44cc15f9add4a8190119eab297e93b07a3efce80 kent Mon Dec 4 13:38:05 2017 -0800 Done first pass of conversion table. diff --git src/hca/v3v4/v3v4 src/hca/v3v4/v3v4 index c100164..65ae056 100644 --- src/hca/v3v4/v3v4 +++ src/hca/v3v4/v3v4 @@ -1,276 +1,274 @@ KEEP assay.core.schema_url assay.core.schema_url KEEP assay.core.schema_version assay.core.schema_version KEEP assay.core.type assay.core.type RENAME assay.id assay.assay_id DELETE assay.rna.core.schema_url DELETE assay.rna.core.schema_version DELETE assay.rna.core.type KEEP assay.rna.end_bias assay.rna.end_bias KEEP assay.rna.library_construction assay.rna.library_construction KEEP assay.rna.library_protocol assay.rna.library_protocol 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 KEEP assay.sample_id assay.sample_id DELETE assay.seq.core.schema_url DELETE assay.seq.core.schema_version DELETE assay.seq.core.type RENAME assay.seq.ena_experiment assay.seq.insdc_experiment RENAME assay.seq.ena_run.[] assay.seq.insdc_run.[] KEEP assay.seq.instrument_model assay.seq.instrument_model KEEP assay.seq.instrument_platform assay.seq.instrument_platform KEEP assay.seq.library_construction assay.seq.library_construction KEEP assay.seq.library_protocol assay.seq.library_protocol KEEP assay.seq.local_machine_name assay.seq.local_machine_name KEEP assay.seq.molecule assay.seq.molecule KEEP assay.seq.paired_ends assay.seq.paired_ends RENAME assay.seq.sra_experiment assay.seq.insdc_experiment RENAME assay.seq.sra_run.[] assay.seq.insdc_run.[] DELETE assay.seq.umi_barcode.core.schema_url DELETE assay.seq.umi_barcode.core.schema_version DELETE assay.seq.umi_barcode.core.type 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 KEEP assay.seq.umi_barcode.white_list_file assay.seq.umi_barcode.white_list_file DELETE assay.single_cell.barcode.core.schema_url DELETE assay.single_cell.barcode.core.schema_version DELETE assay.single_cell.barcode.core.type RENAME assay.single_cell.barcode.offset assay.single_cell.cell_barcode.offset RENAME assay.single_cell.barcode.read assay.single_cell.cell_barcode.read RENAME assay.single_cell.barcode.size assay.single_cell.cell_barcode.size RENAME assay.single_cell.barcode.white_list_file assay.single_cell.cell_barcode.white_list_file KEEP assay.single_cell.cell_handling assay.single_cell.cell_handling DELETE assay.single_cell.core.schema_url DELETE assay.single_cell.core.schema_version DELETE assay.single_cell.core.type KEEP project.array_express_investigation project.array_express_investigation KEEP project.contributors.[].address project.contributors.[].address KEEP project.contributors.[].city project.contributors.[].city DELETE project.contributors.[].core.schema_url DELETE project.contributors.[].core.schema_version DELETE project.contributors.[].core.type KEEP project.contributors.[].country project.contributors.[].country KEEP project.contributors.[].country_division project.contributors.[].country_division KEEP project.contributors.[].email project.contributors.[].email DELETE project.contributors.[].id KEEP project.contributors.[].institution project.contributors.[].institution KEEP project.contributors.[].laboratory project.contributors.[].laboratory KEEP project.contributors.[].name project.contributors.[].name KEEP project.core.schema_url project.core.schema_url KEEP project.core.schema_version project.core.schema_version KEEP project.core.type project.core.type DELETE project.ddjb_trace KEEP project.description project.description KEEP project.experimental_design.[].ontology project.experimental_design.[].ontology KEEP project.experimental_design.[].text project.experimental_design.[].text KEEP project.experimental_factor_name.[] project.experimental_factor_name.[] KEEP project.geo_series project.geo_series RENAME project.id project.project_id DELETE project.ncbi_bioproject project.insdc_study RENAME project.protocols.[].batch_number protocols.[].batch_number RENAME project.protocols.[].core.schema_url protocols.[].core.schema_url RENAME project.protocols.[].core.schema_version protocols.[].core.schema_version RENAME project.protocols.[].core.type protocols.[].core.type RENAME project.protocols.[].description protocols.[].description RENAME project.protocols.[].id protocols.[].id RENAME project.protocols.[].pdf protocols.[].pdf RENAME project.protocols.[].retail_name protocols.[].retail_name RENAME project.protocols.[].submit_date protocols.[].submit_date RENAME project.protocols.[].submitter_id protocols.[].submitter_id RENAME project.protocols.[].type.ontology rotocols.[].type.ontology RENAME project.protocols.[].type.text rotocols.[].type.text RENAME project.protocols.[].update_date protocols.[].update_date RENAME project.protocols.[].updater_id protocols.[].updater_id KEEP project.publications.[].authors.[] project.publications.[].authors.[] DELETE project.publications.[].core.schema_url DELETE project.publications.[].core.schema_version DELETE project.publications.[].core.type KEEP project.publications.[].doi project.publications.[].doi KEEP project.publications.[].pmid project.publications.[].pmid KEEP project.publications.[].title project.publications.[].title KEEP project.publications.[].url project.publications.[].url KEEP project.related_projects.[] project.related_projects.[] RENAME project.sra_project project.insdc_project KEEP project.submit_date project.submit_date RENAME project.submitter.address project.submitters.[].address RENAME project.submitter.city project.submitters.[].city DELETE project.submitter.core.schema_url DELETE project.submitter.core.schema_version DELETE project.submitter.core.type RENAME project.submitter.country project.submitters.[].country RENAME project.submitter.country_division project.submitters.[].country_division RENAME project.submitter.email project.submitters.[].email DELETE project.submitter.id RENAME project.submitter.institution project.submitters.[].institution RENAME project.submitter.laboratory project.submitters.[].laboratory RENAME project.submitter.name project.submitters.[].name NEW project.submitters.[].phone KEEP project.supplementary_files.[] project.supplementary_files.[] RENAME project.title project.name KEEP project.update_date project.update_date DELETE project.updater.address DELETE project.updater.city DELETE project.updater.core.schema_url DELETE project.updater.core.schema_version DELETE project.updater.core.type DELETE project.updater.country DELETE project.updater.country_division DELETE project.updater.email DELETE project.updater.id DELETE project.updater.institution DELETE project.updater.laboratory DELETE project.updater.name -DELETE sample.biosd_sample +RENAME sample.biosd_sample sample.sample_accessions.biosd_sample RENAME sample.body_part.ontology sample.specimen_from_organism.body_part.ontology RENAME sample.body_part.text sample.specimen_from_organism.body_part.text RENAME sample.cell_cycle.ontology sample.immortalized_cell_line.cell_cycle.ontology RENAME sample.cell_cycle.text sample.immortalized_cell_line.cell_cycle.text RENAME sample.cell_line.catalog_number sample.immortalized_cell_line.catalog_number RENAME sample.cell_line.catalog_url sample.immortalized_cell_line.catalog_url RENAME sample.cell_line.cell_type.ontology sample.immortalized_cell_line.cell_type.ontology RENAME sample.cell_line.cell_type.text sample.immortalized_cell_line.cell_type.text DELETE sample.cell_line.core.schema_url DELETE sample.cell_line.core.schema_version DELETE sample.cell_line.core.type DELETE sample.cell_line.culture_protocol RENAME sample.cell_line.date_established sample.immortalized_cell_line.date_established RENAME sample.cell_line.derived_from sample.immortalized_cell_line.derived_from RENAME sample.cell_line.disease.ontology sample.immortalized_cell_line.disease.ontology RENAME sample.cell_line.disease.text sample.immortalized_cell_line.disease.text RENAME sample.cell_line.karyotype sample.immortalized_cell_line.karyotype RENAME sample.cell_line.name.ontology sample.immortalized_cell_line.name.ontology RENAME sample.cell_line.name.text sample.immortalized_cell_line.name.text RENAME sample.cell_line.passage_number sample.immortalized_cell_line.passage_number RENAME sample.cell_line.publication.authors.[] sample.immortalized_cell_line.publication.authors.[] DELETE sample.cell_line.publication.core.schema_url DELETE sample.cell_line.publication.core.schema_version DELETE sample.cell_line.publication.core.type RENAME sample.cell_line.publication.doi sample.immortalized_cell_line.publication.doi RENAME sample.cell_line.publication.pmid sample.immortalized_cell_line.publication.pmid RENAME sample.cell_line.publication.title sample.immortalized_cell_line.publication.title RENAME sample.cell_line.publication.url sample.immortalized_cell_line.publication.url KEEP sample.core.schema_url sample.core.schema_url KEEP sample.core.schema_version sample.core.schema_version KEEP sample.core.type sample.core.type DELETE sample.culture_type DELETE sample.disassociation_protocol KEEP sample.donor.age sample.donor.age KEEP sample.donor.age_unit sample.donor.age_unit KEEP sample.donor.ancestry.[].ontology sample.donor.ancestry.[].ontology KEEP sample.donor.ancestry.[].text sample.donor.ancestry.[].text KEEP sample.donor.body_mass_index sample.donor.body_mass_index DELETE sample.donor.core.schema_url DELETE sample.donor.core.schema_version DELETE sample.donor.core.type RENAME sample.donor.death.cause_of_death sample.donor.death.cause_of_death.text NEW sample.donor.death.cause_of_death.ontology KEEP sample.donor.death.cold_perfused sample.donor.death.cold_perfused DELETE sample.donor.death.core.schema_url DELETE sample.donor.death.core.schema_version DELETE sample.donor.death.core.type KEEP sample.donor.death.days_on_ventilator sample.donor.death.days_on_ventilator KEEP sample.donor.death.hardy_scale sample.donor.death.hardy_scale KEEP sample.donor.death.time_of_death sample.donor.death.time_of_death KEEP sample.donor.development_stage.ontology sample.donor.development_stage.ontology KEEP sample.donor.development_stage.text sample.donor.development_stage.text KEEP sample.donor.disease.[].ontology sample.donor.disease.[].ontology KEEP sample.donor.disease.[].text sample.donor.disease.[].text KEEP sample.donor.genotype sample.donor.genotype KEEP sample.donor.height sample.donor.height -ugly ---- checked above here -DELETE sample.donor.id +NEW sample.donor.alcohol_history +NEW sample.donor.nutritional_state +NEW sample.donor.smoking_history KEEP sample.donor.is_living sample.donor.is_living KEEP sample.donor.life_stage sample.donor.life_stage KEEP sample.donor.medication.[].ontology sample.donor.medication.[].ontology KEEP sample.donor.medication.[].text sample.donor.medication.[].text KEEP sample.donor.sex sample.donor.sex -RENAME sample.donor.species.ontology sample.donor.ancestry.[].ontology -RENAME sample.donor.species.text sample.donor.ancestry.[].text +RENAME sample.donor.species.ontology sample.genus_species.ontology +RENAME sample.donor.species.text sample.genus_species.text KEEP sample.donor.strain.[].ontology sample.donor.strain.[].ontology KEEP sample.donor.strain.[].text sample.donor.strain.[].text -DELETE sample.donor.submitted_id KEEP sample.donor.weight sample.donor.weight -DELETE sample.ena_sample +TODO sample.donor.id sample.sample_id +TODO sample.donor.submitted_id sample.name +DELETE sample.ena_sample sample_accessions.insdc_sample DELETE sample.enrichment.[].core.schema_url DELETE sample.enrichment.[].core.schema_version DELETE sample.enrichment.[].core.type RENAME sample.enrichment.[].markers sample.cell_suspension.enrichment.[].markers RENAME sample.enrichment.[].protocol.[] sample.immortalized_cell_line.publication.authors.[] RENAME sample.enrichment.[].size_max sample.cell_suspension.enrichment.[].size_max RENAME sample.enrichment.[].size_min sample.cell_suspension.enrichment.[].size_min RENAME sample.enrichment.[].type sample.cell_suspension.enrichment.[].type DELETE sample.geo_sample -DELETE sample.id +RENAME sample.id sample.sample_id KEEP sample.name sample.name -DELETE sample.ncbi_biosample +RENAME sample.ncbi_biosample sample.sample_accessions.biosd_sample RENAME sample.organ.ontology sample.specimen_from_organism.organ.ontology RENAME sample.organ.text sample.specimen_from_organism.organ.text RENAME sample.preservation.autolysis_score sample.specimen_from_organism.state_of_specimen.autolysis_score DELETE sample.preservation.core.schema_url DELETE sample.preservation.core.schema_version DELETE sample.preservation.core.type RENAME sample.preservation.gross_description sample.specimen_from_organism.state_of_specimen.gross_description RENAME sample.preservation.gross_image.[] sample.specimen_from_organism.state_of_specimen.gross_image.[] RENAME sample.preservation.ischemic_time sample.specimen_from_organism.state_of_specimen.ischemic_time RENAME sample.preservation.microscopic_description sample.specimen_from_organism.state_of_specimen.microscopic_description RENAME sample.preservation.microscopic_image.[] sample.specimen_from_organism.state_of_specimen.microscopic_image.[] RENAME sample.preservation.postmortem_interval sample.specimen_from_organism.state_of_specimen.postmortem_interval DELETE sample.preservation.preservation_protocol DELETE sample.preservation.storage_protocol -RENAME sample.project_id project.project_id -RENAME sample.protocol_ids.[] sample.immortalized_cell_line.publication.authors.[] +DELETE sample.project_id +KEEP sample.protocol_ids.[] sample.protocol_ids.[] DELETE sample.submit_date DELETE sample.submitter_id KEEP sample.supplementary_files.[] sample.supplementary_files.[] -RENAME sample.title sample.immortalized_cell_line.publication.title +RENAME sample.title sample.description RENAME sample.total_estimated_cells sample.cell_suspension.total_estimated_cells DELETE sample.update_date DELETE sample.updater_id -RENAME sample.well.cell_type.ontology sample.immortalized_cell_line.cell_type.ontology -RENAME sample.well.cell_type.text sample.immortalized_cell_line.cell_type.text +TODO sample.well.cell_type.ontology sample.immortalized_cell_line.cell_type.ontology +TODO sample.well.cell_type.text sample.immortalized_cell_line.cell_type.text RENAME sample.well.col sample.cell_suspension.well.col DELETE sample.well.core.schema_url DELETE sample.well.core.schema_version DELETE sample.well.core.type RENAME sample.well.name sample.cell_suspension.well.name RENAME sample.well.plate sample.cell_suspension.well.plate DELETE sample.well.plating_protocol RENAME sample.well.quality sample.cell_suspension.well.quality RENAME sample.well.row sample.cell_suspension.well.row NEW assay.description NEW assay.imaging.embedding NEW assay.imaging.exposure_time NEW assay.imaging.field_counts.[] NEW assay.imaging.field_microns.[] NEW assay.imaging.field_resolution.[] NEW assay.imaging.fixation NEW assay.imaging.microscope NEW assay.imaging.probes NEW assay.name NEW project.contributors.[].phone NEW project.experimental_design.[].ontology NEW project.experimental_design.[].text NEW project.insdc_project NEW project.name -NEW sample.description NEW sample.donor.alcohol_history NEW sample.donor.nutritional_state NEW sample.donor.smoking_history -NEW sample.genus_species.ontology -NEW sample.genus_species.text NEW sample.immortalized_cell_line.disease.ontology NEW sample.immortalized_cell_line.disease.text NEW sample.ncbi_taxon_id NEW sample.organoid.model_for_organ.ontology NEW sample.organoid.model_for_organ.text NEW sample.primary_cell_line.cell_cycle.ontology NEW sample.primary_cell_line.cell_cycle.text NEW sample.primary_cell_line.cell_type.ontology NEW sample.primary_cell_line.cell_type.text NEW sample.primary_cell_line.date_established NEW sample.primary_cell_line.disease.ontology NEW sample.primary_cell_line.disease.text NEW sample.primary_cell_line.passage_number -NEW sample.sample_accessions