a79774b4bdd70c5531339148277c84b9f7d3c209 kent Wed Nov 29 20:27:49 2017 -0800 Working on v3 to v4 field-by-field conversion for tagstorms. diff --git src/hca/v3v4/v3v4 src/hca/v3v4/v3v4 new file mode 100644 index 0000000..e5bf211 --- /dev/null +++ src/hca/v3v4/v3v4 @@ -0,0 +1,284 @@ +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 +ugly ***************** CHecked to here +DELETE project.ncbi_bioproject +DELETE project.protocols.[].batch_number +DELETE project.protocols.[].core.schema_url +DELETE project.protocols.[].core.schema_version +DELETE project.protocols.[].core.type +RENAME project.protocols.[].description project.description +DELETE project.protocols.[].id +DELETE project.protocols.[].pdf +DELETE project.protocols.[].retail_name +DELETE project.protocols.[].submit_date +DELETE project.protocols.[].submitter_id +RENAME project.protocols.[].type.ontology project.experimental_design.[].ontology +RENAME project.protocols.[].type.text project.experimental_design.[].text +DELETE project.protocols.[].update_date +DELETE project.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.[] +DELETE project.sra_project +DELETE project.submit_date +RENAME project.submitter.address project.contributors.[].address +RENAME project.submitter.city project.contributors.[].city +DELETE project.submitter.core.schema_url +DELETE project.submitter.core.schema_version +DELETE project.submitter.core.type +RENAME project.submitter.country project.contributors.[].country +RENAME project.submitter.country_division project.contributors.[].country_division +RENAME project.submitter.email project.contributors.[].email +DELETE project.submitter.id +RENAME project.submitter.institution project.contributors.[].institution +RENAME project.submitter.laboratory project.contributors.[].laboratory +RENAME project.submitter.name project.contributors.[].name +KEEP project.supplementary_files.[] project.supplementary_files.[] +RENAME project.title project.publications.[].title +DELETE project.update_date +RENAME project.updater.address project.contributors.[].address +RENAME project.updater.city project.contributors.[].city +DELETE project.updater.core.schema_url +DELETE project.updater.core.schema_version +DELETE project.updater.core.type +RENAME project.updater.country project.contributors.[].country +RENAME project.updater.country_division project.contributors.[].country_division +RENAME project.updater.email project.contributors.[].email +DELETE project.updater.id +RENAME project.updater.institution project.contributors.[].institution +RENAME project.updater.laboratory project.contributors.[].laboratory +RENAME project.updater.name project.contributors.[].name +DELETE sample.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.derived_from +RENAME sample.cell_line.disease.ontology sample.donor.disease.[].ontology +RENAME sample.cell_line.disease.text sample.donor.disease.[].text +RENAME sample.cell_line.karyotype sample.immortalized_cell_line.karyotype +RENAME sample.cell_line.name.ontology sample.cell_suspension.target_cell_type.[].ontology +RENAME sample.cell_line.name.text sample.cell_suspension.target_cell_type.[].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 +DELETE sample.donor.death.cause_of_death +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 +DELETE sample.donor.id +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 +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 +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 +KEEP sample.name sample.name +DELETE sample.ncbi_biosample +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.submit_date +DELETE sample.submitter_id +KEEP sample.supplementary_files.[] sample.supplementary_files.[] +RENAME sample.title sample.immortalized_cell_line.publication.title +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 +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.insdc_project +NEW project.insdc_study +NEW project.name +NEW project.submitters.[].address +NEW project.submitters.[].city +NEW project.submitters.[].country +NEW project.submitters.[].country_division +NEW project.submitters.[].email +NEW project.submitters.[].institution +NEW project.submitters.[].laboratory +NEW project.submitters.[].name +NEW project.submitters.[].phone +NEW sample.description +NEW sample.donor.alcohol_history +NEW sample.donor.death.cause_of_death.ontology +NEW sample.donor.death.cause_of_death.text +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