sql.select() calls: Removed order_by=None everywhere that a stable row order is required (i.e. consistent between selects, or consistent between table transformations). This causes several tests to return different inserted row counts, because the input table is now being accessed in pkey order instead of in table order. This fixes a bug where tables with more rows than ~100 would return different results for repeated calls of the same non-ordered select.

sql.py: mk_select(): Use table_order_by() instead of table_pkey_col() to determine what column(s) to order by if order_by is set to order_by_pkey

sql.py: Added table_pkey_index(), index_order_by(), table_cluster_on(), table_order_by()

sql.py: Added index_exprs() and use it in index_cols()

README.TXT: Data import: On local machine: Added `make inputs/.TNRS/cleanup`, which is necessary because the PostgreSQL collation may differ between vegbiendev's and your DB

schemas/vegbien.sql: taxonconcept: taxonconcept_update_ancestors(): Use matched_concept_id's ancestors instead if available. (Recursively applied, this will use the ancestors of the accepted concept.) This facilitates finding all children of and matches to an accepted concept, which will all have an entry for that concept in taxonconcept_ancestor. Note that the concept's own parents will not be indexed in taxonconcept_ancestor, because only accepted ancestors are now stored in taxonconcept_ancestor. Documented that taxonconcept_ancestor now stores the accepted ancestors of a taxonconcept.

schemas/vegbien.sql: taxonconcept: taxonconcept_2_propagate_accepted_concept_id(): Also update accepted_concept_id on concepts that resolve to this concept, which may have been created before this concept was marked as accepted if concepts are not imported in dependency order (accepted concepts first). Added index on matched_concept_id to speed up finding concepts that resolve to this concept.

sql.py: mk_select(): order_by is order_by_pkey: Only order by the table's actual pkey, if it has one, rather than using the first column if it doesn't

inputs/.TNRS/tnrs/test.xml.ref: Updated inserted row count

db_xml.py: partition_size: Increased to 1,000,000 (>= NCBI.higher_taxa's size) so NCBI.higher_taxa can be imported completely in one partition. This is necessary because NCBI's taxonconcepts are not in dependency order (parents first), so a later partition cannot rely on the parents of its taxonconcepts having already been imported. Instead, all taxonconcepts must be imported at once and then separately, the parents of all taxonconcepts must be set.