31139fbd0ac42c06d02e2d534831d719de4b5a0d kent Fri Sep 1 15:51:19 2017 -0700 Renaming stuff for going between metadata versions. diff --git src/hca/hcaV2ToV3/2to3 src/hca/hcaV2ToV3/2to3 deleted file mode 100644 index 0b856a1..0000000 --- src/hca/hcaV2ToV3/2to3 +++ /dev/null @@ -1,134 +0,0 @@ -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