442874e2a5188ef0ca1da03d42c367727f98c372 kent Wed Sep 6 17:21:09 2017 -0700 Fixing a few typos and missing things. diff --git src/hca/v2v3/2to3 src/hca/v2v3/2to3 index 56a2db5..32c14dc 100644 --- src/hca/v2v3/2to3 +++ src/hca/v2v3/2to3 @@ -1,134 +1,135 @@ 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 +DELETE project.contact.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 +DELETE project.geo_parent_series 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 KEEP sample.donor.genotype sample.donor.genotype RENAME sample.donor.id sample.donor.submitted_id KEEP sample.donor.life_stage sample.donor.life_stage -KEEP sample.donor.medication sample.donor.medication.1.text +RENAME sample.donor.medication sample.donor.medication.1.text RENAME sample.donor.ncbi_taxon sample.donor.species.1.ontology KEEP sample.donor.sex sample.donor.sex RENAME 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