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From 04/23/2012 to 05/22/2012

05/22/2012

10:00 PM Revision 2342: exc.py: add_msg(): Fixed bug where msg needed to be converted to a unicode object before appending it to another unicode object
Aaron Marcuse-Kubitza
09:54 PM Revision 2341: mappings/VegX-VegBIEN.stems.csv: Fixed bug where taxonfit was named taxonFit. (This was only recently discovered because column names are now escaped, causing them not to be case-insensitive.)
Aaron Marcuse-Kubitza
09:51 PM Revision 2340: sql.py: Added table_not_null_col()
Aaron Marcuse-Kubitza
09:50 PM Revision 2339: sql.py: Added table_cols() and use it in pkey()
Aaron Marcuse-Kubitza
09:36 PM Revision 2338: schemas/vegbien.sql, schemas/functions.sql: Relational functions: Added dummy not_null column to provide a column to use in LEFT JOIN filter-out filters
Aaron Marcuse-Kubitza
09:24 PM Revision 2337: sql.py: mk_insert_select(): embeddable: Use new sql_gen.NamedTable
Aaron Marcuse-Kubitza
09:23 PM Revision 2336: sql_gen.py: Added NamedTable. Table: Added to_Table().
Aaron Marcuse-Kubitza
09:06 PM Revision 2335: sql_gen.py: Added section labels for each type of SQL code object
Aaron Marcuse-Kubitza
08:25 PM Revision 2334: sql.py: put_table(): DuplicateKeyException: Fixed bug where dict_subset_right_join() was used instead of dict_subset(), adding spurious None values for columns in the constraint which are not in the input tables
Aaron Marcuse-Kubitza
08:23 PM Revision 2333: sql_gen.py: as_Col(): Don't allow None cols
Aaron Marcuse-Kubitza
08:06 PM Revision 2332: schemas/vegbien.ERD.mwb: Synced with schemas/vegbien.sql
Aaron Marcuse-Kubitza
07:39 PM Revision 2331: sql.py: Removed no longer used clean_name()
Aaron Marcuse-Kubitza
07:38 PM Revision 2330: sql.py: mk_insert_select(): embeddable: Removed clean_name() because the function name is now escaped where it's used
Aaron Marcuse-Kubitza
07:36 PM Revision 2329: sql.py: put_table(): Added support for out_table values that are Table objects
Aaron Marcuse-Kubitza
07:31 PM Revision 2328: sql.py: mk_insert_select(): Fixed bug where table for creating the returning column Col object was the already-escaped string, instead of the Table object
Aaron Marcuse-Kubitza
07:24 PM Revision 2327: sql.py: mk_insert_select(): Fixed bug where function name and returning col were not being escaped
Aaron Marcuse-Kubitza
07:08 PM Revision 2326: sql.py: put_table(): log_ignore(): Fixed bug where in_col needed to be passed through str() because it's a column object
Aaron Marcuse-Kubitza
07:03 PM Revision 2325: sql.py: put_table(): Fixed bug where the filter_out join should only be used in the insert, not in the select of existing/inserted rows. insert_select() call: Fixed compatibility bug where old versions of Python did not support mixing keyword args and ** args.
Aaron Marcuse-Kubitza
06:32 PM Revision 2324: sql.py: put_table(): Fixed bug where "add_row_num(db, out_pkeys_ref[0])" was mistakenly put under the "if row_ct_ref != None" if statement
Aaron Marcuse-Kubitza
06:26 PM Revision 2323: sql_gen.py: Renamed NamedCode to NamedCol to better reflect its specific use
Aaron Marcuse-Kubitza
06:23 PM Revision 2322: sql.py: Removed unnecessary calls to check_name()
Aaron Marcuse-Kubitza
06:22 PM Revision 2321: sql.py: mk_insert_select(): Fixed bug where returning col was not being escaped
Aaron Marcuse-Kubitza
06:20 PM Revision 2320: sql.py: add_row_num(): Fixed bug where table name was not being escaped
Aaron Marcuse-Kubitza
06:13 PM Revision 2319: sql.py: run_query_into(): Fixed bug where into table name was not being escaped
Aaron Marcuse-Kubitza
06:07 PM Revision 2318: sql.py: mk_insert_select(): Fixed bug where utput column names were not being escaped
Aaron Marcuse-Kubitza
05:57 PM Revision 2317: sql.py: put_table(): Fixed bug where only string columns were being included in the distinct_on, but columns are now always sql_gen.Col instances
Aaron Marcuse-Kubitza
05:53 PM Revision 2316: sql.py: put_table(): Put together varying insert_select() args using dict instead of individual vars
Aaron Marcuse-Kubitza
05:51 PM Revision 2315: sql.py: mk_select(): Fixed bug where order_by needed to default to None if distinct_on was used. Fixed bug where cond values were being treated as %s params in addition to being parsed by sql_gen.as_ValueCond().to_str().
Aaron Marcuse-Kubitza
05:40 PM Revision 2314: sql_gen.py: Col: Added to_Col()
Aaron Marcuse-Kubitza
05:31 PM Revision 2313: db_xml.py: put_table(): Accept sql_gen.Table objects or strings instead of separate table and schema names
Aaron Marcuse-Kubitza
05:10 PM Revision 2312: sql.py: put_table(): Require all in_table_cols to be sql_gen.Col objects
Aaron Marcuse-Kubitza
05:03 PM Revision 2311: sql_gen.py: ValueCond: Unwrap NamedCode objects
Aaron Marcuse-Kubitza
04:55 PM Revision 2310: sql_gen.py: NamedCode: Inherit from Col so that its name can be retrieved using the same attribute as Col's
Aaron Marcuse-Kubitza
04:43 PM Revision 2309: sql.py: put_table(): Debug-log each caught exception
Aaron Marcuse-Kubitza
04:41 PM Revision 2308: exc.py: str_(): Added first_line_only param to return just the first line
Aaron Marcuse-Kubitza
04:26 PM Revision 2307: sql.py: ConstraintException: Changed text of message to specify that a constraint was violated
Aaron Marcuse-Kubitza
04:14 PM Revision 2306: sql.py: Renamed ExceptionWithColumns to ConstraintException and added name field to contain the constraint name, if any
Aaron Marcuse-Kubitza
04:06 PM Revision 2305: sql.py: put_table(): If there are join_cols, don't get output pkeys of inserted rows and instead select all rows (existing and inserted) after the insert
Aaron Marcuse-Kubitza
04:04 PM Revision 2304: sql_gen.py: Join.to_str(): Fixed bug where order of right_table_col and left_table_col was reversed when applying as_ValueCond() and as_Col()
Aaron Marcuse-Kubitza
03:33 PM Revision 2303: sql.py: put_table(): Moved things outside of the try clause which should not produce the exceptions
Aaron Marcuse-Kubitza
03:21 PM Revision 2302: sql_gen.py: Code: Extend new strings.DebugPrintable instead of implementing __str__(), __repr__() itself
Aaron Marcuse-Kubitza
03:20 PM Revision 2301: strings.py: Added DebugPrintable
Aaron Marcuse-Kubitza
03:17 PM Revision 2300: sql_gen.py: Code: __str__(): Added class name. Added __repr__().
Aaron Marcuse-Kubitza
03:16 PM Revision 2299: util.py: Added class_name()
Aaron Marcuse-Kubitza
02:55 PM Revision 2298: sql_gen.py: Join.to_str(): Fixed bug in USING syntax where columns were not escaped
Aaron Marcuse-Kubitza
02:48 PM Revision 2297: sql.py: put_table(): Order selects by in_tables0's pkey to avoid undefined orderings on multiple runs of the same query
Aaron Marcuse-Kubitza
02:42 PM Revision 2296: sql.py: mk_select(): Removed no longer used esc_name_()
Aaron Marcuse-Kubitza
02:41 PM Revision 2295: sql_gen.py: as_Table() Removed no longer used support for (schema, table) tuples
Aaron Marcuse-Kubitza
02:39 PM Revision 2294: sql_gen.py: Removed no longer used unescape_table() and table2sql_gen()
Aaron Marcuse-Kubitza
02:38 PM Revision 2293: sql.py: mk_select(): Removed no longer used table_is_esc
Aaron Marcuse-Kubitza
02:37 PM Revision 2292: sql.py: mk_insert_select(): Removed no longer used table_is_esc
Aaron Marcuse-Kubitza
02:34 PM Revision 2291: sql.py: pkey(): Removed no longer used table_is_esc
Aaron Marcuse-Kubitza
02:31 PM Revision 2290: sql.py: cleanup_table(): Switched from table_is_esc to sql_gen.as_Table.to_str()
Aaron Marcuse-Kubitza
02:19 PM Revision 2289: csv2db: Switched to using plain table names rather than table_is_esc
Aaron Marcuse-Kubitza
02:13 PM Revision 2288: bin/map: Switched to using sql_gen rather than table_is_esc
Aaron Marcuse-Kubitza
02:05 PM Revision 2287: sql_gen.py: Removed no longer needed col2sql_gen() and value2sql_gen()
Aaron Marcuse-Kubitza
02:04 PM Revision 2286: sql.py: Replaced sql_gen.value2sql_gen() with sql_gen.as_Col()
Aaron Marcuse-Kubitza
02:00 PM Revision 2285: sql.py: Replaced sql_gen.col2sql_gen() with sql_gen.as_Col()
Aaron Marcuse-Kubitza
01:57 PM Revision 2284: sql.py: mk_select(): Inline cond() and don't use sql_gen.as_Col because sql_gen.as_ValueCond.to_str() calls it
Aaron Marcuse-Kubitza
01:54 PM Revision 2283: sql_gen.py: Removed no longer needed cond2sql_gen()
Aaron Marcuse-Kubitza
01:53 PM Revision 2282: sql.py: mk_select(): cond(): Parse conditions using sql_gen-only functions
Aaron Marcuse-Kubitza
01:47 PM Revision 2281: sql_gen.py: Removed no longer needed join2sql_gen()
Aaron Marcuse-Kubitza
01:44 PM Revision 2280: sql.py: put_table(): Switched joins to sql_gen.Join objects. mk_select(): Only accept joins which are sql_gen.Join objects.
Aaron Marcuse-Kubitza
01:38 PM Revision 2279: sql.py: put_table(): Removed no longer used table_is_esc param
Aaron Marcuse-Kubitza
01:36 PM Revision 2278: sql.py: put_table(): Switched joins to sql_gen.Join objects
Aaron Marcuse-Kubitza
01:28 PM Revision 2277: sql.py: mk_select(): joins: Switched to using sql_gen.Join.to_str() to render joins to SQL
Aaron Marcuse-Kubitza
01:24 PM Revision 2276: sql_gen.py: Join.to_str(): Fixed bugs revealed in first test of function
Aaron Marcuse-Kubitza

05/21/2012

11:05 PM Revision 2275: db_xml.py: put_table(): Turn off table_is_esc when calling sql.put_table() and don't escape out_table
Aaron Marcuse-Kubitza
11:04 PM Revision 2274: sql.py: mk_insert_select(): Use sql_gen.table2sql_gen().to_str() to escape the table
Aaron Marcuse-Kubitza
10:57 PM Revision 2273: db_xml.py: put_table(): First in_tables table is sql_gen.Table object
Aaron Marcuse-Kubitza
10:49 PM Revision 2272: db_xml.py: put_table(): Converted row (mapping) values to sql_gen objects
Aaron Marcuse-Kubitza
10:45 PM Revision 2271: sql.py: mk_select(): Accept main tables (table0's) that are Table objects. This change requires plain SQL code to be wrapped in a CustomCode object if it should not be unescaped and converted to a Table object.
Aaron Marcuse-Kubitza
10:42 PM Revision 2270: sql_gen.py: as_Table(): Accept tables that are Code objects, not just Table objects
Aaron Marcuse-Kubitza
10:40 PM Revision 2269: sql_gen.py: CustomCode: Fixed bug where needed to inherit from Code
Aaron Marcuse-Kubitza
10:19 PM Revision 2268: sql.py: put_table(): Return a sql_gen.Col object instead of an old-style tuple
Aaron Marcuse-Kubitza
10:00 PM Revision 2267: sql.py: mk_select(): joins: Switched to using filter_out as an attribute of the Join object instead of a sentinel value for the first column. Filter by the right table's pkey being NULL instead of each joined column being NULL, because some joined columns may contain NULL values which would mess things up, but the pkey presumably is NOT NULL.
Aaron Marcuse-Kubitza
09:56 PM Revision 2266: sql_gen.py: Join.to_str(): Fixed bug where type_ None was being concatenated with the JOIN str
Aaron Marcuse-Kubitza
09:31 PM Revision 2265: sql_gen.py: Join.to_str(): Fixed bug where USING syntax could not be used for filter_out join type, because a separate right column is required for filtering
Aaron Marcuse-Kubitza
09:20 PM Revision 2264: sql_gen.py: Use new table2sql_gen() in col2sql_gen(), join2sql_gen()
Aaron Marcuse-Kubitza
09:18 PM Revision 2263: sql.py: mk_select(): joins: Convert all joins to sql_gen format using join2sql_gen()
Aaron Marcuse-Kubitza
09:17 PM Revision 2262: sql_gen.py: Added table2sql_gen()
Aaron Marcuse-Kubitza
08:44 PM Revision 2261: sql_gen.py: Added join2sql_gen()
Aaron Marcuse-Kubitza
08:33 PM Revision 2260: sql_gen.py: Added as_Col(). as_ValueCond(): Added support for assuming the value is a column rather than a literal value, using the default_table param. Added Join.
Aaron Marcuse-Kubitza
07:10 PM Revision 2259: sql_gen.py: Put parameterized SQL code objects in separate section
Aaron Marcuse-Kubitza
07:08 PM Revision 2258: sql.py: put_table(): DuplicateKeyException: Assert that join_cols has changed to avoid infinite loops
Aaron Marcuse-Kubitza
06:59 PM Revision 2257: sql.py: put_table(): Moved getting pkeys of already existing rows from DuplicateKeyException to try clause, so that it always runs if there are join_cols. DuplicateKeyException: Add new duplicate key cols to join_cols instead of replacing join_cols so that multiple unique constraints being violated causes the union of their columns to be used for join_cols.
Aaron Marcuse-Kubitza
06:23 PM Revision 2256: sql_gen.py: Added CustomCode
Aaron Marcuse-Kubitza
06:05 PM Revision 2255: sql.py: mk_select(): joins: Fixed bug where joins dict was being modified without first being copied, causing the input value to be modified
Aaron Marcuse-Kubitza
05:52 PM Revision 2254: Compare object()-based sentinel values using is. Where sentinel values must be compared using ==, use rand.rand_int() instead.
Aaron Marcuse-Kubitza
05:13 PM Revision 2253: sql.py: put_table(): Added debug messages for every action performed
Aaron Marcuse-Kubitza
04:45 PM Revision 2252: sql.py: put_table(): Moved assignment of in_pkeys_ref outside loop so it wouldn't need to be re-versioned every iteration
Aaron Marcuse-Kubitza
04:42 PM Revision 2251: sql.py: put_table(): Changed temp_suffix to temp_prefix so all temp tables for a given out_table would have the same prefix. (Existing name collisions due to truncated names are not a problem because version prefixes are automatically added.)
Aaron Marcuse-Kubitza
04:23 PM Revision 2250: mappings/DwC2-VegBIEN.specimens.csv: Filter dates through _toTimestamp
Aaron Marcuse-Kubitza
04:20 PM Revision 2249: schemas/functions.sql: Added _toTimestamp
Aaron Marcuse-Kubitza
04:15 PM Revision 2248: mappings/DwC2-VegBIEN.specimens.csv: Filter coordsaccuracy through _toDouble
Aaron Marcuse-Kubitza
04:12 PM Revision 2247: sql.py: FunctionValueException parsing: Support values containing non-word and non-ASCII characters
Aaron Marcuse-Kubitza
04:11 PM Revision 2246: exc.py: Support exception messages containing non-ASCII characters
Aaron Marcuse-Kubitza

05/18/2012

07:10 PM Revision 2245: sql.py: put_table(): Print debug messages about how exceptions are being handled
Aaron Marcuse-Kubitza
06:45 PM Revision 2244: sql.py: put_table(): After getting pkeys of already existing rows, insert new rows
Aaron Marcuse-Kubitza
06:42 PM Revision 2243: sql.py: put_table(): Handle FunctionValueExceptions by excluding rows with the invalid value in their "value" column
Aaron Marcuse-Kubitza
06:41 PM Revision 2242: sql.py: run_query(): Also parse "invalid input *syntax* at assignment" errors as FunctionValueExceptions
Aaron Marcuse-Kubitza
06:39 PM Revision 2241: sql_gen.py: Col: Convert string table names to Table objects
Aaron Marcuse-Kubitza
06:09 PM Revision 2240: sql.py: run_query(): Parse "invalid input value at assignment" errors' values as well
Aaron Marcuse-Kubitza
05:55 PM Revision 2239: sql.py: run_query(): Parse "invalid input value at assignment" errors as FunctionValueExceptions
Aaron Marcuse-Kubitza
05:27 PM Revision 2238: sql.py: mk_select(): joins: filter_out: Pass NULLs through. Use sql_gen.*2sql_gen() to add the left and right table names to the columns.
Aaron Marcuse-Kubitza
05:26 PM Revision 2237: sql_gen.py: cond2sql_gen(): Take assume_col param and pass it to value2sql_gen()
Aaron Marcuse-Kubitza
04:45 PM Revision 2236: sql.py: put_table(): Use table-qualified pkey col names whenever possible, to avoid ambiguous column references
Aaron Marcuse-Kubitza
04:12 PM Revision 2235: mappings/DwC2-VegBIEN.specimens.csv: placenames: Convert ranks using _toPlacerank to work with multi-inserts
Aaron Marcuse-Kubitza
04:11 PM Revision 2234: sql.py: DbConn._db(): Fixed bug where the isolation level was not set to "SERIALIZABLE" in a portable way
Aaron Marcuse-Kubitza
04:04 PM Revision 2233: sql.py: mk_select(): distinct_on is turned off when distinct_on == [] rather than when it's None
Aaron Marcuse-Kubitza
03:48 PM Revision 2232: schemas/vegbien.sql: Added _toPlacerank
Aaron Marcuse-Kubitza
03:43 PM Revision 2231: schemas/vegbien.sql: Added _toTaxonrank
Aaron Marcuse-Kubitza
03:35 PM Revision 2230: sql.py: put_table(): Handle NullValueExceptions by removing invalid rows
Aaron Marcuse-Kubitza
03:31 PM Revision 2229: sql_gen.py: Added NamedCode
Aaron Marcuse-Kubitza
03:30 PM Revision 2228: sql_gen.py: Added __str__() to base classes for debugging
Aaron Marcuse-Kubitza
02:46 PM Revision 2227: sql.py: mk_select() (and sql_gen.py): Fixed bugs where literal strings were treated as literal values when they should have been treated as column names. Take default_table param to determine default table to use if a column doesn't have an explicit table. put_table(): mk_main_select(): Pass in_tables0 as mk_select()'s default_table.
Aaron Marcuse-Kubitza
12:54 PM Revision 2226: sql.py: mk_select(): cond(): Run additional sql_gen translation functions cond2sql_gen() and col2sql_gen() on the left and right sides of the comparison
Aaron Marcuse-Kubitza
12:50 PM Revision 2225: sql_gen.py: ValueCond: Fixed bug where values which are Code objects were being converted to Literals. Added cond2sql_gen().
Aaron Marcuse-Kubitza

05/17/2012

08:01 PM Revision 2224: sql.py: mk_select(): join(): Use cond() now that it supports sql_gen format
Aaron Marcuse-Kubitza
07:50 PM Revision 2223: sql_gen.py: Added col2sql_gen() and use it in value2sql_gen()
Aaron Marcuse-Kubitza
07:25 PM Revision 2222: sql_gen.py: CompareCond: By default, compare NULL values literally. Support operator values to pass NULLs through.
Aaron Marcuse-Kubitza
07:23 PM Revision 2221: strings.py: remove_prefix(), remove_suffix(): Added removed_ref param
Aaron Marcuse-Kubitza
06:28 PM Revision 2220: sql.py: mk_select(): parse_col(): Use sql_gen.value2sql_gen().to_str()
Aaron Marcuse-Kubitza
06:22 PM Revision 2219: sql_gen.py: Added as_Table(), unescape_table(), value2sql_gen()
Aaron Marcuse-Kubitza
03:37 PM Revision 2218: sql.py: mk_select(): Documented conds param
Aaron Marcuse-Kubitza
03:32 PM Revision 2217: sql.py: mk_select(): cond(): Switched to using sql_gen so that custom conds would be supported
Aaron Marcuse-Kubitza
03:19 PM Revision 2216: sql_gen.py: ValueCond.to_str(): Made value_code a Code object instead of a string, and renamed it to left_value to reflect where it goes. Added as_ValueCond().
Aaron Marcuse-Kubitza
03:11 PM Revision 2215: sql.py: esc_value(): Fixed bug where db needed to be referenced through self
Aaron Marcuse-Kubitza
02:22 PM Revision 2214: sql_gen.py: ValueCond.to_str(): Added value_code param
Aaron Marcuse-Kubitza
02:16 PM Revision 2213: sql_gen.py: Literal, CompareCond: Implemented to_str(). ValueCond: Autoconvert literal values to Literals.
Aaron Marcuse-Kubitza
02:14 PM Revision 2212: sql.py: DbConn: Added esc_value()
Aaron Marcuse-Kubitza
01:52 PM Revision 2211: Moved SQL code generation classes from sql.py to new sql_gen.py. sql_gen.py: Added Code, Literal, ValueCond, and CompareCond. sql.py: Removed Query because we will use a different approach.
Aaron Marcuse-Kubitza
12:43 PM Revision 2210: sql.py: Added Query, Table, Col
Aaron Marcuse-Kubitza
11:28 AM Revision 2209: sql.py: get(): Fixed bug where limit=1 needs to be passed to select() as a keyword arg now that the distinct_on param comes before it
Aaron Marcuse-Kubitza
11:01 AM Revision 2208: sql.py: put_table(): mk_main_select(): Pass outer var conds to mk_select()
Aaron Marcuse-Kubitza
10:57 AM Revision 2207: sql.py: put_table(): mk_select_(): Fixed bug where it was sometimes being called without distinct_on, causing it to return a different # of rows. Renamed mk_select_() to mk_main_select() for clarity.
Aaron Marcuse-Kubitza
10:48 AM Revision 2206: sql.py: put_table(): Do inserts and selects in a loop so that it will keep retrying the operation with additional constraints until it succeeds
Aaron Marcuse-Kubitza

05/15/2012

03:56 PM Revision 2205: sql.py: put_table(): mk_select_(): Fixed bug where order_by needed to be None because otherwise it wouldn't match the distinct_on cols if they were specified
Aaron Marcuse-Kubitza
03:55 PM Revision 2204: sql.py: put_table(): insert_(): Fixed bug where distinct_on was not passed to mk_select_()
Aaron Marcuse-Kubitza
03:30 PM Revision 2203: sql.py: put_table(): mk_select_(): Fixed bug where distinct_on needed to be passed as a keyword param
Aaron Marcuse-Kubitza
03:21 PM Revision 2202: sql.py: put_table(): insert_() and mk_select_() take distinct_on param
Aaron Marcuse-Kubitza
03:10 PM Revision 2201: sql.py: put_table(): Factored out code that inserts into pkeys table into run_query_into_pkeys() helper function
Aaron Marcuse-Kubitza
02:55 PM Revision 2200: sql.py: mk_select(): Implemented DISTINCT ON according to the distinct_on param
Aaron Marcuse-Kubitza
02:48 PM Revision 2199: sql.py: mk_select(): Added distinct_on param to set the columns to SELECT DISTINCT ON
Aaron Marcuse-Kubitza
02:31 PM Revision 2198: sql.py: clean_name(): Convert names to lowercase so that PostgreSQL will behave the same whether the name is escaped with "" or not. This will help avoid bugs in code that uses temp tables created by the sql module.
Aaron Marcuse-Kubitza
02:29 PM Revision 2197: sql.py: put_table(): Added order_by=None wherever rows were not supposed to be re-ordered. On DuplicateKeyException: Save existing pkeys in temp table for joining on.
Aaron Marcuse-Kubitza
01:31 PM Revision 2196: db_xml.py: put_table(): Pass limit and start to sql.put_table()
Aaron Marcuse-Kubitza
01:09 PM Revision 2195: db_xml.py: put_table(): Added limit and start options
Aaron Marcuse-Kubitza
11:54 AM Revision 2194: sql.py: When creating a temporary entity (table, function, etc.), instead create it as a permanent entity in debug mode so it can be viewed after the program is run
Aaron Marcuse-Kubitza
11:40 AM Revision 2193: sql.py: DbConn: Store whether in debug mode (log_debug != log_debug_none) for easy use by methods
Aaron Marcuse-Kubitza
11:31 AM Revision 2192: bin/map: connect_db(): Turn on autocommit mode in debug mode if commit is on, so that incremental results can be seen in the DB
Aaron Marcuse-Kubitza
11:30 AM Revision 2191: sql.py: DbConn: Use internal autocommit handling instead of DB connection autocommit attr to avoid autocommits inside a savepoint
Aaron Marcuse-Kubitza
11:15 AM Revision 2190: sql.py: DbConn: Added autocommit option to turn on autocommit mode. Use set_session() instead of SQL command to set isolation level.
Aaron Marcuse-Kubitza

05/14/2012

05:50 PM Revision 2189: sql.py: mk_insert_select(): embeddable: Fixed bug where the function may do different things when run, because the function (and other statements whose cached strings depend on the function name) may be run after the function definition would have changed, by versioning the function name and using CREATE FUNCTION instead of CREATE OR REPLACE FUNCTION so that its definition never changes
Aaron Marcuse-Kubitza
05:28 PM Revision 2188: sql.py: Parse "function already exists" errors as DuplicateFunctionException
Aaron Marcuse-Kubitza
05:13 PM Revision 2187: sql.py: mk_select(): joins: Fixed bug where join_not_equal did not do what it was designed for, which is filtering out matches of the join condition (before the bug fix, it effectively did a cross join with matching rows excluded, causing duplication of rows). Renamed join_not_equal to filter_out to reflect its intended use. Support table-scoped column names in the WHERE conds list.
Aaron Marcuse-Kubitza
04:22 PM Revision 2186: sql.py: put_table(): Fixed bug where ORDER BY column needed to have table0 name prefixed (if it didn't already have a table name), to avoid ambiguous column references
Aaron Marcuse-Kubitza
04:11 PM Revision 2185: sql.py: mk_select(): Fixed bug in joins where right_col had the table name prepended *before* it was copied for use with a different table name in join_using and join_not_equal
Aaron Marcuse-Kubitza
03:42 PM Revision 2184: Mapped some unmapped fields in DwC inputs
Aaron Marcuse-Kubitza
02:19 PM Revision 2183: Added mappings/for_review/DwC2-VegBIEN.specimens.fields.csv
Aaron Marcuse-Kubitza
01:21 PM Revision 2182: db_xml.py: put_table(): Fixed bug where didn't commit right after inserting node, but instead waited until children with fkeys to parent (independent of the node itself) were inserted
Aaron Marcuse-Kubitza
01:16 PM Revision 2181: sql.py: put_table(): insert_(): Use insert_select() instead of run_query_into() if new option pkeys_table_exists is on
Aaron Marcuse-Kubitza
12:51 PM Revision 2180: sql.py: mk_select(): Support joins with !=
Aaron Marcuse-Kubitza
12:45 PM Revision 2179: sql.py: mk_select(): Support only some join columns being join_using
Aaron Marcuse-Kubitza
12:40 PM Revision 2178: sql.py: put_table(): Renamed in_joins to insert_joins and joins to select_joins for clarity
Aaron Marcuse-Kubitza
12:21 PM Revision 2177: db_xml.py: put_table(): Support children with fkeys to parent
Aaron Marcuse-Kubitza
12:11 PM Revision 2176: sql.py: mk_select(): Make tuple optional for None literal values
Aaron Marcuse-Kubitza

05/13/2012

02:05 PM Revision 2175: sql.py: put_table(): Removed "SELECT statement missing a WHERE, LIMIT, or OFFSET clause" warnings
Aaron Marcuse-Kubitza
02:02 PM Revision 2174: bin/map: by_col: row_ct = 0 because it's unknown for now
Aaron Marcuse-Kubitza
02:00 PM Revision 2173: mk_select(): Support join conditions with literal values
Aaron Marcuse-Kubitza
01:42 PM Revision 2172: sql.py: mk_insert_select(): embeddable: Don't cache function_query because function def could change and then change back
Aaron Marcuse-Kubitza
01:35 PM Revision 2171: sql.py: with_savepoint(): Renamed savepoints to have "level" prefix, since the # indicates the level #
Aaron Marcuse-Kubitza
01:32 PM Revision 2170: sql.py: get_cur_query(): Also accept input params to combine with input_query, and pass input params when get_cur_query() is called
Aaron Marcuse-Kubitza
01:26 PM Revision 2169: sql.py: DbConn.run_query(): Pass input query to get_cur_query()
Aaron Marcuse-Kubitza
01:19 PM Revision 2168: sql.py: get_cur_query() and _add_cursor_info(): Support input_query param that will be used if the raw query is None. Pass input_query in DbConn.execute().
Aaron Marcuse-Kubitza
01:09 PM Revision 2167: sql.py: DbConn.run_query(): Check that query != None
Aaron Marcuse-Kubitza
01:05 PM Revision 2166: bin/map: out_is_db: Only rollback() and close() out_db if it was connected
Aaron Marcuse-Kubitza
01:04 PM Revision 2165: sql.py: DbConn: Added connected()
Aaron Marcuse-Kubitza
01:01 PM Revision 2164: sql.py: Wrapped calls to get_cur_query() that are used as strings in str(), because get_cur_query() can return None
Aaron Marcuse-Kubitza
12:57 PM Revision 2163: sql.py: next_version(): Versions start from 1, because first existing name was version 0
Aaron Marcuse-Kubitza
12:55 PM Revision 2162: put_table(): Use short name for temp_suffix now that version # will be added if needed
Aaron Marcuse-Kubitza
12:51 PM Revision 2161: sql.py: mk_select(): Parse join columns for literal values and table-scoped names as well
Aaron Marcuse-Kubitza
11:54 AM Revision 2160: mappings/DwC2-VegBIEN.specimens.csv: establishmentMeans: Call _toGrowthform on growthform
Aaron Marcuse-Kubitza
11:53 AM Revision 2159: schemas/vegbien.sql: Added _toGrowthform
Aaron Marcuse-Kubitza
11:19 AM Revision 2158: sql.py: put_table(): Changed temp_prefix to a suffix so main name won't be removed if name is truncated
Aaron Marcuse-Kubitza
11:14 AM Revision 2157: sql.py: mk_select(): fields: Support columns with tables. Changed syntax for literal values so that it wouldn't conflict with new syntax for columns with tables.
Aaron Marcuse-Kubitza
11:08 AM Revision 2156: iters.py: flatten(): If not an iterable, just return the value
Aaron Marcuse-Kubitza
10:32 AM Revision 2155: sql.py: put_table(): Pass in_pkeys and out_pkeys to run_query_into() by ref so they will be updated if the table names are changed
Aaron Marcuse-Kubitza
10:28 AM Revision 2154: sql.py: put_table(): Pass pkeys to run_query_into() by ref so it will be updated if the table name is changed
Aaron Marcuse-Kubitza
10:15 AM Revision 2153: sql.py: run_query_into(): If CREATE TABLE AS generates a DuplicateTableException, rename the table with a version # prepended
Aaron Marcuse-Kubitza
10:08 AM Revision 2152: sql.py: run_query_into(): Made into param a reference so that the function can change it, and renamed it to into_ref
Aaron Marcuse-Kubitza
09:36 AM Revision 2151: sql.py: run_query_into(): Made into param a reference so that the function can change it, and renamed it to into_ref
Aaron Marcuse-Kubitza
09:11 AM Revision 2150: sql.py: put_table(): If DuplicateKeyException: run_query_into() recoverably, so that DB errors such as DuplicateTableException will be parsed
Aaron Marcuse-Kubitza
09:07 AM Revision 2149: sql.py: Removed no-longer-needed try_insert()
Aaron Marcuse-Kubitza
09:05 AM Revision 2148: sql.py: Merged with_parsed_errors() into run_query() so all recoverable queries would automatically benefit from DB error message parsing. DbConn: Moved _add_cursor_info() to DbCursor.execute().
Aaron Marcuse-Kubitza
07:45 AM Revision 2147: sql.py: with_parsed_errors(): Raise DuplicateTableException for "relation already exists" errors instead of "table name specified more than once" errors
Aaron Marcuse-Kubitza
07:43 AM Revision 2146: sql.py: run_query_into(): Removed "DROP TABLE IF EXISTS" because sometimes when there are collisions in the temp table names, the code actually uses both "copies" of the temp table. Eventually, this situation will be resolved by adding a counter to the temp table name.
Aaron Marcuse-Kubitza
07:26 AM Revision 2145: sql.py: Cleaned up DbException's and subclasses' messages
Aaron Marcuse-Kubitza
07:26 AM Revision 2144: exc.py: ExceptionWithCause: Added cause_newline option to put the cause on its own line instead of on the message line
Aaron Marcuse-Kubitza
07:10 AM Revision 2143: sql.py: with_parsed_errors(): Also parse "table name specified more than once" errors as DuplicateTableExceptions
Aaron Marcuse-Kubitza
06:56 AM Revision 2142: sql.py: put_table(): Handle DuplicateKeyExceptions by running a select query on the unique constraint columns
Aaron Marcuse-Kubitza
06:14 AM Revision 2141: sql.py: mk_select(): Support tuples of tables, not just lists
Aaron Marcuse-Kubitza
05:29 AM Revision 2140: sql.py: with_parsed_errors(): Support table names that start with "_"
Aaron Marcuse-Kubitza
05:20 AM Revision 2139: sql.py: DbConn: Added with_savepoint(). with_savepoint(): Use new DbConn.with_savepoint().
Aaron Marcuse-Kubitza
04:13 AM Revision 2138: schemas/functions.sql: Added _toBool
Aaron Marcuse-Kubitza
04:12 AM Revision 2137: mappings/DwC2-VegBIEN.specimens.csv: establishmentMeans: Use _toBool on iscultivated, isnative
Aaron Marcuse-Kubitza
04:11 AM Revision 2136: schemas/functions.sql: Added _toBool
Aaron Marcuse-Kubitza
04:01 AM Revision 2135: schemas/functions.sql: Made trigger functions IMMUTABLE since they do not modify other tables
Aaron Marcuse-Kubitza
03:51 AM Revision 2134: sql.py: put_table(): Added support for putting just a window subset of the rows in the table. Removed "SELECT statement missing a WHERE, LIMIT, or OFFSET clause" warnings.
Aaron Marcuse-Kubitza
03:30 AM Revision 2133: sql.py: put_table(): Return the column where the pkeys are made available (the out_pkey) instead of taking it as an argument
Aaron Marcuse-Kubitza
03:20 AM Revision 2132: sql.py: put_table(): Get input pkeys corresponding to rows in insert and join together out_pkeys and in_pkeys into final pkeys table
Aaron Marcuse-Kubitza
01:04 AM Revision 2131: sql.py: put_table(): Fully support multiple in_tables, joined together using the main input table's pkey
Aaron Marcuse-Kubitza
01:02 AM Revision 2130: sql.py: mk_select(): joins: Fixed bug where USING-based joins did not have closing ")"
Aaron Marcuse-Kubitza
12:28 AM Revision 2129: db_xml.py: put_table(): Fixed bug where in_table was last in in_tables instead of first, causing it to be ignored by the current put_table() implementation, which only considers the first table name
Aaron Marcuse-Kubitza
12:17 AM Revision 2128: db_xml.py: put_table(): Fixed bug where pkeys_table returned by recursive call to put_table() needed to be prefixed with $ to be treated as an input column name rather than a literal value
Aaron Marcuse-Kubitza

05/09/2012

05:29 AM Revision 2127: sql.py: mk_select(): Support joins with USING, which can be used to merge multiple input cols into the same output col
Aaron Marcuse-Kubitza
04:42 AM Revision 2126: sql.py: mk_insert_select(): embeddable: Fixed bug where query that uses function was being sorted by its first column (the default mk_select() setting), when it should be left in its original order
Aaron Marcuse-Kubitza
04:36 AM Revision 2125: sql.py: put_table(): Take a dict mapping out to in cols instead of separate in and out cols lists
Aaron Marcuse-Kubitza
04:08 AM Revision 2124: sql.py: mk_select(): Joins: Reversed order of left_col and right_col in the joins dict as well, so the joined table's columns are the keys
Aaron Marcuse-Kubitza
04:05 AM Revision 2123: sql.py: mk_select(): Joins: Reversed order of left_col and right_col so the column of the table being joined is first, to match the form of a WHERE clause
Aaron Marcuse-Kubitza
03:56 AM Revision 2122: sql.py: mk_select(): Support joins
Aaron Marcuse-Kubitza
03:27 AM Revision 2121: sql.py: mk_select(): Accept a list of tables to join together (initial implementation just uses the first table)
Aaron Marcuse-Kubitza
02:26 AM Revision 2120: sql.py: mk_select(): Support ORDER BY clause. By default, order by the pkey, since PostgreSQL apparently doesn't do this automatically (and this was causing some staging table tests to fail).
Aaron Marcuse-Kubitza
02:04 AM Revision 2119: bin/map: In debug mode, print the row # and input row just like in error messages
Aaron Marcuse-Kubitza
01:51 AM Revision 2118: bin/map: verbose_errors also defaults to on in debug mode
Aaron Marcuse-Kubitza
01:39 AM Revision 2117: sql.py: add_row_num(): Make the row number column the primary key
Aaron Marcuse-Kubitza
12:36 AM Revision 2116: csv2db: Use new sql.cleanup_table() to map NULL-equivalents to NULL. Consider the empty string to be NULL.
Aaron Marcuse-Kubitza
12:35 AM Revision 2115: sql.py: Added cleanup_table()
Aaron Marcuse-Kubitza
12:33 AM Revision 2114: csvs.py: Added row filters
Aaron Marcuse-Kubitza

05/07/2012

11:14 PM Revision 2113: db_xml.py: put_table(): Fixed bug where relational functions were not being treated as value nodes, and thus their containing child was treated as a child with a backwards pointer instead of a field
Aaron Marcuse-Kubitza
11:12 PM Revision 2112: xml_func.py: Added is_func*() and is_xml_func*() and use them where their definitions were used
Aaron Marcuse-Kubitza
10:40 PM Revision 2111: db_xml.py: Added value() and use it where xml_dom.first_elem() was used
Aaron Marcuse-Kubitza
10:12 PM Revision 2110: mappings/DwC2-VegBIEN.specimens.csv: *Latitude/*Longitude: Moved _toDouble directly after the output col name, so that it's run after any translation functions (which all return strings). *ElevationInMeters: Added _toDouble around all output cols.
Aaron Marcuse-Kubitza
09:56 PM Revision 2109: xpath.py: get(): Create attrs: Fixed bug where attrs were created with last_only on, which caused attrs to get created multiple times if there were multiple attrs of the same name but different values, becase the last_only optimization would only check the last attr of that name
Aaron Marcuse-Kubitza
09:19 PM Revision 2108: mappings/DwC2-VegBIEN.specimens.csv: *Latitude/*Longitude: Use new _toDouble to convert strings to doubles (needed for by_col)
Aaron Marcuse-Kubitza
09:16 PM Revision 2107: schemas/functions.sql: Added _toDouble
Aaron Marcuse-Kubitza
09:16 PM Revision 2106: bin/map: When calling xml_func.process(), pass DB connection if available
Aaron Marcuse-Kubitza
09:15 PM Revision 2105: xml_func.py: process(): If DB with relational functions available (passed in via db param), call any non-local XML functions as relational funcs
Aaron Marcuse-Kubitza
09:09 PM Revision 2104: sql.py: put(): pkey param (now pkey_) defaults to table's pkey
Aaron Marcuse-Kubitza
08:30 PM Revision 2103: bin/map: by_col: In debug mode, print stripped XML tree that guides import
Aaron Marcuse-Kubitza
08:03 PM Revision 2102: vegbien_dest: Fixed bug where there was a missing line continuation char before schemas var
Aaron Marcuse-Kubitza
08:02 PM Revision 2101: sql.py: DbConn: Fixed bug where schemas db_config value needed to be split apart into strings. Fixed bug where current_setting() returned a value rather than an identifier, so it had to be used with set_config() instead of SET, and run after SET TRANSACTION ISOLATION LEVEL. Moved Input validation section before Database connections because it's used by Database connections.
Aaron Marcuse-Kubitza
07:29 PM Revision 2100: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
07:26 PM Revision 2099: vegbien.ERD.mwb: Changed lines to a configuration that MySQLWorkbench wouldn't keep resetting whenever the ERD was reopened
Aaron Marcuse-Kubitza
07:21 PM Revision 2098: vegbien_dest: Added "functions" to schemas
Aaron Marcuse-Kubitza
07:20 PM Revision 2097: sql.py: db_config: Added schemas param. DbConn: Use any schemas db_config value to set search_path.
Aaron Marcuse-Kubitza
06:58 PM Revision 2096: sql.py: add_row_num(): Name the column "_row_num" so that it doesn't conflict with any "row_num" column that's part of the table schema
Aaron Marcuse-Kubitza
06:50 PM Revision 2095: main Makefile: VegBIEN DB: functions schema: Renamed schemas/functions/clear to .../reset to reflect that it also resets the schema to what's in the dump file. schemas/functions/reset: Use now-available schemas/functions.sql to create the schema.
Aaron Marcuse-Kubitza
06:45 PM Revision 2094: Added autogen schemas/functions.sql
Aaron Marcuse-Kubitza
06:41 PM Revision 2093: schemas/vegbien.sql.make: Use new pg_dump_vegbien
Aaron Marcuse-Kubitza
06:41 PM Revision 2092: Added pg_dump_vegbien to dump a schema of the vegbien db
Aaron Marcuse-Kubitza
06:34 PM Revision 2091: main Makefile: VegBIEN DB: Added functions schema targets
Aaron Marcuse-Kubitza
06:09 PM Revision 2090: Makefile: $(confirm): Support a separate line outside of the highlighted line. Include the "Continue?" in the macro since all prompts include it.
Aaron Marcuse-Kubitza
05:55 PM Revision 2089: Makefile: VegBIEN DB: Display different warning message depending on whether entire DB or just current public schema is being deleted
Aaron Marcuse-Kubitza
05:38 PM Revision 2088: db_xml.py: put_table(): Recurse into forward pointers
Aaron Marcuse-Kubitza

05/05/2012

09:55 PM Revision 2087: sql.py: put_table(): Take multiple in_tables. Initial implementation just used the first in_table.
Aaron Marcuse-Kubitza
09:48 PM Revision 2086: sql.py: Added add_row_num(). put_table(): Add row_num to pkeys_table, so it can be joined with in_table's pkeys.
Aaron Marcuse-Kubitza
09:38 PM Revision 2085: sql.py: Added run_query_into() and use it in insert_select()
Aaron Marcuse-Kubitza
08:53 PM Revision 2084: sql.py: pkey(): Support escaped table names
Aaron Marcuse-Kubitza
07:32 PM Revision 2083: sql.py: mk_insert_select(): embeddable: Name the function alias "f" since it will just be wrapped in a nested SELECT, so the exact name doesn't matter (and won't be visible outside the nested SELECT anyway)
Aaron Marcuse-Kubitza
07:08 PM Revision 2082: db_xml.py: put_table(): Return the (table, col) where the pkeys are made available, now that this information is available from sql.put_table()
Aaron Marcuse-Kubitza
07:05 PM Revision 2081: sql.py: put_table(): Return just the name of the table where the pkeys are made available, since the column name in that table now equals the pkey name
Aaron Marcuse-Kubitza
06:58 PM Revision 2080: sql.py: mk_insert_select(): embeddable: Make the column returned by the function have the same name as the returning column
Aaron Marcuse-Kubitza
06:39 PM Revision 2079: db_xml.py: put_table() Use new sql.put_table()
Aaron Marcuse-Kubitza
06:39 PM Revision 2078: sql.py: Added put_table()
Aaron Marcuse-Kubitza
06:37 PM Revision 2077: sql.py: Added clean_name(). Use it where needed to make an escaped name appendable as a string.
Aaron Marcuse-Kubitza
05:53 PM Revision 2076: sql.py: Added with_parsed_errors() and use it in try_insert()
Aaron Marcuse-Kubitza
05:30 PM Revision 2075: sql.py: insert_select(): into != None: Fixed bug where cacheable was not passed through to DROP TABLE's run_query(), even though it was passed through to CREATE TABLE AS's run_query()
Aaron Marcuse-Kubitza
05:27 PM Revision 2074: db_xml.py: put_table(): Place pkeys in temp table
Aaron Marcuse-Kubitza
05:26 PM Revision 2073: sql.py: mk_insert_select(): Document that embeddable will cause the query to be fully cached, not just if it raises an exception. insert_select(): into != None: Pass recover and cacheable through to each run_query()
Aaron Marcuse-Kubitza
05:17 PM Revision 2072: sql.py: insert_select(): Support placing RETURNING values in temp table
Aaron Marcuse-Kubitza
04:40 PM Revision 2071: db_xml.py: put_table(): Support returning pkey from INSERT SELECT
Aaron Marcuse-Kubitza
04:38 PM Revision 2070: sql.py: mk_insert_select(): Support using an INSERT RETURNING statement as a nested SELECT
Aaron Marcuse-Kubitza

05/04/2012

07:15 PM Revision 2069: sql.py: mk_insert_select(): Removed unused params recover and cacheable
Aaron Marcuse-Kubitza
07:10 PM Revision 2068: sql.py: Added mogrify()
Aaron Marcuse-Kubitza
07:00 PM Revision 2067: db_xml.py: put_table(): Corrected @return doc
Aaron Marcuse-Kubitza
06:32 PM Revision 2066: sql.py: Added mk_insert_select() and use it in insert_select()
Aaron Marcuse-Kubitza
06:21 PM Revision 2065: db_xml.py: put_table(): Use new insert_select()
Aaron Marcuse-Kubitza
06:15 PM Revision 2064: sql.py: insert_select(): Changed order of cols and params arguments so select_query and params would be together
Aaron Marcuse-Kubitza
06:12 PM Revision 2063: sql.py: Added insert_select() and use it in insert()
Aaron Marcuse-Kubitza
04:55 PM Revision 2062: Calls to sql.esc_name*(): Removed preserve_case=True because it is now the default
Aaron Marcuse-Kubitza
04:51 PM Revision 2061: sql.py: esc_name_by_module(): Changed preserve_case to ignore_case, which defaults to False
Aaron Marcuse-Kubitza
04:49 PM Revision 2060: Calls to sql.esc_name*(): Removed preserve_case=True because it is now the default
Aaron Marcuse-Kubitza
04:47 PM Revision 2059: sql.py: esc_name_by_module(): preserve_case defaults to True
Aaron Marcuse-Kubitza
04:44 PM Revision 2058: sql.py: mk_select(): Escape all names used (table, column, cond, etc.)
Aaron Marcuse-Kubitza
04:33 PM Revision 2057: sql.py: esc_name_by_module(): If not enclosing name in quotes, call check_name() on it
Aaron Marcuse-Kubitza
04:30 PM Revision 2056: sql.py: mk_select(): Support literal values in the list of cols to select
Aaron Marcuse-Kubitza
03:22 PM Revision 2055: sql.py: mk_select(): Don't escape the table name, because it will either be check_name()d or it's already been escaped
Aaron Marcuse-Kubitza
03:11 PM Revision 2054: sql.py: Added mk_select(), and use it in select()
Aaron Marcuse-Kubitza
02:14 PM Revision 2053: bin/map: Always pass qual_name(table) to sql.select(). This is possible now that qual_name() can handle None schemas.
Aaron Marcuse-Kubitza
02:08 PM Revision 2052: db_xml.py: put_table(): Take separate in_table and in_schema names, instead of in_table and table_is_esc, because the in_schema is needed to scope the temp tables appropriately
Aaron Marcuse-Kubitza
02:04 PM Revision 2051: sql.py: qual_name(): If schema is None, don't prepend schema
Aaron Marcuse-Kubitza

05/03/2012

06:59 PM Revision 2050: bin/map, sql.py: Turned SQL query caching back on because benchmarks of just the caching on vs. off reveal that it does reduce processing time significantly. However, there is a slowdown that was introduced between the time caching was added and the time the same XML tree was used for each node, which was giving the false indication that the slowdown was due to the caching.
Aaron Marcuse-Kubitza
06:44 PM Revision 2049: bin/map: Turn SQL query caching off by default
Aaron Marcuse-Kubitza
06:39 PM Revision 2048: bin/map: Added cache_sql env var to enable SQL query caching
Aaron Marcuse-Kubitza
06:39 PM Revision 2047: sql.py: Make caching DbConn enablable. Turn caching off by default because recent benchmarks (n=1000) were showing that it slows things down.
Aaron Marcuse-Kubitza
04:53 PM Revision 2046: bin/map: Added new verbose_errors mode, enabled in test mode and off otherwise, which controls whether the output row and tracebacks are included in error messages. Having this off in import mode will reduce the size of error logs so they don't fill up the vegbiendev hard disk as quickly.
Aaron Marcuse-Kubitza
04:51 PM Revision 2045: exc.py: print_ex(): Added detail option to turn off traceback
Aaron Marcuse-Kubitza
04:10 PM Revision 2044: bin/map: Turn parallel processing off by default. This should fix "Cannot allocate memory" errors in large imports.
Aaron Marcuse-Kubitza

05/01/2012

07:58 AM Revision 2043: bin/map: in_is_db: Don't cache the main SELECT query
Aaron Marcuse-Kubitza
07:56 AM Revision 2042: bin/map: by_col: Use the created template, which already has the column names in it, instead of mapping a sample row
Aaron Marcuse-Kubitza
07:50 AM Revision 2041: bin/map: Fixed bug where db_xml could not be imported twice, or it was treated as an undefined variable for some reason
Aaron Marcuse-Kubitza
07:45 AM Revision 2040: bin/map: map_table(): Make each column a db_xml.ColRef instead of a bare index, so that it will appear as the column name when converted to a string. This will provide better debugging info in the template tree and also avoid needing to create a separate sample row in by_col.
Aaron Marcuse-Kubitza
07:33 AM Revision 2039: db_xml.py: Added ColRef
Aaron Marcuse-Kubitza
06:33 AM Revision 2038: bin/map: Fixed bug where row count was off by one if all rows in the input were exhausted, because the row that raises StopIteration was counting as a row
Aaron Marcuse-Kubitza
06:13 AM Revision 2037: main Makefile: VegBIEN DB: mk_db: Use template1 because it has PROCEDURAL LANGUAGE plpgsql already installed and we aren't using an encoding other than UTF8
Aaron Marcuse-Kubitza
06:11 AM Revision 2036: Moved "CREATE PROCEDURAL LANGUAGE plpgsql" to main Makefile so that it would only run when the DB is created, not when the public schema is reinstalled. This is only relevant on PostgreSQL < 9.x, where the plpgsql language is not part of template0.
Aaron Marcuse-Kubitza
05:56 AM Revision 2035: Renamed parallel.py to parallelproc.py to avoid conflict with new system parallel module on vegbiendev
Aaron Marcuse-Kubitza
05:43 AM Revision 2034: Makefile: VegBIEN DB: public schema: Added schemas/rotate
Aaron Marcuse-Kubitza
05:34 AM Revision 2033: bin/map: Fixed bug in input rows processed count where the count would be off by 1, because the for loop would leave i at the index of the last row instead of one-past-the-last
Aaron Marcuse-Kubitza
04:44 AM Revision 2032: bin/map: Use the same XML tree for each row in DB outputs, to eliminate time spent creating the tree from the XPaths for each row
Aaron Marcuse-Kubitza
04:08 AM Revision 2031: bin/map: map_table(): Resolve each prefix into a separate mapping, which is collision-eliminated, instead of resolving values from multiple prefixes when each individual row is mapped
Aaron Marcuse-Kubitza
03:50 AM Revision 2030: bin/map: Moved collision-prevention code to map_rows() so it would only run if there were mappings, and so that it would run after any mappings preprocessing by map_table() that creates more collisions
Aaron Marcuse-Kubitza
03:45 AM Revision 2029: bin/map: Prevent collisions if multiple inputs mapping to same output
Aaron Marcuse-Kubitza
02:02 AM Revision 2028: mappings/DwC1-DwC2.specimens.csv: Mapped collectorNumber and recordNumber to recordNumber with _alt so they wouldn't collide when every input column, even empty ones, are created in the XML tree
Aaron Marcuse-Kubitza
12:42 AM Revision 2027: bin/map: If out_is_db, in debug mode, print each row's XML tree and each value that it's putting
Aaron Marcuse-Kubitza
12:36 AM Revision 2026: bin/map: If out_is_db, in debug mode, print the template XML tree used to insert a sample row into the DB
Aaron Marcuse-Kubitza

04/30/2012

11:57 PM Revision 2025: bin/map: map_table(): When translating mappings to column indexes, use appends to a new list instead of deletions from an existing list to simplify the algorithm
Aaron Marcuse-Kubitza
11:20 PM Revision 2024: union: Omit mappings that are mapped *to* in the input map, in addition to mappings that were overridden. This prevents multiple outputs being created for both the renamed and original mappings, causing duplicate output nodes when one XML tree is used for all rows.
Aaron Marcuse-Kubitza
11:18 PM Revision 2023: union: Omit mappings that are mapped *to* in the input map, in addition to mappings that were overridden. This prevents multiple outputs being created for both the renamed and original mappings, causing duplicate output nodes when one XML tree is used for all rows.
Aaron Marcuse-Kubitza
11:17 PM Revision 2022: input.Makefile: Maps building: Via maps cleanup: subtract: Include comment column so commented mappings are never removed
Aaron Marcuse-Kubitza
11:07 PM Revision 2021: subtract: Support "ragged rows" that have fewer columns than the specified column numbers
Aaron Marcuse-Kubitza
11:06 PM Revision 2020: util.py: list_subset(): Added default param to specify the value to use for invalid indexes (if any)
Aaron Marcuse-Kubitza
09:44 AM Revision 2019: mappings/VegX-VegBIEN.stems.csv: Mappings with multiple inputs for the same output: Use _alt, etc. to map the multiple inputs to different places in the XML tree, so that when using a pregenerated tree, the empty leaves for each input will not collide with each other
Aaron Marcuse-Kubitza
09:20 AM Revision 2018: mappings/VegX-VegBIEN.stems.csv: Changed XPath references (using "$") to XML function references using _ref where needed to make them work even on a pre-made XML tree used by all rows
Aaron Marcuse-Kubitza
09:13 AM Revision 2017: xml_func.py: Added _ref to retrieve a value from another XML node
Aaron Marcuse-Kubitza
06:12 AM Revision 2016: xml_func.py: Made all functions take a 2nd node param, which contains the func node itself
Aaron Marcuse-Kubitza
04:15 AM Revision 2015: bin/map: If outputting to a DB, also create output XML elements for NULL input values. This will help with the transition to using the same XML tree for all rows.
Aaron Marcuse-Kubitza
04:09 AM Revision 2014: xml_func.py: _label: return None on empty input
Aaron Marcuse-Kubitza
03:46 AM Revision 2013: mappings/VegX-VegBIEN.stems.csv: Added _collapse around subtrees that need to be removed if they are created around a NULL value
Aaron Marcuse-Kubitza
03:40 AM Revision 2012: xml_func.py: Added _collapse to collapse a subtree if the "value" element in it is NULL
Aaron Marcuse-Kubitza
01:44 AM Revision 2011: schemas/vegbien.sql: definedvalue: Made definedvalue nullable so that each row of a datasource can have a uniform structure in VegBIEN, and to support reusing the same XML DOM tree for each row
Aaron Marcuse-Kubitza
01:11 AM Revision 2010: xpath.py: Added is_xpath()
Aaron Marcuse-Kubitza
01:10 AM Revision 2009: xml_dom.py: set_value(): If value is None and node is Element, remove value node entirely instead of setting node's value to None
Aaron Marcuse-Kubitza
01:02 AM Revision 2008: xml_dom.py: Added value_node(). Use new value_node() in value() and set_value(). set_value(): If the node already has a value node, reuse it instead of appending a new value node.
Aaron Marcuse-Kubitza
12:35 AM Revision 2007: xpath.py: put_obj(): Return the id_attr_node using get_1() because it should only be one node
Aaron Marcuse-Kubitza
12:30 AM Revision 2006: xml_func.py: _simplifyPath: Also treat the elem as empty if the required node exists but is empty
Aaron Marcuse-Kubitza
12:04 AM Revision 2005: db_xml.py: put_table(): Added part of put() code that should be common to both functions
Aaron Marcuse-Kubitza

04/27/2012

06:16 PM Revision 2004: xpath.py: put_obj(): Return a tuple of the inserted node and the id attr node
Aaron Marcuse-Kubitza
06:13 PM Revision 2003: xpath.py: set_id(): When creating the id_path, use obj() (which deepcopy()s the entire path) because it prevents pointers w/o targets
Aaron Marcuse-Kubitza
06:05 PM Revision 2002: xpath.py: set_id(): When creating the id_path, deepcopy() the id_elem because its keys will change in the main copy
Aaron Marcuse-Kubitza
05:47 PM Revision 2001: xpath.py: set_id(): Return the path to the ID attr, which can be used to change the ID
Aaron Marcuse-Kubitza
05:25 PM Revision 2000: xpath.py: put_obj(): Return the inserted node so it can be used to change the inserted value
Aaron Marcuse-Kubitza
05:08 PM Revision 1999: main Makefile: Maps validation: Fixed bug where there would be infinite recursion with the Maps validation section before the Subdir forwarding section (it's unknown why this is necessary)
Aaron Marcuse-Kubitza

04/26/2012

07:12 PM Revision 1998: db_xml.py: put_table(): Added commit param to specify whether to commit after each query
Aaron Marcuse-Kubitza
06:55 PM Revision 1997: bin/map: in_is_db: by_col: Use new put_table() (defined but not implemented yet)
Aaron Marcuse-Kubitza
06:54 PM Revision 1996: db_xml.py: Added put_table() (without implementation)
Aaron Marcuse-Kubitza
06:52 PM Revision 1995: xml_func.py: strip(): Remove _ignore XML funcs completely instead of replacing them with their values
Aaron Marcuse-Kubitza
06:26 PM Revision 1994: bin/map: in_is_db: by_col: Prefix each input column name by "$"
Aaron Marcuse-Kubitza
06:11 PM Revision 1993: bin/map: in_is_db: by_col: Strip off XML functions
Aaron Marcuse-Kubitza
06:09 PM Revision 1992: xml_func.py: Added strip(). pop_value(): Support custom name of value param.
Aaron Marcuse-Kubitza
05:44 PM Revision 1991: bin/map: in_is_db: by_col: Create XML tree of sample row, with the input column names as the values. This tree will guide the sequencing and creation of the column-based queries.
Aaron Marcuse-Kubitza
05:43 PM Revision 1990: input.Makefile: use_staged env var: defaults to on if by_col is on
Aaron Marcuse-Kubitza
05:00 PM Revision 1989: bin/map: Only turn on by_col optimization if mapping to same DB, rather than requiring each place that checks by_col to also check whether mapping to same DB
Aaron Marcuse-Kubitza

04/24/2012

06:32 PM Revision 1988: input.Makefile: Testing: Don't abort tester if only staging test fails, in case staging table missing
Aaron Marcuse-Kubitza
06:25 PM Revision 1987: input.Makefile: Testing: When cleaning up test outputs, remove everything that doesn't end in .ref
Aaron Marcuse-Kubitza
06:11 PM Revision 1986: input.Makefile: Testing: Added test/import.%.staging.out test to test the staging tables. Sources: cat: Updated Usage comment to include the "inputs/<datasrc>/" prefix the user would need to add when running make.
Aaron Marcuse-Kubitza
05:33 PM Revision 1985: bin/map: Fixed bug where mapping to same DB wouldn't work because by-column optimization wasn't implemented yet, by turning it off by default and allowing it to be enabled with an env var
Aaron Marcuse-Kubitza
05:25 PM Revision 1984: bin/map: DB inputs: Use by-column optimization if mapping to same DB (with skeleton code for optimization's implementation)
Aaron Marcuse-Kubitza
05:12 PM Revision 1983: input.Makefile: Mapping: Use the staging tables instead of any flat files if use_staged is specified
Aaron Marcuse-Kubitza
05:10 PM Revision 1982: bin/map: Support custom schema name. Support input table/schema override via env vars, in case the map spreadsheet was written for a different input format.
Aaron Marcuse-Kubitza
05:01 PM Revision 1981: sql.py: qual_name(): Fixed bugs where esc_name() nested func couldn't have same name as outer func, and esc_name() needed to be invoked without the module name because it's in the same module. select(): Support already-escaped table names.
Aaron Marcuse-Kubitza
04:16 PM Revision 1980: main Makefile: $(psqlAsAdmin): Tell sudo to preserve env vars so PGOPTIONS is passed to psql
Aaron Marcuse-Kubitza
03:33 PM Revision 1979: root map: Fill in defaults for inputs from VegBIEN, as well as outputs to it
Aaron Marcuse-Kubitza
02:59 PM Revision 1978: disown_all: Updated to use main function, local vars, $self, etc. like other bash scripts run using "."
Aaron Marcuse-Kubitza
02:55 PM Revision 1977: vegbien_dest: Fixed bug where it would give a usage error if run from a makefile rule, because the BASH_LINENO would be 0, by also checking if ${BASH_ARGV[0]} is ${BASH_SOURCE[0]}
Aaron Marcuse-Kubitza
02:28 PM Revision 1976: postgres_vegbien: Fixed bug where interpreter did not match vegbien_dest's new required interpreter of /bin/bash
Aaron Marcuse-Kubitza
02:23 PM Revision 1975: vegbien_dest: Changed interpreter to /bin/bash. Removed comment that it requires var bien_password.
Aaron Marcuse-Kubitza
02:20 PM Revision 1974: postgres_vegbien: Removed no longer needed retrieval of bien_password
Aaron Marcuse-Kubitza
02:20 PM Revision 1973: vegbien_dest: Get bien_password by searching relative to $self, which we now have a way to get in a bash script (${BASH_SOURCE[0]}), rather than requiring the caller to set it. Provide usage error if run without initial ".".
Aaron Marcuse-Kubitza
02:12 PM Revision 1972: input.Makefile: Staging tables: import/install-%: Use new quiet option to determine whether to tee output to terminal. Don't use log option because that's always set to true except in test mode, which doesn't apply to installs.
Aaron Marcuse-Kubitza
02:12 PM Revision 1971: input.Makefile: Staging tables: import/install-%: Use new quiet option to determine whether to tee output to terminal. Don't use log option because that's always set to true except in test mode, which doesn't apply to installs.
Aaron Marcuse-Kubitza
01:56 PM Revision 1970: main Makefile: PostgreSQL: Edit /etc/phppgadmin/apache.conf to replace "deny from all" with "allow from all", instead of uncommenting an "allow from all" that may not be there
Aaron Marcuse-Kubitza
01:35 PM Revision 1969: input.Makefile: Sources: Fixed bug where cat was defined before $(tables), by moving Sources after Existing maps discovery and putting just $(inputFiles) and $(dbExport) from Sources at the beginning of Existing maps discovery
Aaron Marcuse-Kubitza
01:05 PM Revision 1968: sql.py: Made truncate(), tables(), empty_db() schema-aware. Added qual_name(). tables(): Added option to filter tables by a LIKE pattern.
Aaron Marcuse-Kubitza
12:34 PM Revision 1967: main Makefile: VegBIEN DB: Install public schema in a separate step, so that it can be dropped without dropping the entire DB (which also contains staging tables that shouldn't be dropped when there is a schema change). Added schemas/install, schemas/uninstall, implicit schemas/reinstall to manage the public schema separately from the rest of the DB. Moved Subdir forwarding to the bottom so overridden targets are not forwarded. README.TXT: Since `make reinstall_db` would drop the entire DB, tell user to run new `make schemas/reinstall` instead to reinstall (main) DB from schema.
Aaron Marcuse-Kubitza
12:30 PM Revision 1966: schemas/postgresql.Mac.conf: Set unix_socket_directory to the new dir it seems to be using, which is now /tmp
Aaron Marcuse-Kubitza
11:43 AM Revision 1965: csv2db: Fixed bug where extra columns were not truncated in INSERT mode. Replace empty column names with the column # to avoid errors with CSVs that have trailing ","s, etc.
Aaron Marcuse-Kubitza
11:41 AM Revision 1964: streams.py: StreamIter: Define readline() as a separate method so it can be overridden, and all calls to self.next() will use the overridden readline(). This fixes a bug in ProgressInputStream where incremental counts would not be displayed and it would end with "not all input read" if the StreamIter interface was used instead of readline().
Aaron Marcuse-Kubitza

04/23/2012

09:57 PM Revision 1963: csv2db: Fall back to manually inserting each row (autodetecting the encoding for each field) if COPY FROM doesn't work
Aaron Marcuse-Kubitza
09:56 PM Revision 1962: streams.py: FilterStream: Inherit from StreamIter so that all descendants automatically have StreamIter functionality
Aaron Marcuse-Kubitza
09:42 PM Revision 1961: sql.py: insert(): Support using the default value for columns designated with the special value sql.default
Aaron Marcuse-Kubitza
09:21 PM Revision 1960: sql.py: insert(): Support rows that are just a list of values, with no columns. Support already-escaped table names.
Aaron Marcuse-Kubitza
08:54 PM Revision 1959: strings.py: Added contains_any()
Aaron Marcuse-Kubitza
08:54 PM Revision 1958: csvs.py: reader_and_header(): Use make_reader()
Aaron Marcuse-Kubitza
08:07 PM Revision 1957: Added reinstall_all to reinstall all inputs at once
Aaron Marcuse-Kubitza
08:06 PM Revision 1956: with_all: Documented that it must be run from the root svn directory
Aaron Marcuse-Kubitza
08:05 PM Revision 1955: input.Makefile: Staging tables: import/install-%: Only install staging table if input contains only CSV sources. Changed $(isXml) to $(isCsv) (negated) everywhere because rules almost always only run something if input contains only CSV sources, rather than if input contains XML sources.
Aaron Marcuse-Kubitza
07:21 PM Revision 1954: input.Makefile: Staging tables: import/install-%: Output load status to log file if log option is set
Aaron Marcuse-Kubitza
07:00 PM Revision 1953: Scripts that are meant to be run in the calling shell: Fixed bug where running the script inside another script would make the script think it was being run as a program, and abort with a usage error
Aaron Marcuse-Kubitza
06:56 PM Revision 1952: Scripts that are meant to be run in the calling shell: Fixed bug where running the script as a program (without initial ".") wouldn't be able to call return in something that was not a function. Converted all code to a <script_name>_main method so that return would work properly again. Converted all variables to local variables.
Aaron Marcuse-Kubitza
06:38 PM Revision 1951: env_password: return instead of exit if password not yet stored, in case user is running it from a shell without the initial "-" argument. (This would be the case if the user is just testing out the script, instead of using a command that env_password directs them to run.)
Aaron Marcuse-Kubitza
05:43 PM Revision 1950: env_password: Use ${BASH_SOURCE[0]} for $self and $self for $0. return instead of exit on usage error in case user is running it from a shell.
Aaron Marcuse-Kubitza
05:36 PM Revision 1949: stop_imports: Use ${BASH_SOURCE[0]} for $self and $self for $0
Aaron Marcuse-Kubitza
05:36 PM Revision 1948: import_all: Use new with_all. Use ${BASH_SOURCE[0]} for $self and $self for $0.
Aaron Marcuse-Kubitza
05:34 PM Revision 1947: Added with_all to run a make target on all inputs at once
Aaron Marcuse-Kubitza
05:05 PM Revision 1946: Made row #s 1-based to the user to match up with the staging table row #s
Aaron Marcuse-Kubitza
04:59 PM Revision 1945: bin/map: Fixed bug where limit passed to sql.select() was end instead of the # rows, causing extra rows to be fetched when start > 0. Documented that row #s start with 0.
Aaron Marcuse-Kubitza
04:19 PM Revision 1944: Removed no longer needed csv2ddl
Aaron Marcuse-Kubitza
04:19 PM Revision 1943: input.Makefile: Staging tables: import/install-%: Use new csv2db instead of csv2ddl/$(psqlAsBien), because it handles translating encodings properly
Aaron Marcuse-Kubitza
04:14 PM Revision 1942: Added csv2db to load a command's CSV output stream into a PostgreSQL table
Aaron Marcuse-Kubitza
 

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