5f0479c39a7257c46305e8eb377f4bbc5d49d8b7 kent Thu Nov 30 13:30:55 2017 -0800 Saving another round of changes, a little more than half way through manual pass through file. diff --git src/hca/v3v4/v3v4 src/hca/v3v4/v3v4 index e5bf211..c100164 100644 --- src/hca/v3v4/v3v4 +++ src/hca/v3v4/v3v4 @@ -56,140 +56,142 @@ 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 +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.[] -DELETE project.sra_project -DELETE project.submit_date -RENAME project.submitter.address project.contributors.[].address -RENAME project.submitter.city project.contributors.[].city +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.contributors.[].country -RENAME project.submitter.country_division project.contributors.[].country_division -RENAME project.submitter.email project.contributors.[].email +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.contributors.[].institution -RENAME project.submitter.laboratory project.contributors.[].laboratory -RENAME project.submitter.name project.contributors.[].name +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.publications.[].title -DELETE project.update_date -RENAME project.updater.address project.contributors.[].address -RENAME project.updater.city project.contributors.[].city +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 -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.country +DELETE project.updater.country_division +DELETE project.updater.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 project.updater.institution +DELETE project.updater.laboratory +DELETE project.updater.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.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.cell_suspension.target_cell_type.[].ontology -RENAME sample.cell_line.name.text sample.cell_suspension.target_cell_type.[].text +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 -DELETE sample.donor.death.cause_of_death +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 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 @@ -236,46 +238,36 @@ 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.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