56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f
kent
  Mon Oct 30 11:12:25 2017 -0700
Final round of HCA v3 metadata changes.  This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.

diff --git src/hca/v2v3/2to3 src/hca/v2v3/2to3
index 32c14dc..f3e2e6f 100644
--- src/hca/v2v3/2to3
+++ src/hca/v2v3/2to3
@@ -99,37 +99,37 @@
 KEEP	sample.characteristics_facs_gating	sample.characteristics_facs_gating
 KEEP	sample.characteristics_inferred_cell_type	sample.characteristics_inferred_cell_type
 KEEP	sample.characteristics_plate	sample.characteristics_plate
 KEEP	sample.characteristics_time	sample.characteristics_time
 DELETE	sample.data_processing
 KEEP	sample.donor.age	sample.donor.age
 KEEP	sample.donor.age_unit	sample.donor.age_unit.text
 KEEP	sample.donor.body_mass_index	sample.donor.body_mass_index
 RENAME	sample.donor.development_stage	sample.donor.development_stage.text
 RENAME	sample.donor.disease	sample.donor.disease.1.text
 RENAME	sample.donor.ethnicity	sample.donor.ancestry.1.text
 KEEP	sample.donor.genotype	sample.donor.genotype
 RENAME	sample.donor.id	sample.donor.submitted_id
 KEEP	sample.donor.life_stage sample.donor.life_stage
 RENAME	sample.donor.medication	sample.donor.medication.1.text
-RENAME	sample.donor.ncbi_taxon	sample.donor.species.1.ontology
+RENAME	sample.donor.ncbi_taxon	sample.donor.species.ontology
 KEEP	sample.donor.sex	sample.donor.sex
-RENAME	sample.donor.species	sample.donor.species.1.text
+RENAME	sample.donor.species	sample.donor.species.text
 RENAME	sample.donor.strain	sample.donor.strain.1.text
 RENAME	sample.donor.uuid	sample.donor.core.id
 KEEP	sample.ena_sample	sample.ena_sample
 KEEP	sample.geo_sample	sample.geo_sample
 RENAME	sample.id	sample.submitter_id
 RENAME	sample.last_update_date	sample.update_date
 RENAME	sample.long_label	sample.title
 KEEP	sample.ncbi_biosample	sample.ncbi_biosample
 RENAME	sample.passage_number	sample.cell_line.passage_number
-RENAME	sample.protocol_types	sample.supplementary_protocols.1.type
-RENAME	sample.protocols	sample.supplementary_protocols.1.description
+MODIFY	sample.protocol_types	project.protocols.1.type
+MODIFY	sample.protocols	project.protocols.1.description
 RENAME	sample.short_label	sample.name
 RENAME	sample.storage	sample.preservation.storage_protocol.description
 RENAME	sample.submission_date	sample.submit_date
 KEEP	sample.supplementary_files	sample.supplementary_files
 RENAME	sample.treatment.culture_type	sample.culture_type
 RENAME	sample.treatment.enrichment	sample.enrichment.markers
 RENAME	sample.treatment.enrichment_method	sample.enrichment.protocol.text
 RENAME	sample.uuid	sample.core.id