cfa79208aac247b068c2049273305dfa279d9965 kent Wed Dec 20 16:43:31 2017 -0800 A little polishing. diff --git src/hca/v3v4/v3v4 src/hca/v3v4/v3v4 index da54b00..dfb9b43 100644 --- src/hca/v3v4/v3v4 +++ src/hca/v3v4/v3v4 @@ -49,76 +49,76 @@ 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 +RENAME project.ddjb_trace project.insdc_project KEEP project.description project.description -KEEP project.experimental_design.[].ontology project.experimental_design.[].ontology -KEEP project.experimental_design.[].text project.experimental_design.[].text +DELETE project.experimental_design.[].ontology +RENAME project.experimental_design.[].text project.experimental_design.[] 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.ontology protocols.[].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.submit_date project.submit_date +RENAME project.submitter.address project.submitters.0.address +RENAME project.submitter.city project.submitters.0.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 +RENAME project.submitter.country project.submitters.0.country +RENAME project.submitter.country_division project.submitters.0.country_division +RENAME project.submitter.email project.submitters.0.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 +RENAME project.submitter.institution project.submitters.0.institution +RENAME project.submitter.laboratory project.submitters.0.laboratory +RENAME project.submitter.name project.submitters.0.name +NEW project.submitters.0.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 @@ -175,37 +175,37 @@ 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 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.genus_species.ontology -RENAME sample.donor.species.text sample.genus_species.text +RENAME sample.donor.species.ontology sample.ncbi_taxon_id +RENAME sample.donor.species.text sample.genus_species KEEP sample.donor.strain.[].ontology sample.donor.strain.[].ontology KEEP sample.donor.strain.[].text sample.donor.strain.[].text KEEP sample.donor.weight sample.donor.weight -TODO sample.donor.id sample.sample_id -TODO sample.donor.submitted_id sample.name +COMPLEX sample.donor.id sample.sample_id +COMPLEX 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 DELETE sample.enrichment.[].protocol 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 RENAME sample.id sample.sample_id KEEP sample.name sample.name 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 @@ -218,32 +218,32 @@ 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 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.description RENAME sample.total_estimated_cells sample.cell_suspension.total_estimated_cells DELETE sample.update_date DELETE sample.updater_id -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 +COMPLEX sample.well.cell_type.ontology sample.immortalized_cell_line.cell_type.ontology +COMPLEX 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.[]