f3256f82f0a5eb915068c65290675b315ee20678 kent Fri Sep 1 14:02:27 2017 -0700 Adding table that describes how v2 metadata fields move to v3. diff --git src/hca/hcaV2ToV3/2to3 src/hca/hcaV2ToV3/2to3 new file mode 100644 index 0000000..0b856a1 --- /dev/null +++ src/hca/hcaV2ToV3/2to3 @@ -0,0 +1,134 @@ +HANDADD assay.core.id +RENAME assay.ena_experiment assay.seq.ena_experiment +RENAME assay.ena_run assay.seq.ena_run +MODIFY assay.files assay.seq.lane_REFORMAT_NEEDED +RENAME assay.rna.prep assay.rna.library_construction +KEEP assay.rna.primer assay.rna.primer +KEEP assay.rna.spike_in assay.rna.spike_in +KEEP assay.rna.spike_in_dilution assay.rna.spike_in_dilution +KEEP assay.rna.strand assay.rna.strand +HANDADD assay.rna.end_bias +RENAME assay.seq.machine assay.seq.instrument_model +HANDADD assay.instrument_platform +KEEP assay.seq.molecule assay.seq.molecule +KEEP assay.seq.paired_ends assay.seq.paired_ends +RENAME assay.seq.prep assay.seq.library_construction +KEEP assay.seq.umi_barcode_offset assay.seq.umi_barcode_offset +KEEP assay.seq.umi_barcode_read assay.seq.umi_barcode_read +KEEP assay.seq.umi_barcode_size assay.seq.umi_barcode_size +RENAME assay.single_cell.cell_barcode_offset assay.single_cell.barcode_offset +RENAME assay.single_cell.cell_barcode_read assay.single_cell.barcode_read +RENAME assay.single_cell.cell_barcode_size assay.single_cell.barcode_size +RENAME assay.single_cell.method assay.single_cell.cell_handling +RENAME assay.sra_experiment assay.seq.sra_experiment +RENAME assay.sra_run assay.seq.sra_run +DELETE assay.submitted_file_names +RENAME cell.cell_cycle sample.cell_cycle.text +RENAME cell.characteristics_cd10 sample.characteristics_cd10 +RENAME cell.characteristics_cd135 sample.characteristics_cd135 +RENAME cell.characteristics_cd34 sample.characteristics_cd34 +RENAME cell.characteristics_cd38 sample.characteristics_cd38 +RENAME cell.characteristics_cd45ra sample.characteristics_cd45ra +RENAME cell.characteristics_cd49f sample.characteristics_cd49f +RENAME cell.characteristics_cd7 sample.characteristics_cd7 +RENAME cell.characteristics_cd90 sample.characteristics_cd90 +RENAME cell.characteristics_facs_time sample.characteristics_facs_time +RENAME cell.characteristics_fsc_a sample.characteristics_fsc_a +RENAME cell.characteristics_fsc_h sample.characteristics_fsc_h +RENAME cell.characteristics_fsc_w sample.characteristics_fsc_w +RENAME cell.characteristics_lin sample.characteristics_lin +RENAME cell.characteristics_ssc-w sample.characteristics_ssc-w +RENAME cell.characteristics_ssc_a sample.characteristics_ssc_a +RENAME cell.characteristics_ssc_h sample.characteristics_ssc_h +RENAME cell.id sample.well.core.id +RENAME cell.ontology sample.well.cell_type.ontology +RENAME cell.type sample.well.cell_type.text +RENAME cell.well_quality sample.well.quality +RENAME project.array_express.accession project.array_express_investigation +DELETE project.array_express.experiment_type +RENAME project.array_express.related_experiment project.related_projects +DELETE project.array_express.term_source_file +DELETE project.array_express.term_source_name +RENAME project.contact.address project.submitter.address +RENAME project.contact.city project.submitter.city +RENAME project.contact.country project.submitter.country +DELETE project.contacts.department +RENAME project.contact.email project.submitter.email +RENAME project.contact.institute project.submitter.institution +RENAME project.contact.laboratory project.submitter.laboratory +RENAME project.contact.name project.submitter.name +DELETE project.contact.phone +DELETE project.contact.postal_code +RENAME project.contact.state project.submitter.country_division +DELETE project.contact.street_address +MODIFY project.contributor project.contributors +RENAME project.ddjb_trace_project project.ddjb_trace +KEEP project.experimental_factor_name project.experimental_factor_name +DELETE project.geo_doc_id +RENAME project.array_express.related_experiment project.related_projects +KEEP project.geo_series project.geo_series +RENAME project.id project.core.id +RENAME project.last_update_date project.update_date +DELETE project.mage_tab_version project.mage_tab_version +KEEP project.ncbi_bioproject project.ncbi_bioproject +RENAME project.overall_design project.experimental_design.1.text +RENAME project.pmid project.publications.1.pmid +RENAME project.publication_author_list project.publications.1.author_list +DELETE project.release_status +KEEP project.sra_project project.sra_project +RENAME project.submission_date project.submit_date +RENAME project.summary project.description +KEEP project.supplementary_files project.supplementary_files +KEEP project.title project.title +DELETE project.uuid +KEEP sample.biosd_sample sample.biosd_sample +RENAME sample.body_part.cell_count sample.total_estimated_cells +RENAME sample.body_part.name sample.body_part.text +RENAME sample.body_part.ontology sample.body_part.ontology +RENAME sample.body_part.organ sample.organ.text +RENAME sample.body_part.organ_ontology sample.organ.ontology +DELETE sample.body_part.source +RENAME sample.cell_line sample.cell_line.name.text +KEEP sample.characteristics_c1_chip_id sample.characteristics_c1_chip_id +KEEP sample.characteristics_cef sample.characteristics_cef +KEEP sample.characteristics_clone.info sample.characteristics_clone.info +KEEP sample.characteristics_cross sample.characteristics_cross +KEEP sample.characteristics_donor_age sample.characteristics_donor_age +KEEP sample.characteristics_experiment_sample_name sample.characteristics_experiment_sample_name +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 +MODIFY sample.donor.genotype sample.donor.strain_REFORMAT_NEEDED +RENAME sample.donor.id sample.donor.submitted_id +MODIFY sample.donor.life_stage +KEEP sample.donor.medication sample.donor.medication.1.text +RENAME sample.donor.ncbi_taxon sample.donor.species.ontology +KEEP sample.donor.sex sample.donor.sex +MODIFY sample.donor.species sample.donor.species.1.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 +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