Create templates for improved curation [IN PROGRESS]#28
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allenbaron wants to merge 34 commits into
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Rely on INTERNAL googlesheets4 functions.
- curation_template() creates a curation template in a Google sheet... can't write data yet - spreadhseet_range() calculates and returns a range as expected by Excel or Google Sheets
PROBLEM: Adding validation fails when trying to create a new Google Sheet from scratch. FIX: Pass newly created ss identifier to validation & freeze functions.
Shorten and standardize so future languages are easily managed. Using IETF BCP 47 language tags to identify different languages.
No effect on outputs
.data argument moved to first for improved use in function pipelines. Includes only NULL method currently, which creates a blank curation template with a specified number of rows.
To extract all anonymous relations from an OBO Foundry ontology in Manchester format.
To make values which are IRIs human understandable with less work
- Rename 'annotation' to 'data_type' to reflect that not all data are annotations - Drop 'remove' column and use dropdown-validated 'status' instead for more flexible & powerful data handling - 'status' validation options are all documented in curation_status and include'retain', 'add', 'remove', 'exclude', 'ignore', 'restore' - Add new 'sparql_dt_motif' column to schema and ingest as internal data to support full conversion of obo-data.rq output to 'data_type's
To create curation templates with input data from an OBO ontology
To better reflect that this column and included notes indicate how the data should be acted upon and not its present status.
Original letter calculation would only have worked for first 26 columns. colnum_to_sht_letter() works for any number of columns.
- Rename 'type' column in schema sheet to 'inclusion' - Remove 'deprecated' column from schema and use "deprecated" in inclusion instead - Add .sparql_dt_motif as internal data
Error caused by addition of missing 'sheet' parameter in GS validation functions.
Tests: PASS
Modification of #34 for full curation template work
To sort obo_data according to .curation_opts schema in curation_template()
To add a specified number of empty rows between different ID data
New internal functions: - filter_max_ids() - pivot_obo_to_curation()
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This is a major new feature supporting creation of curation templates in Google Sheets.
EXPECTED when complete:
MAY exist when complete:
inventory_omim()orinventory_mappings()(not sure if this complete)inventory_mappings()