>
* bl/vl/sample/kb/drivers/omero/samples_container.py (TiterPlate):
moved barcode, label and virtualContainer handling to superclass
* tests/bl/vl/individual/kb/test_ikb.py (TestIKB.test_enrollment): in phase ...
* bl/vl/individual/kb/drivers/omero/individual.py (Individual): in phase ...
* bl/vl/sample/kb/drivers/omero/study.py (Study): in phase with ...
* bl/vl/individual/kb/drivers/omero/enrollment.py
(Enrollment): in phase with new convoluted...
* bl/vl/sample/kb/drivers/omero/proxy_core.py (ProxyCore.save):
Added support for the convoluted dynamic object fetching mechanism.
* bl/vl/sample/kb/drivers/omero/wrapper.py (OmeroWrapper): Added a
convoluted mechanism to allow dynamic object fetching.
2011-04-28 <zag@manzanillo>
* bl/vl/app/importer/plate_well.py (Recorder): same as below...
* bl/vl/app/importer/titer_plate.py (Recorder): same as below...
* bl/vl/app/importer/blood_sample.py (import_blood_sample_implementation): same as below..
* bl/vl/app/importer/bio_sample.py (BioSampleRecorder): added
keep_tokens support. Humm, why am i not using **kw???
* bl/vl/app/importer/core.py (Core.__init__): added keep_tokens support.
* bl/vl/app/importer/individual.py (Recorder): added keep_tokens support.
* tools/importer (App.make_parser): added keep-token flag
* tests/bl/vl/sample/kb/test_skb.py (OME_KEEP): in phase with new
keep_section_open mechanism.
* bl/vl/sample/kb/drivers/omero/proxy_core.py (ProxyCore): Added a
simple keep_session_open mechanism to speed-up operations.
* tools/importer (App): added titer_plate module.
* bl/vl/app/importer/plate_well.py: moved all the titer_plate
stuff to titer_plate.py.
* bl/vl/app/importer/titer_plate.py: Added.
2011-04-27 <zag@manzanillo>
* tests/bl/vl/sample/kb/skb_object_creator.py: labLabel -> label
* models/sample/samples_container.ome.xml: labLabel -> label
* bl/vl/sample/kb/drivers/omero/proxy.py (Proxy.get_bio_sample): labLabel -> label
* models/sample/bio_sample.ome.xml: changed labLabel to label
* tools/extract_individuals.py (load_individuals): now we keep the
first record found when there is a 'parental' conflict between
records.
2011-04-24 <zag@pflip>
* bl/vl/individual/pedigree.py (import_pedigree): Changed
algorithm. Now it should be able to handle a large number of individuals.
2011-04-22 <zag@pflip>
* examples/load_data.py (network_builder.call_genotypes): in phase
with SNPMarkersSet and GenotypeDataSample
* tests/bl/vl/sample/kb/skb_object_creator.py (SKBObjectCreator.create_snp_markers_set): added.
(SKBObjectCreator.create_genotype_data_sample): added. Added also relates tests in test_skb.py
* bl/vl/sample/kb/drivers/omero/genotyping.py (SNPMarkersSet): added.
(GenotypeDataSample): added.
* bl/vl/app/importer/core.py (Core.get_device): in phase with new device API
* examples/load_data.py (network_builder.get_device): in phase
with new device API
* tests/bl/vl/sample/kb/test_skb.py (TestSKB.test_device): updated
to the new API
* bl/vl/sample/kb/drivers/omero/proxy.py (Proxy.get_device): now
we search by label.
* tests/bl/vl/sample/kb/skb_object_creator.py
(SKBObjectCreator.create_device): in phase with changes to new
python interface.
* bl/vl/sample/kb/drivers/omero/device.py (Device): in phase with
changes to the ome model.
* models/sample/device.ome.xml: Added a required, unique,
attribute name. We need it to distinguish between, e.g., physical
instances of a given class. Changed 'vendor' to a politically
neutral 'maker'