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From 08/19/2013 to 09/17/2013

09/17/2013

10:05 PM Revision 11000: bugfix: lib/runscripts/*: calls to rm: use `rm -f` instead to avoid an error (which aborts the program) if the file does not yet exist
Aaron Marcuse-Kubitza

09/16/2013

07:51 AM Revision 10999: inputs/VegBank/: added taxon_observation.** left-join of the tables, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource
Aaron Marcuse-Kubitza
07:48 AM Revision 10998: inputs/VegBank/taxonobservation_/create.sql: join starting with taxoninterpretation so that we can use the taxoninterpretation_id as the row_num (text strings, formed from concatenated #s cannot be used as a row_num). there is only 1 taxonobservation without a taxoninterpretation, so we can just include one row for each taxoninterpretation.
Aaron Marcuse-Kubitza
02:32 AM Revision 10997: bugfix: inputs/VegBank/taxonobservation_/test.xml.ref: updated after reloading staging table. this fixed a bug where observationGranularity apparently either did not exist or was not the right type of constant column to be properly inlined the last time the tester was run. the inlining is important for using metadata switches to generate the correct XML import script.
Aaron Marcuse-Kubitza
12:13 AM Revision 10996: bugfix: lib/sh/make.sh: don't allow rm to override remake if an invoked script uses this file. this fixes a bug in `rm=1 inputs/.../.../run` where the remake action would be invoked on the map_table command even though it had been suppressed, because it was run externally (i.e. make.sh was reloaded) and the rm=1 flag was still active
Aaron Marcuse-Kubitza

09/15/2013

10:50 PM Revision 10995: schemas/VegCore/ERD/VegCore.ERD.png.map.htm: reordered in dependency order: moved traceable before party because party is a subclass of it
Aaron Marcuse-Kubitza
10:02 PM Revision 10994: bugfix: inputs/input.Makefile: `%/install: %/create.sql`: don't include %/header.csv as a target, so that it won't get deleted if the install fails (especially on a step that happens *after* the header is exported)
Aaron Marcuse-Kubitza
09:07 PM Revision 10993: inputs/VegBank/taxonobservation_/postprocess.sql: added primary key. note that the inserted row count changes, most likely because the rows are now in sorted order.
Aaron Marcuse-Kubitza
01:54 PM Revision 10992: inputs/VegBank/stemcount_/postprocess.sql: added primary key. note that the inserted row count changes, most likely because the rows are now in sorted order.
Aaron Marcuse-Kubitza
01:27 PM Revision 10991: bugfix: schemas/util.sql: mk_subset_by_row_num_func(): need explicit ORDER BY on the row_num_col, to prevent PostgreSQL from sorting the rows in reverse (they will be sorted because of the index scan, but the direction is otherwise indeterminate)
Aaron Marcuse-Kubitza
01:20 PM Revision 10990: schemas/util.sql: mk_subset_by_row_num_func(): support tables whose pkeys don't start with 1 (such as the VegBank tables), by calculating the smallest row_num from the table
Aaron Marcuse-Kubitza
01:03 PM Revision 10989: schemas/util.sql: offset2row_num(), limit2row_num(): added optional min_row_num, for tables whose serial pkeys start from a value other than 1
Aaron Marcuse-Kubitza
12:36 PM Revision 10988: schemas/util.sql: added qual_name(regclass)
Aaron Marcuse-Kubitza
08:36 AM Revision 10987: schemas/util.sql: added esc_name__append()
Aaron Marcuse-Kubitza
08:09 AM Revision 10986: schemas/util.sql: added col__min()
Aaron Marcuse-Kubitza
07:34 AM Revision 10985: schemas/util.sql: added limit2row_num() and use it in mk_subset_by_row_num_func() for clarity
Aaron Marcuse-Kubitza
07:26 AM Revision 10984: schemas/util.sql: added offset2row_num() and use it in mk_subset_by_row_num_func() for clarity
Aaron Marcuse-Kubitza
07:25 AM Revision 10983: bugfix: schemas/Makefile: `%/install: vegbien.sql`: when replacing public with the specified schema name, only perform the replacement if the schema is named something other than public. this prevents text like "public schema" inside comments from being "-escaped.
Aaron Marcuse-Kubitza
06:50 AM Revision 10982: planning/timeline/timeline.2013.xls: updated for progress
Aaron Marcuse-Kubitza
06:25 AM Revision 10981: bugfix: /README.TXT: to backup files not in Time Machine: need to use -E option to sudo to preserve env, after installing the latest system update
Aaron Marcuse-Kubitza
05:47 AM Revision 10980: schemas/VegCore/ERD/VegCore.ERD.png.map.htm: reordered in dependency order
Aaron Marcuse-Kubitza
05:40 AM Revision 10979: schemas/VegCore/VegCore.ERD.mwb: regenerated exports and udpated image map
Aaron Marcuse-Kubitza
05:17 AM Revision 10978: schemas/VegCore/VegCore.ERD.mwb: party: added required name field
Aaron Marcuse-Kubitza
05:12 AM Revision 10977: schemas/VegCore/VegCore.ERD.mwb: fixed table positions
Aaron Marcuse-Kubitza
05:09 AM Revision 10976: schemas/VegCore/VegCore.ERD.mwb: event: added event_unique_within_parent, event_unique_within_place unique indexes
Aaron Marcuse-Kubitza
04:57 AM Revision 10975: schemas/VegCore/VegCore.ERD.mwb: source: split into source and dataset tables, since many of the source fields (first_publisher, data_owners, contacts) were only applicable to datasets. note that a dataset is specifically something *requiring attribution*, while a source just indicates where something came from. non-dataset sources are useful e.g. as the taxon_concept.according_to.
Aaron Marcuse-Kubitza
03:48 AM Revision 10974: schemas/VegCore/VegCore.ERD.mwb: source.owners: renamed to data_owners for clarity. documented that this is the parties who must be given attribution, such as copyrightholders.
Aaron Marcuse-Kubitza
03:39 AM Revision 10973: schemas/VegCore/VegCore.ERD.mwb: source: allow multiple contacts
Aaron Marcuse-Kubitza
03:34 AM Revision 10972: schemas/VegCore/VegCore.ERD.mwb: source: added contact (different from owners)
Aaron Marcuse-Kubitza
03:23 AM Revision 10971: schemas/VegCore/VegCore.ERD.mwb: model options: templates for new column names, etc.: configured to our conventions (pkey is "id"; columns are unique within the table rather than being prefixed with the table name)
Aaron Marcuse-Kubitza
03:08 AM Revision 10970: schemas/VegCore/VegCore.ERD.mwb: source: allow multiple data owners
Aaron Marcuse-Kubitza
03:04 AM Revision 10969: schemas/VegCore/VegCore.ERD.mwb: documented that record is the record in the *source* data, and traceable is a row that can have associated source information
Aaron Marcuse-Kubitza
03:03 AM Revision 10968: schemas/VegCore/VegCore.ERD.mwb: removed relationship table, because this is too general, and custom relationships between entities are better indicated in the applicable hstore extender field for the table in question. record: split into record and traceable tables, where record is instead the record in the *source* data, and traceable indicates that a row has associated source information.
Aaron Marcuse-Kubitza
02:36 AM Revision 10967: bugfix: schemas/VegCore/VegCore.ERD.mwb: party_list_entry: use just a single id field as the primary key, because the pkey must be a single text string in order to uniquely identify the row by a global ID
Aaron Marcuse-Kubitza
02:25 AM Revision 10966: schemas/VegCore/VegCore.ERD.mwb: party_list_entry: added role field
Aaron Marcuse-Kubitza
02:01 AM Revision 10965: schemas/VegCore/VegCore.ERD.mwb: regenerated exports and udpated image map
Aaron Marcuse-Kubitza
01:53 AM Revision 10964: schemas/VegCore/VegCore.ERD.mwb: taxa_sampling_event: link directly to project, so that you don't have to search the parent event hierarchy to find the associated project
Aaron Marcuse-Kubitza
01:50 AM Revision 10963: schemas/VegCore/VegCore.ERD.mwb: fixed table positions
Aaron Marcuse-Kubitza
01:48 AM Revision 10962: schemas/VegCore/VegCore.ERD.mwb: spaced tables out more
Aaron Marcuse-Kubitza
01:36 AM Revision 10961: schemas/VegCore/VegCore.ERD.mwb: taxon_occurrence: require all taxon_occurrences to have an associated within_place (which may be set to Earth if the coordinates/placename is unknown)
Aaron Marcuse-Kubitza
01:30 AM Revision 10960: schemas/VegCore/VegCore.ERD.mwb: moved the plot table next the the section label for the plots half of the page
Aaron Marcuse-Kubitza
01:19 AM Revision 10959: schemas/VegCore/VegCore.ERD.mwb: taxon_observation: allow any taxon_observation to link directly to a taxa_sampling_event, not just aggregate_observation. this allows any taxon_observation's methodology information to be found directly by joining to taxa_sampling_event. previously, one had to join to event.parent and then taxa_sampling_event, and it was not clear that event.parent would even *be* a taxa_sampling_event.
Aaron Marcuse-Kubitza
01:07 AM Revision 10958: schemas/VegCore/VegCore.ERD.mwb: aggregate_observation: link to rather than being a taxa_sampling_event, because taxa_sampling_event was actually intended to be the container event in which various types of taxon_observations occur, rather than a type of taxon_observation itself. rearranged tables to avoid them covering any lines.
Aaron Marcuse-Kubitza

09/14/2013

11:53 PM Revision 10957: schemas/VegCore/VegCore.ERD.mwb: renamed GNRS & geovalidation steps to just geoscrubbing steps for clarity
Aaron Marcuse-Kubitza
11:48 PM Revision 10956: schemas/VegCore/VegCore.ERD.mwb: taxon_occurrence: added within_place to allow easily locating all the taxon_occurrences in a plot. (some taxon_occurrences require within_place, but there was no common superclass field to allow joining to just a single table.)
Aaron Marcuse-Kubitza
11:24 PM Revision 10955: schemas/VegCore/ERD/VegCore.ERD.png.map.htm: moved reobservable tables (individual, specimen, etc.) before aggregate_observation tables because these are less abstract
Aaron Marcuse-Kubitza
11:21 PM Revision 10954: schemas/VegCore/VegCore.ERD.mwb: regenerated exports and udpated image map
Aaron Marcuse-Kubitza
11:15 PM Revision 10953: schemas/VegCore/VegCore.ERD.mwb: individual_count: inherit from taxon_presence because this is also a type of taxon_observation (and specifically, a taxon_presence), in addition to the general taxon_presence it's associated with. it is possible e.g. for different diameter classes to be counted by different collectors, and thus to need separate taxon_observations to store the different collectors.
Aaron Marcuse-Kubitza
11:07 PM Revision 10952: schemas/VegCore/VegCore.ERD.mwb: added taxon_occurrence to store the underlying occurrence for each taxon_observation. we cannot use reobservable for this because not all taxon_observations are reobservable, but the one-time observations still have an associated occurrence. moved reobservable.current_determination to taxon_occurrence and renamed it to current_observation (this can be used to find the latest observation for each occurrence).
Aaron Marcuse-Kubitza
09:47 PM Revision 10951: planning/timeline/timeline.2013.xls: added spacing between later column and weeks to make clear that dots in the later column do not correspond to a week
Aaron Marcuse-Kubitza
09:26 PM Revision 10950: inputs/FIA/occurrence_all/: renamed to taxon_observation.** to clarify what an occurrence is. taxon_observation has the same meaning as in VegCore, where *each taxon_determination is considered a separate taxon_observation* of the associated specimen or vouchered plant (vegpath.org/VegCore/ERD/). (note that having multiple taxon_determinations only makes sense when there is something to reobserve.) the .** is SQL dotpath syntax (wiki.vegpath.org/SQL_dotpaths) for the recursive expansion of all tables to which taxon_observation has forward fkeys (i.e. "the left-join").
Aaron Marcuse-Kubitza
09:01 PM Revision 10949: inputs/FIA/occurrence_all/postprocess.sql: use :table_str var instead of hardcoding the table name as occurrence_all, to avoid needing to change this file when renaming the view
Aaron Marcuse-Kubitza
05:38 PM Revision 10948: inputs/FIA/occurrence_all/postprocess.sql: renamed occurrence_all--row_num to just row_num because this is for the entire view, rather than a specific table in it, and thus does not need a disambiguating table prefix. this also avoids embedding the view name in its own columns.
Aaron Marcuse-Kubitza
04:34 PM Revision 10947: inputs/FIA/*/map.csv: use -- to separate the table and column name instead of - , to conform with the u-name format (wiki.vegpath.org/u-name#format), which works even when only one of _- can be used in the name. -s are needed in this case to linewrap the column on a separate line as the table in phpPgAdmin.
Aaron Marcuse-Kubitza
04:20 PM Revision 10946: lib/runscripts/datasrc_dir.run: added postprocess target to run postprocess in just the table subdirs, skipping any additional subdirs that don't have this target
Aaron Marcuse-Kubitza
04:19 PM Revision 10945: lib/runscripts/datasrc_dir.run: @subdirs: moved import_order.txt subdirs into separate @table_subdirs, which provides access to just the table subdirs when the user adds other dirs to @subdirs
Aaron Marcuse-Kubitza

09/12/2013

06:43 PM Revision 10944: inputs/VegBank/: prepended the table name to each column name to prevent column collisions, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource
Aaron Marcuse-Kubitza
06:17 PM Revision 10943: inputs/VegBank/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource
Aaron Marcuse-Kubitza
06:13 PM Revision 10942: bugfix: inputs/VegBank/stemlocation_/map.csv: put columns in table order, which is needed by new-style import
Aaron Marcuse-Kubitza
05:57 PM Revision 10941: inputs/VegBank/stemlocation_/: translated one-to-many mappings to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
Aaron Marcuse-Kubitza
05:49 PM Revision 10940: bugfix: inputs/VegBank/taxonobservation_/map.csv: put columns in table order, which is needed by new-style import
Aaron Marcuse-Kubitza
05:26 PM Revision 10939: bugfix: inputs/VegBank/plot_/postprocess.sql: coordinateUncertaintyInMeters: need to use GREATEST() instead of _alt() to handle cases where the coordinate uncertainty is > than the fuzzing uncertainty, where you wouldn't want to just use the smaller fuzzing uncertainty
Aaron Marcuse-Kubitza
05:20 PM Revision 10938: inputs/VegBank/plot_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
Aaron Marcuse-Kubitza
05:11 PM Revision 10937: inputs/VegBank/plot_/postprocess.sql: map_*() derived cols: updated runtime
Aaron Marcuse-Kubitza
05:10 PM Revision 10936: inputs/VegBank/plot_/: translated single-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
Aaron Marcuse-Kubitza
04:36 PM Revision 10935: inputs/VegBank/stemcount_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
Aaron Marcuse-Kubitza
04:31 PM Revision 10934: inputs/VegBank/stemlocation_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
Aaron Marcuse-Kubitza
04:30 PM Revision 10933: inputs/VegBank/taxonobservation_/postprocess.sql: scientificName: recorded runtime (15 s)
Aaron Marcuse-Kubitza
04:15 PM Revision 10932: inputs/VegBank/taxonobservation_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
Aaron Marcuse-Kubitza
04:14 PM Revision 10931: inputs/VegBank/taxonobservation_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
Aaron Marcuse-Kubitza
03:37 PM Revision 10930: inputs/FIA/occurrence_all/postprocess.sql: use much simpler LEFT JOINs instead of nested RIGHT JOINs, which required lots of () to get them to happen in the right order. note that the columns are now provided in reverse instead of forwards path order, but this is still much clearer than the nested mess of RIGHT JOINs. this approach can also be used to simplify VegBank's joins.
Aaron Marcuse-Kubitza
03:34 PM Revision 10929: bugfix: lib/runscripts/view.run: remake_VegBIEN_mappings(): also need to remake header.csv, not just map.csv as for tables, because view columns may change when the view is regenerated
Aaron Marcuse-Kubitza
02:42 PM Revision 10928: schemas/VegCore/VegCore.ERD.mwb: specimen: changed definition to "something collected from a plant" rather than just "a physical part of a plant", to support using this table for identifying pictures and descriptions of a plant (as DwC does)
Aaron Marcuse-Kubitza
02:28 PM Revision 10927: schemas/VegCore/VegCore.ERD.mwb: regenerated exports and udpated image map
Aaron Marcuse-Kubitza
02:24 PM Revision 10926: schemas/VegCore/VegCore.ERD.mwb: reobservable_presence: allow it to be vouchered by any reobservable element (including a tagged individual), not just a specimen
Aaron Marcuse-Kubitza
02:01 PM Revision 10925: schemas/VegCore/VegCore.ERD.mwb: specimen.defining_data: clarified that the observations in this are actually a subset of individual_observation.traits (specifically, the subset that can be used to make a taxonomic redetermination). information in this field should therefore always also be stored in individual_observation.traits.
Aaron Marcuse-Kubitza
01:54 PM Revision 10924: schemas/VegCore/VegCore.ERD.mwb: specimen: added specimen_unique_in_individual_observation unique constraint, analogous to specimen_unique_in_individual
Aaron Marcuse-Kubitza
01:34 PM Revision 10923: schemas/VegCore/VegCore.ERD.mwb: regenerated exports and udpated image map
Aaron Marcuse-Kubitza
01:29 PM Revision 10922: schemas/VegCore/VegCore.ERD.mwb: specimen: added defining_data, which for a digital-only specimen, stores the information that comprises the specimen. note that a taxon_presence without a physical voucher can still qualify as reobservable if a detailed description of it is provided in this field, to make taxonomic redeterminations on. for datasources like VegBank, which incorrectly allow multiple taxon_determinations for *any* type of taxon_observation, their taxonomic redeterminations would actually be considered invalid if made on a purely taxon_presence observation (i.e. just a taxon name) without a detailed description that could be used to make a redetermination. this is different than the scrubbing of a taxon name, which relates a taxon name to another taxon name, rather than a taxon_observation to a completely different taxon name.
Aaron Marcuse-Kubitza
12:35 PM Revision 10921: bugfix: lib/sh/util.sh: set_fds(): don't add surrounding quotes to empty redirect dest
Aaron Marcuse-Kubitza
12:31 PM Revision 10920: bugfix: lib/sh/util.sh: set_fds(): need to check if redirect is empty *before* escaping it with `printf %q`, which may add surrounding quotes to an empty string
Aaron Marcuse-Kubitza
11:40 AM Revision 10919: planning/timeline/timeline.2013.xls: attribution and conditions of use: documented that Brad/Brian/Bob should work on this, as decided in the conference call (wiki.vegpath.org/2013-09-12_conference_call#data-provider-metadata)
Aaron Marcuse-Kubitza
05:47 AM Revision 10918: planning/timeline/timeline.2013.xls: reformatted to fit all rows and all per-week columns on one page
Aaron Marcuse-Kubitza
05:30 AM Revision 10917: planning/timeline/timeline.2013.xls: streamline process of mapping and adding a new datasource: added subtask to create interactive scripts for each import step
Aaron Marcuse-Kubitza
05:15 AM Revision 10916: planning/timeline/timeline.2013.xls: improve and complete data provider metadata: moved to end because this can also been added manually to the source table, and does not have to be in place before running column-based import
Aaron Marcuse-Kubitza
05:09 AM Revision 10915: planning/timeline/timeline.2013.xls: flatten the datasources to a common schema: added subtask to left-join unvalidated datasources since they need the flattening in order to validate them properly
Aaron Marcuse-Kubitza
04:21 AM Revision 10914: planning/timeline/timeline.2013.xls: rebalanced dots
Aaron Marcuse-Kubitza
04:15 AM Revision 10913: planning/timeline/timeline.2013.xls: moved items marked later to separate section at bottom
Aaron Marcuse-Kubitza
04:13 AM Revision 10912: planning/timeline/timeline.2013.xls: moved revisions to schema under datasource validations because schema changes are largely driven by validations problems uncovered
Aaron Marcuse-Kubitza
04:12 AM Revision 10911: planning/timeline/timeline.2013.xls: split tasks into weeks
Aaron Marcuse-Kubitza
03:47 AM Revision 10910: planning/timeline/timeline.2013.xls: updated for progress
Aaron Marcuse-Kubitza
03:35 AM Revision 10909: planning/timeline/timeline.2013.xls: split months into (currently identical) weeks
Aaron Marcuse-Kubitza
03:19 AM Revision 10908: planning/timeline/timeline.2013.xls: added During month of label above months
Aaron Marcuse-Kubitza
03:09 AM Revision 10907: planning/timeline/timeline.2013.xls: switched to portrait mode to better fit the new format, which hides columns for past months
Aaron Marcuse-Kubitza
03:05 AM Revision 10906: planning/timeline/timeline.2013.xls: hid crossed out rows to show just the remaining tasks
Aaron Marcuse-Kubitza
03:03 AM Revision 10905: planning/timeline/timeline.2013.xls: crossed out avoid DB restructuring when ingesting a new datasource, because FIA (which is flattened before import) *does* properly support optional subplots and diamond linking of subplots to parent plot events, which were necessary to ingest an arbitrary flattened plots datasource
Aaron Marcuse-Kubitza
02:55 AM Revision 10904: planning/timeline/timeline.2013.xls: crossed out fully-completed tasks. rebalanced dots.
Aaron Marcuse-Kubitza
02:46 AM Revision 10903: planning/timeline/timeline.2013.xls: moved switching to new-style import to top of streamline process of mapping and adding a new datasource because this puts all the datasource adding steps (except filling in the mappings) into one rerunnable script
Aaron Marcuse-Kubitza
02:36 AM Revision 10902: planning/timeline/timeline.2013.xls: hid columns for past months so that the current and future months are right next to each task
Aaron Marcuse-Kubitza
02:31 AM Revision 10901: planning/timeline/timeline.2013.xls: moved streamline process of mapping and adding a new datasource before documentation testing because this will assist the documentation tester in running the import process
Aaron Marcuse-Kubitza
02:26 AM Revision 10900: planning/timeline/timeline.2013.xls: moved geoscrubbing re-run under add any missing columns because this is needed to fully populate the geoscrubbing columns
Aaron Marcuse-Kubitza
02:20 AM Revision 10899: planning/timeline/timeline.2013.xls: added documentation testing, usability testing priority tasks (wiki.vegpath.org/Priority_tasks). lowercased tasks for consistency with the wiki and to avoid needing to sentence case new subtasks.
Aaron Marcuse-Kubitza
01:53 AM Revision 10898: planning/timeline/timeline.2013.xls: moved Flatten the datasources to a common schema under Datasource validations because the query left-joining the tables is needed for validation, and it is much easier to validate datasources when there is only one input table to validate
Aaron Marcuse-Kubitza

09/11/2013

02:52 PM Revision 10897: added derived/biengeo/Geovalidation_and_geoscrubbing_update.presentation.url
Aaron Marcuse-Kubitza

09/09/2013

06:12 PM Revision 10896: added BIEN2/traits_observation_counts.xls
Aaron Marcuse-Kubitza
05:44 PM Revision 10895: /README.TXT: Single datasource import: removed rescrub step because this is not needed by the current TNRS process
Aaron Marcuse-Kubitza
02:04 PM Revision 10894: web/links/index.htm: updated to Firefox bookmarks. MySQL: added steps to add a user if you are not root but have sudo access.
Aaron Marcuse-Kubitza

09/07/2013

08:19 PM Revision 10893: BIEN2/country_species/: svn:ignore the .tsv exports
Aaron Marcuse-Kubitza
08:19 PM Revision 10892: BIEN2/country_species/run: documented runtime (1 min)
Aaron Marcuse-Kubitza
08:15 PM Revision 10891: added BIEN2/country_species/run, which exports each BIEN2 country's species list
Aaron Marcuse-Kubitza
08:14 PM Revision 10890: bugfix: lib/sh/util.sh: set_fds(): need to escape redirect destinations which are files, because they may contain special shell characters
Aaron Marcuse-Kubitza
08:10 PM Revision 10889: lib/sh/util.sh: added rm_prefix()
Aaron Marcuse-Kubitza
07:11 PM Revision 10888: lib/sh/db.sh: mysql_cmd(): added caller usage with connection/login opts
Aaron Marcuse-Kubitza
07:08 PM Revision 10887: lib/sh/db.sh: mysql(), mysql_export(): usage: added database=...
Aaron Marcuse-Kubitza
12:30 AM Revision 10886: planning/timeline/timeline.2013.xls: Data provider validations: renamed to Datasource validations to clarify that this is a validation *of the datasources*, but not necessarily *by the data providers*
Aaron Marcuse-Kubitza

09/05/2013

07:19 PM Revision 10885: /README.TXT: Full database import: added Running individual steps separately label for the section that is not part of the main import, but is useful if the import is aborted part of the way through
Aaron Marcuse-Kubitza
05:02 PM Revision 10884: /README.TXT: moved Single datasource import, Datasource setup to top since these are the most important howtos
Aaron Marcuse-Kubitza
04:14 PM Revision 10883: bugfix: schemas/Makefile: enclose schema names in "" so that they won't be lowercased
Aaron Marcuse-Kubitza
03:56 PM Revision 10882: bugfix: schemas/Makefile, lib/common.Makefile: enclose schema names in "" so that they won't be lowercased
Aaron Marcuse-Kubitza
03:26 PM Revision 10881: /run: geoscrub_input/make(): updated runtime (20 s)
Aaron Marcuse-Kubitza
01:31 PM Revision 10880: planning/timeline/timeline.2013.xls: Data provider validations (spot-checking): moved ahead of Individual datasource refresh as decided in conference call
Aaron Marcuse-Kubitza
01:29 PM Revision 10879: schemas/vegbien.sql: analytical_plot: added aggregateOrganismObservationID from analytical_stem
Aaron Marcuse-Kubitza
08:38 AM Revision 10878: planning/timeline/timeline.2013.xls: updated for progress
Aaron Marcuse-Kubitza
08:37 AM Revision 10877: planning/timeline/timeline.2013.xls: Data provider validations: added subtask for Aggregated validations (counts)
Aaron Marcuse-Kubitza
01:17 AM Revision 10876: inputs/import.stats.xls: analytical DB: updated rowcount
Aaron Marcuse-Kubitza
01:14 AM Revision 10875: inputs/import.stats.xls: updated import times
Aaron Marcuse-Kubitza
01:01 AM Revision 10874: inputs/input.Makefile: reimport: don't remove the existing import first, because it will instead be removed by the publish step. this ensures there is always one complete copy of the datasource in the DB.
Aaron Marcuse-Kubitza
01:00 AM Revision 10873: added backups/vegbien.r10848.backup.md5
Aaron Marcuse-Kubitza
12:59 AM Revision 10872: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
12:11 AM Revision 10871: bugfix: bin/import_all: use reimport_scrub instead of import_scrub so that the temp suffix of the datasource name is removed
Aaron Marcuse-Kubitza
12:02 AM Revision 10870: inputs/input.Makefile: reimport: use import_publish instead of import so that the reimport replaces the previous import
Aaron Marcuse-Kubitza

09/04/2013

11:59 PM Revision 10869: inputs/input.Makefile: added import_publish, which removes the temp suffix when the import is done
Aaron Marcuse-Kubitza
11:48 PM Revision 10868: bugfix: bin/after_import: run backups/fix_perms right after the backup files are created to make them private
Aaron Marcuse-Kubitza
11:32 PM Revision 10867: bugfix: backups/fix_perms: just make the backups themselves private, since the other files are in svn, and their permissions should match their accessibility through Redmine
Aaron Marcuse-Kubitza
11:06 PM Revision 10866: inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix
Aaron Marcuse-Kubitza
05:27 PM Revision 10865: bugfix: bin/make_analytical_db: `/run export_`: don't take input from the terminal, because this causes rm to prompt the user (from a background task) about overwriting the previous export
Aaron Marcuse-Kubitza
05:26 PM Revision 10864: /README.TXT: Full database import: Publish the new import: added runtime (1 min)
Aaron Marcuse-Kubitza
03:00 PM Revision 10863: inputs/input.Makefile: $(map2db): import to datasrc.new instead of plain datasrc, so that the current import of the datasrc is not overwritten
Aaron Marcuse-Kubitza
02:59 PM Revision 10862: inputs/input.Makefile: added publish (`make inputs/src/publish`)
Aaron Marcuse-Kubitza
02:55 PM Revision 10861: bugfix: schemas/vegbien.sql: source: removed testing row that had gotten in during `make schemas/remake`
Aaron Marcuse-Kubitza
02:43 PM Revision 10860: inputs/input.Makefile: added %/publish (`make inputs/src/src.version/publish`)
Aaron Marcuse-Kubitza
02:32 PM Revision 10859: bugfix: schemas/vegbien.sql: datasource_publish(): need to remove the *current* live datasource instead of the datasource to publish. note that datasource_rename() does not currently generate an error if the specified datasource doesn't exist.
Aaron Marcuse-Kubitza
02:27 PM Revision 10858: bugfix: schemas/vegbien.sql: datasource_publish(): run it in a nested transaction so that there is always one published copy of the datasource. (note that a nested transaction is not automatically created for each function, http://stackoverflow.com/questions/6274457/set-isolation-level-for-postgresql-stored-procedures?In_PG_your_procedures_aren%27t_separate_transactions#answer-6283201 .)
Aaron Marcuse-Kubitza
01:57 PM Revision 10857: schemas/vegbien.sql: added datasource_publish()
Aaron Marcuse-Kubitza
01:53 PM Revision 10856: schemas/vegbien.sql: added datasource_rename()
Aaron Marcuse-Kubitza
01:51 PM Revision 10855: schemas/vegbien.sql: added rm_version_suffix()
Aaron Marcuse-Kubitza
01:28 PM Revision 10854: bin/map: allow user to override the source env var, which is used as the source.shortname value in the DB
Aaron Marcuse-Kubitza
09:43 AM Revision 10853: exports/: svn:ignore *.zip
Aaron Marcuse-Kubitza
09:42 AM Revision 10852: inputs/WIN/Specimen/unmapped_terms.csv: updated
Aaron Marcuse-Kubitza
09:37 AM Revision 10851: inputs/import.stats.xls: updated import times
Aaron Marcuse-Kubitza

08/31/2013

07:47 PM Revision 10850: /README.TXT: Full database import: time to wait for the import to finish: updated to time in inputs/import.stats.xls
Aaron Marcuse-Kubitza
07:44 PM Revision 10849: bugfix: bin/import_all: `rm inputs/.TNRS/tnrs/tnrs.make.lock`: need to use `"rm"` instead of `rm` so that we don't use any rm alias the user might have in their shell (import_all is run in the calling shell so that the jobs are owned by the calling shell)
Aaron Marcuse-Kubitza
07:36 PM Revision 10848: bugfix: mappings/VegCore-VegBIEN.csv: don't map datasetURL to source.url for taxa-only data (this mapping should only occur for Source tables)
Aaron Marcuse-Kubitza
07:27 PM Revision 10847: bin/import_all: added step to remove any leftover TNRS lockfile (previously done manually)
Aaron Marcuse-Kubitza
06:46 PM Revision 10846: planning/timeline/timeline.2013.xls: updated for progress
Aaron Marcuse-Kubitza
06:32 PM Revision 10845: bugfix: lib/sql_io.py: put_table(): Getting output table pkeys of existing/inserted rows: need to include the index cond in the join condition here, too (using var join_custom_cond), so that an index scan can be used instead of a much slower full-table sort
Aaron Marcuse-Kubitza
06:01 PM Revision 10844: bugfix: schemas/vegbien.sql: locationevent: locationevent_unique_within_location unique index: added COALESCE(...) expression around location_id since it is nullable, and this is needed for the left and right sides of the join to exactly match up to use an index scan
Aaron Marcuse-Kubitza
05:52 PM Revision 10843: bugfix: lib/sql_io.py: put_table(): DuplicateKeyException: need to include any index cond in the join condition, so that an index scan can be used instead of a much slower full-table sort (otherwise the query planner will not know that it can restrict results to rows satisfying the index cond)
Aaron Marcuse-Kubitza
05:48 PM Revision 10842: lib/sql_gen.py: Join: added custom_cond param that can be used to add to the JOIN condition
Aaron Marcuse-Kubitza
01:02 AM Revision 10841: lib/sql.py: distinct_table(): support custom filters on the distincting query
Aaron Marcuse-Kubitza
01:01 AM Revision 10840: lib/sql_gen.py: ColValueCond: support conds that are just plain SQL (without separate left and right sides) using special custom_cond flag value
Aaron Marcuse-Kubitza

08/30/2013

11:18 PM Revision 10839: bugfix: inputs/input.Makefile: %/test: in by_col mode, also need to run %/test.by_col.xml
Aaron Marcuse-Kubitza
10:38 PM Revision 10838: lib/sql_io.py: ensure_cond(): documented meaning of passed, failed params (at least one row passed/failed the constraint)
Aaron Marcuse-Kubitza
06:28 PM Revision 10837: fix: web/links/index.htm: PostgreSQL: vacuuming: moved info about autovacuum process being aborted to correct bookmark
Aaron Marcuse-Kubitza
06:25 PM Revision 10836: web/links/index.htm: updated to Firefox bookmarks. PostgreSQL: added info on vacuuming and analyzing.
Aaron Marcuse-Kubitza
06:06 PM Revision 10835: lib/runscripts/util.run: usage: documented that this usage also applies to all files that include this file
Aaron Marcuse-Kubitza
06:06 PM Revision 10834: lib/runscripts/util.run: usage: clarified that the cmd to run is a function
Aaron Marcuse-Kubitza
06:03 PM Revision 10833: added schemas/postgresql*.conf.run, which installs these config files and takes care of restarting the server
Aaron Marcuse-Kubitza
06:02 PM Revision 10832: added lib/runscripts/pg.conf.run, which installs PostgreSQL config files
Aaron Marcuse-Kubitza
06:01 PM Revision 10831: added lib/runscripts/install.run, analogous to import.run
Aaron Marcuse-Kubitza
04:39 PM Revision 10830: fix: schemas/postgresql*.conf: turn on autovacuum logging (log_autovacuum_min_duration = 0) so we can verify if autovacuum is happening
Aaron Marcuse-Kubitza
04:35 PM Revision 10829: bugfix: lib/db_xml.py: put_table(): turned off db.autoanalyze, since forcing an ANALYZE after every bulk insert is inefficient for small datasources. the default autovacuum settings in schemas/postgresql.conf should be fine; however, the frequency and/or threshold may need to be increased if autovacuum does not ANALYZE frequently enough to replace db.autoanalyze.
Aaron Marcuse-Kubitza
03:37 PM Revision 10828: /run: taxon_trait/make(): order by scientificName, measurementType as described in the taxon_trait table comment
Aaron Marcuse-Kubitza
03:36 PM Revision 10827: lib/sh/db.sh: mk_select(): added support for ORDER BY
Aaron Marcuse-Kubitza
03:30 PM Revision 10826: /run: added taxon_trait/make()
Aaron Marcuse-Kubitza
03:28 PM Revision 10825: lib/sh/db.sh: added pg_export_table_to_dir(), analogous to pg_export_table_to_dir_no_header()
Aaron Marcuse-Kubitza
03:03 PM Revision 10824: schemas/vegbien.sql: taxon_trait: added query to use to export
Aaron Marcuse-Kubitza
02:52 PM Revision 10823: inputs/NVS/*/map.csv: Taxon Growth Form: mapped to VegBIEN.growthform enum, using http://www.fgdc.gov/standards/projects/FGDC-standards-projects/vegetation/NVCS_V2_FINAL_2008-02.pdf#page=83&section.page=76 . documented values used by each table.
Aaron Marcuse-Kubitza
02:18 PM Revision 10822: lib/sh/util.sh: is_array(): handle unset vars (=false). this fixes a bug in pg_export_table_no_header, which produced the error "lib/sh/util.sh: line 290: declare: cols: not found".
Aaron Marcuse-Kubitza
02:06 PM Revision 10821: fix: lib/sh/util.sh: join(): documented that delim must be a single char
Aaron Marcuse-Kubitza
07:15 AM Revision 10820: bugfix: /README.TXT: on a live machine, you should put the following in your .profile: need to make svn files web-accessible, because these are used by fs.vegpath.org links (such as to the ERD, etc.). note that this does not affect unversioned files, because these get the right permissions on the local machine instead (see Testing > On a development machine, you should put the following in your .profile).
Aaron Marcuse-Kubitza
07:07 AM Revision 10819: /README.TXT: to backup files not in Time Machine: added command to start the PostgreSQL server
Aaron Marcuse-Kubitza
06:58 AM Revision 10818: bugfix: /README.TXT: to synchronize a Mac's settings with my testing machine's: don't upload ~/.profile, etc. to jupiter because these files are different on each machine. they can instead be synced manually.
Aaron Marcuse-Kubitza
06:52 AM Revision 10817: /README.TXT: to backup files not in Time Machine: added command to stop the PostgreSQL server
Aaron Marcuse-Kubitza
06:49 AM Revision 10816: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: noted that ./fix_perms should be run on all machines
Aaron Marcuse-Kubitza
06:36 AM Revision 10815: removed unused dir analysis/ (originally requested by Jim)
Aaron Marcuse-Kubitza
06:31 AM Revision 10814: bugfix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine:: added step to run `make backups/TNRS.backup/download live=1`, because bin/sync_upload does not sync this due to filters in backups/.rsync_filter.download
Aaron Marcuse-Kubitza
06:11 AM Revision 10813: /README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: added step to run ./fix_perms so that there are fewer permissions diffs to review
Aaron Marcuse-Kubitza
06:07 AM Revision 10812: bugfix: /README.TXT: to synchronize a Mac's settings with my testing machine's: upload: `(cd ~/Dropbox/svn/; svn up)`: use `up` instead so that the needed --force option is applied
Aaron Marcuse-Kubitza
05:37 AM Revision 10811: inputs/VegBank/*/postprocess.sql: added primary keys to derived tables
Aaron Marcuse-Kubitza
05:15 AM Revision 10810: schemas/VegCore/VegCore.ERD.mwb: regenerated exports and udpated image map
Aaron Marcuse-Kubitza
05:11 AM Revision 10809: schemas/VegCore/VegCore.ERD.mwb: individual_observation.individual: documented that it is optional because an individual_observation cannot have an associated individual unless the individual is traceable to a specific plant
Aaron Marcuse-Kubitza
05:09 AM Revision 10808: schemas/VegCore/VegCore.ERD.mwb: individual_observation.place_observed_at: made it optional because some individual_observations (e.g. of the plant a specimen was collected from) may be missing location information. however, an individual_observation cannot have an associated individual unless the individual is traceable to a specific plant.
Aaron Marcuse-Kubitza
05:03 AM Revision 10807: schemas/VegCore/VegCore.ERD.mwb: specimen: added individual_observation, which stores observations about the plant the specimen was collected from. (some specimens may not be traceable to a reobservable individual, but will still have these plant observations.) specimen_observation: adjusted position to fully display the HAS-A connector to specimen.
Aaron Marcuse-Kubitza
03:44 AM Revision 10806: planning/timeline/timeline.2013.xls: updated for progress. rebalanced dots.
Aaron Marcuse-Kubitza
01:39 AM Revision 10805: planning/timeline/timeline.2013.xls: added separate task for Individual datasource refresh (separate from Individual datasource *removal*), because we also need to optimize the reload of datasources. the reload is most likely slow because rows are being added to very large tables.
Aaron Marcuse-Kubitza
01:21 AM Revision 10804: /README.TXT: Single datasource import: run commands in the background, since these are long-running commands
Aaron Marcuse-Kubitza
12:57 AM Revision 10803: planning/timeline/timeline.2013.xls: moved Attribution and conditions of use before Flatten the datasources as suggested in meeting with Mark
Aaron Marcuse-Kubitza
12:42 AM Revision 10802: schemas/vegbien.sql: datasource_rm(): runtime: added runtime of MO (55 min, 0.85 ms/row), which has a much larger # of rows than ACAD (4 million instead of 45,000). updated GBIF runtime estimate (~13 h) with more accurate ms/row from MO.
Aaron Marcuse-Kubitza

08/29/2013

11:19 PM Revision 10801: schemas/vegbien.sql: datasource_rm(): estimated runtime for GBIF (~10 h). note that this is still significantly shorter than the import time (3.4 days).
Aaron Marcuse-Kubitza
11:11 PM Revision 10800: schemas/vegbien.sql: datasource_rm(): documented how to calculate runtime
Aaron Marcuse-Kubitza
11:04 PM Revision 10799: schemas/vegbien.sql: datasource_rm(): documented runtime for ACAD: 30 s; 0.61 ms/row
Aaron Marcuse-Kubitza
05:09 PM Revision 10798: inputs/input.Makefile: rm: use new datasource_rm(), which encapsulates the schema-specific aspects of removing a datasource
Aaron Marcuse-Kubitza
04:59 PM Revision 10797: bugfix: schemas/vegbien.sql: datasource_rm(): set_config(): don't name the is_local param because it is not a named parameter
Aaron Marcuse-Kubitza
04:50 PM Revision 10796: schemas/vegbien.sql: added datasource_rm(). this uses an internal schema-scoping parameter to ensure that the function always operates on tables in the schema it was *defined* in, rather than tables in the search_path. this ensures that when the public schema is renamed (e.g. from an imported version), the function will continue to operate on its own schema rather than whichever schema happens to be called public. this avoids any surprises if you are trying to remove a datasource in one schema, and don't want it to unintentionally be removed in another schema instead.
Aaron Marcuse-Kubitza
04:20 PM Revision 10795: schemas/util.sql: added schema_ident()
Aaron Marcuse-Kubitza
03:20 PM Revision 10794: schemas/util.sql: added schema(regtype), schema(anyelement)
Aaron Marcuse-Kubitza
02:07 PM Revision 10793: inputs/.TNRS/schema.sql: added covering indexes on foreign keys where needed. this enables rows to be cascadingly deleted without a full table scan.
Aaron Marcuse-Kubitza
01:58 PM Revision 10792: schemas/vegbien.sql: added covering indexes on foreign keys where needed. this enables rows to be cascadingly deleted without a full table scan.
Aaron Marcuse-Kubitza

08/27/2013

11:11 PM Revision 10791: planning/timeline/timeline.2013.xls: increased font size for better readability at 100% (which is also the printed size). note that the timeline is normally zoomed in, so you don't see the actual font size.
Aaron Marcuse-Kubitza
10:52 PM Revision 10790: inputs/.TNRS/schema.sql: tnrs: instructions for when changing this table's schema: updated to use new `inputs/.TNRS/data.sql.run refresh`
Aaron Marcuse-Kubitza
10:50 PM Revision 10789: inputs/.TNRS/data.sql.run: added refresh() target which runs inputs/test_taxonomic_names/test_scrub
Aaron Marcuse-Kubitza
10:34 PM Revision 10788: inputs/test_taxonomic_names/test_scrub: added step to update inputs/.TNRS/data.sql to the now-refreshed TNRS sample data (this updating step is now automated)
Aaron Marcuse-Kubitza
10:32 PM Revision 10787: inputs/.TNRS/schema.sql: tnrs: updated steps to run when changing this table's schema, to use new TNRS editing workflow
Aaron Marcuse-Kubitza
10:14 PM Revision 10786: inputs/.TNRS/data.sql: re-ran TNRS using `inputs/test_taxonomic_names/test_scrub; rm=1 inputs/.TNRS/data.sql.run export_`
Aaron Marcuse-Kubitza
10:13 PM Revision 10785: /README.TXT: Full database import: fixing TNRS errors: noted that inputs/test_taxonomic_names/test_scrub re-runs TNRS
Aaron Marcuse-Kubitza
10:12 PM Revision 10784: /README.TXT: Full database import: fixing TNRS errors: updated instructions for new TNRS schema editing workflow
Aaron Marcuse-Kubitza
09:53 PM Revision 10783: inputs/.TNRS/data.sql: generate from the DB using `rm=1 inputs/.TNRS/data.sql.run export_` instead of being a hand-edited file
Aaron Marcuse-Kubitza
09:50 PM Revision 10782: added inputs/.TNRS/data.sql.run for syncing data.sql directly with the DB without needing to use inputs/test_taxonomic_names/test_scrub just to export the sample data. (however, when modifying the tnrs table, it may still be easier to generate new sample data using test_scrub rather than refactoring the table in place.)
Aaron Marcuse-Kubitza
09:35 PM Revision 10781: added lib/runscripts/data.pg.sql.run (analogous to schema.pg.sql.run for data-only SQL scripts)
Aaron Marcuse-Kubitza
09:32 PM Revision 10780: added lib/runscripts/file.pg.sql.run and use it in schema.pg.sql.run
Aaron Marcuse-Kubitza
09:25 PM Revision 10779: added lib/runscripts/schema.pg.sql.run and use it in inputs/.TNRS/schema.sql.run
Aaron Marcuse-Kubitza
09:18 PM Revision 10778: inputs/.TNRS/schema.sql: generate from the DB using `rm=1 inputs/.TNRS/schema.sql.run export_` instead of being a hand-edited file. this makes it much easier to edit the (now frequently-changing) TNRS schema directly in pgAdmin (which is graphical), rather than having to manually copy SQL changes from pgAdmin to the file.
Aaron Marcuse-Kubitza
09:15 PM Revision 10777: inputs/.TNRS/schema.sql.run: export_(): added usage
Aaron Marcuse-Kubitza
09:12 PM Revision 10776: added inputs/.TNRS/schema.sql.run, which syncs schema.sql with the DB
Aaron Marcuse-Kubitza
09:07 PM Revision 10775: bugfix: lib/sh/db.sh: pg_dump(): don't default $struct flag to on, because both structure and data should be printed by default
Aaron Marcuse-Kubitza
09:02 PM Revision 10774: lib/sh/db.sh: pg_dump(): added create_schema= flag to remove CREATE SCHEMA statements (useful if the schema already exists)
Aaron Marcuse-Kubitza
08:59 PM Revision 10773: bugfix: lib/sh/util.sh: set_fds(): remove empty redirects resulting from using `redirs= cmd...` to clear the redirs and then using $redirs as an array
Aaron Marcuse-Kubitza
08:47 PM Revision 10772: fix: lib/sh/util.sh: set_fds(): documented that it does not currently support redirecting an fd to itself (due to bash bugs that require the dest fd to be closed before it can be reopened)
Aaron Marcuse-Kubitza
08:44 PM Revision 10771: bugfix: lib/sh/util.sh: stdout2fd(): don't add >&$fd redirect if the fd is 1, because redir does not currently support redirecting an fd to itself (due to bash bugs that require the dest fd to be closed before it can be reopened)
Aaron Marcuse-Kubitza
08:40 PM Revision 10770: lib/sh/util.sh: filter_fd(): factored out >() subshell command into stdout2fd() for clarity
Aaron Marcuse-Kubitza
08:33 PM Revision 10769: bugfix: lib/sh/util.sh: redir(): unset redirs so that you don't redirect again in the invoked command
Aaron Marcuse-Kubitza
08:29 PM Revision 10768: fix: lib/sh/util.sh: filter_fd(): documented that ${redirs[@]} must not be set to an outer value
Aaron Marcuse-Kubitza
07:41 PM Revision 10767: fix: inputs/ARIZ/omoccurrences/map.csv: occurrenceID: remapped to EQUIV#to:occid instead of DUPLICATE#of:occid since these are not exact duplicates
Aaron Marcuse-Kubitza
07:30 PM Revision 10766: lib/runscripts/util.run: added to_top_file alias for use with $top_file
Aaron Marcuse-Kubitza
07:10 PM Revision 10765: lib/sh/local.sh: added pg_dump_local()
Aaron Marcuse-Kubitza
07:09 PM Revision 10764: lib/sh/db.sh: added pg_dump(), using the code in bin/pg_dump_vegbien with clarity improvements
Aaron Marcuse-Kubitza
07:06 PM Revision 10763: lib/sh/db.sh: added pg_cmd() (analogous to mysql_cmd() for PostgreSQL), and use it in psql(), so that other PostgreSQL operations can use this to set the PG* connection/login vars
Aaron Marcuse-Kubitza
05:36 PM Revision 10762: planning/timeline/timeline.2013.xls: updated dots for new priority order
Aaron Marcuse-Kubitza
05:33 PM Revision 10761: planning/timeline/timeline.2013.xls: moved optimization of individual datasource removal before flattening the datasources to a common schema as suggested in meeting with Mark
Aaron Marcuse-Kubitza
04:00 PM Revision 10760: lib/runscripts/datasrc_dir.run: include of import.run: use .rel instead of `. "$(dirname "${BASH_SOURCE[0]}")"/...`
Aaron Marcuse-Kubitza
03:59 PM Revision 10759: lib/runscripts/datasrc_dir.run: moved commands related to any runscript in the datasrc dir to new in_datasrc_dir.run
Aaron Marcuse-Kubitza
03:57 PM Revision 10758: inputs/*/Specimen/test.xml.ref with eventDate->dateCollected mappings: updated test outputs to match mapping
Aaron Marcuse-Kubitza
03:52 PM Revision 10757: some inputs/*/*/unmapped_terms.csv: updated now that datasetURL is mapped (this does not affect the mappings because it is only mapped for Source tables)
Aaron Marcuse-Kubitza
03:43 PM Revision 10756: bugfix: inputs/ARIZ/omoccurrences/map.csv: fixed one-to-many mapping for modified (created by the automapper?)
Aaron Marcuse-Kubitza
02:38 PM Revision 10755: lib/sh/db.sh: pg_export(): added usage
Aaron Marcuse-Kubitza
01:54 PM Revision 10754: inputs/.TNRS/schema.sql: moved source code comments to in-schema COMMENT ON comments so all the info in schema.sql is in the DB
Aaron Marcuse-Kubitza
01:47 PM Revision 10753: inputs/.TNRS/schema.sql: views that use * as the column list: added comments to indicate that this is the case, so that the views can be updated in place rather than only by reinstalling the TNRS schema
Aaron Marcuse-Kubitza
01:20 PM Revision 10752: updated backups/TNRS.backup.md5
Aaron Marcuse-Kubitza
01:19 PM Revision 10751: planning/timeline/timeline.2013.xls: clarified note about the purpose of the dots
Aaron Marcuse-Kubitza
01:03 PM Revision 10750: added backups/vegbien.r10548.backup.md5
Aaron Marcuse-Kubitza
01:03 PM Revision 10749: bugfix: backups/: svn:ignore: removed *.md5, which should be under version control
Aaron Marcuse-Kubitza
12:55 PM Revision 10748: inputs/input.Makefile: scrub: documented that using & (background process) ignores TNRS errors, so that TNRS bugs do not prevent the remaining tables from being imported even if TNRS can't be run
Aaron Marcuse-Kubitza
12:49 PM Revision 10747: inputs/.TNRS/schema.sql: tnrs: util.set_col_types() runtime: updated for most recent ALTER COLUMN TYPE command (9 min)
Aaron Marcuse-Kubitza
12:25 PM Revision 10746: inputs/.TNRS/schema.sql: tnrs.Time_submitted: renamed to batch and added fkey to batch.id. this requires including the batch table in inputs/.TNRS/data.sql, so that the fkey is satisfied (batch entries are already added by bin/tnrs_db.
Aaron Marcuse-Kubitza
11:42 AM Revision 10745: updated backups/TNRS.backup
Aaron Marcuse-Kubitza
11:38 AM Revision 10744: /README.TXT: Full database import: To back up DB (staging tables and last import) separately: added step to upload backups to jupiter
Aaron Marcuse-Kubitza
11:30 AM Revision 10743: /README.TXT: Full database import: To back up DB (staging tables and last import) separately: added step to remake backups/TNRS.backup
Aaron Marcuse-Kubitza

08/26/2013

08:45 PM Revision 10742: bin/tnrs_db: add entry to new batch table
Aaron Marcuse-Kubitza
07:48 PM Revision 10741: inputs/.TNRS/schema.sql: batch: reset name of id_by_time unique constraint since this field is now in the batch table
Aaron Marcuse-Kubitza
07:46 PM Revision 10740: inputs/.TNRS/schema.sql: download_settings: renamed to batch_download_settings because this table is actually specific to the batch, and it does not make sense to have a download settings file without a batch
Aaron Marcuse-Kubitza
07:32 PM Revision 10739: inputs/.TNRS/schema.sql: download_settings.id: added fkey to batch.id to create a 1:1 relationship with optional participation by download_settings. note that this relationship happens to be the same as SQL inheritance, as used in VegCore, but in this case, the 1:1 relationship is not related to inheritance.
Aaron Marcuse-Kubitza
06:30 PM Revision 10738: inputs/.TNRS/schema.sql: client_version: added table, column comments with info on how to retrieve each value
Aaron Marcuse-Kubitza
06:28 PM Revision 10737: inputs/.TNRS/schema.sql: added client_version table for svn revisions, with fkey from batch
Aaron Marcuse-Kubitza
06:23 PM Revision 10736: inputs/.TNRS/schema.sql: added batch table and moved download_settings.time_submitted, id_by_time to it since these are not related to the download_settings file
Aaron Marcuse-Kubitza
05:04 PM Revision 10735: fix: planning/timeline/timeline.2013.xls: Switching to new-style import: updated hyperlink
Aaron Marcuse-Kubitza
05:02 PM Revision 10734: planning/timeline/timeline.2013.xls: moved Individual datasource removal under Streamline process of mapping and adding a new datasource
Aaron Marcuse-Kubitza
04:49 PM Revision 10733: planning/timeline/timeline.2013.xls: added note that the purpose of the dots is to show what tasks should be worked on. in some cases, they are also proportional to the complexity of the task, but this may not be the case if e.g. a task was given different priorities in different months, or worked on in different amounts.
Aaron Marcuse-Kubitza
04:38 PM Revision 10732: fix: planning/timeline/timeline.2013.xls: matched supertask status to subtask status
Aaron Marcuse-Kubitza
04:35 PM Revision 10731: planning/timeline/timeline.2013.xls: made Switching to new-style import a subtask of Streamline process of mapping and adding a new datasource because new-style import automates many of the datasource-mapping tasks that previously needed to be done by hand
Aaron Marcuse-Kubitza
04:33 PM Revision 10730: planning/timeline/timeline.2013.xls: reordered for priorities and to-do assignments from last conference call (wiki.vegpath.org/2013-08-22_conference_call#Decisions-made)
Aaron Marcuse-Kubitza
04:32 PM Revision 10729: planning/timeline/timeline.2013.xls: updated for August progress and recently-added tasks
Aaron Marcuse-Kubitza
01:49 PM Revision 10728: inputs/.TNRS/schema.sql: added VegCore-style id column as the primary key, instead of using time_submitted directly. this enables always using the same name for the pkey. the pkey is now autopopulated from time_submitted in a trigger, using helper column id_by_time. the user is now also able to specify their own globally-unique ID that is not based on the time_submitted.
Aaron Marcuse-Kubitza

08/25/2013

11:22 PM Revision 10727: inputs/.TNRS/schema.sql: download_settings comment: changed name of button to Download settings, which had gotten auto-replaced to download_settings
Aaron Marcuse-Kubitza
11:08 PM Revision 10726: inputs/.TNRS/schema.sql: Download settings table: renamed to download_settings because although Download settings is the verbatim name of the button that this info comes from, it is not necessary to name the table a particular way in order to match up data to it correctly, so we can just use the standard naming convention (wiki.vegpath.org/u-name#format) and avoid the need to enclose the name in ""
Aaron Marcuse-Kubitza

08/24/2013

06:00 PM Revision 10725: inputs/.TNRS/schema.sql: added Download settings table, which stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt
Aaron Marcuse-Kubitza
04:07 PM Revision 10724: inputs/.TNRS/Source/map.csv: mapped datasetURL
Aaron Marcuse-Kubitza

08/23/2013

11:43 PM Revision 10723: inputs/.geoscrub/Source/map.csv: mapped datasetURL
Aaron Marcuse-Kubitza
11:41 PM Revision 10722: mappings/VegCore-VegBIEN.csv: mapped datasetURL
Aaron Marcuse-Kubitza
11:38 PM Revision 10721: mappings/VegCore-VegBIEN.csv: mapped datasetURL
Aaron Marcuse-Kubitza

08/22/2013

06:12 PM Revision 10720: fix: mappings/VegCore-VegBIEN.csv: source__modified_date: remapped to pubdate instead of datelastmodified because this is actually metadata for the source itself, rather than for the VegBIEN record *of* the source
Aaron Marcuse-Kubitza
05:56 PM Revision 10719: fix: inputs/.geoscrub/Source/map.csv: source__modified_date: use the mtime of the CSV file instead, since this is closer to the actual version of the biengeo code at the time it was run
Aaron Marcuse-Kubitza
05:41 PM Revision 10718: inputs/.geoscrub/Source/map.csv: mapped source__modified_date. note that the test must be run with inputs/.geoscrub/Source/run instead of `make inputs/.geoscrub/Source/test` to add these metadata columns to the staging table.
Aaron Marcuse-Kubitza
05:38 PM Revision 10717: mappings/VegCore-VegBIEN.csv: mapped source__modified_date (different from vegcore.vegpath.org?modified, which is for the data record)
Aaron Marcuse-Kubitza
05:36 PM Revision 10716: mappings/VegCore.htm: regenerated from wiki. added source__version (= edition), source__modified_date.
Aaron Marcuse-Kubitza
05:33 PM Revision 10715: bugfix: schemas/util.sql: set_col_names_with_metadata(): *rename* any metadata cols rather than re-adding them with new names
Aaron Marcuse-Kubitza
04:38 PM Revision 10714: mappings/VegCore-VegBIEN.csv: mapped edition
Aaron Marcuse-Kubitza
04:36 PM Revision 10713: bugfix: inputs/.geoscrub/{Source,geoscrub_output}/VegBIEN.csv: switched to the version needed for new-style datasources
Aaron Marcuse-Kubitza
04:12 PM Revision 10712: inputs/.geoscrub/Source/map.csv: mapped edition (the version), using `svn info derived/biengeo/`
Aaron Marcuse-Kubitza
03:53 PM Revision 10711: schemas/vegbien.sql: source.revision: renamed to import_revision for clarity
Aaron Marcuse-Kubitza
03:52 PM Revision 10710: schemas/vegbien.my.sql: updated with `make schemas/remake`
Aaron Marcuse-Kubitza
03:44 PM Revision 10709: schemas/vegbien.sql: source: datecreated, datelastmodified: default to now() like in VegBank (schemas/VegBank/vegbank.sql)
Aaron Marcuse-Kubitza
03:29 PM Revision 10708: schemas/vegbien.sql: source: added datecreated, datelastmodified, etc. for source-level tracking of import and revision (wiki.vegpath.org/2013-08-22_conference_call#source-level-tracking-of-import-and-revision)
Aaron Marcuse-Kubitza
02:54 PM Revision 10707: added derived/biengeo/ from https://projects.nceas.ucsb.edu/nceas/projects/biengeo/repository/
Aaron Marcuse-Kubitza
02:50 PM Revision 10706: added /derived
Aaron Marcuse-Kubitza
01:04 PM Revision 10705: web/links/index.htm: updated to Firefox bookmarks. Gmvault: added steps to do full backup and to backup only new e-mails
Aaron Marcuse-Kubitza
12:48 PM Revision 10704: planning/timeline/timeline.2013.xls: flagged timeline issues that can be done by iPlant personnel: Attribution and conditions of use, Geoscrubbing re-run, Geoscrubbing automated pipeline, Improve and complete data provider metadata, Obtain any additional new data
Aaron Marcuse-Kubitza
11:12 AM Revision 10703: web/links/index.htm: updated to Firefox bookmarks. Gmvault: added run instructions for Mac.
Aaron Marcuse-Kubitza
10:50 AM Revision 10702: web/links/index.htm: updated to Firefox bookmarks. added link to Gmvault (Gmail backup), which wouldn't install for me on Mac (but that may be because I'm using 10.8, and Gmvault is for 10.7/10.6)
Aaron Marcuse-Kubitza
10:26 AM Revision 10701: added planning/meetings/BIEN conference call availability.xlsx (backup of Google spreadsheet)
Aaron Marcuse-Kubitza
10:10 AM Revision 10700: planning/timeline/timeline.2013.xls: updated for changes made in the conference call: moved Data provider validations (spot-checking) to beginning since that seems to have been decided to be a higher priority than architectural changes
Aaron Marcuse-Kubitza

08/21/2013

06:50 PM Revision 10699: schemas/util.sql: combining functions taking anyelement params which could be text: take text param instead, so that other argument types (e.g. integer) will first be implicitly cast to text instead of trying to concatenate integers directly. this fixes a bug in the VegBank.stemcount_,stemlocation_ _join() of two integer pkeys, which first needed to be cast to text. anyelement was previously used so that other text-like types such as varchar could also be used, but varchar is implicitly castable to text so keeping anyelement should not be necessary.
Aaron Marcuse-Kubitza
06:07 PM Revision 10698: planning/timeline/timeline.2013.xls: added tasks to Avoid DB restructuring when ingesting a new datasource and Streamline process of mapping and adding a new datasource (not yet put in priority order)
Aaron Marcuse-Kubitza

08/20/2013

08:49 PM Revision 10697: inputs/VegBank/observation_/test.xml.ref: updated inserted row count
Aaron Marcuse-Kubitza
02:40 PM Revision 10696: bugfix: inputs/VegBank/stemlocation_/map.csv: also _join together taxonimportance_id, stemcount_id for aggregateOrganismObservationID so that the aggregateoccurrence pkeys match up with those imported from stemcount_
Aaron Marcuse-Kubitza
01:40 PM Revision 10695: bugfix: inputs/VegBank/stemcount_/map.csv: aggregateOrganismObservationID: prepend taxonimportance_id so that rows with only a taxonimportance entry (no stemcounts) will also have the required sourceaccessioncode
Aaron Marcuse-Kubitza
12:59 PM Revision 10694: schemas/vegbien.sql: analytical_stem: synced with analytical_stem_view using sync_analytical_stem_to_view()
Aaron Marcuse-Kubitza
12:58 PM Revision 10693: bugfix: schemas/vegbien.sql: sync_analytical_stem_to_view(): added re-creation of range_modeling_input view
Aaron Marcuse-Kubitza
11:40 AM Revision 10692: schemas/vegbien.sql: analytical_stem_view: added aggregateOrganismObservationID (aggregateoccurrence.sourceaccessioncode) so aggregateoccurrences can be matched back up to their input rows (e.g. VegBank.stemcount)
Aaron Marcuse-Kubitza
10:31 AM Revision 10691: inputs/VegBank/taxonobservation_/map.csv: plantname: remapped to DUPLICATE#of:plantconcept_plantname because this is an exact duplicate
Aaron Marcuse-Kubitza
10:24 AM Revision 10690: bugfix: inputs/VegBank/taxonobservation_/map.csv: updated input column names for renamings in inputs/VegBank/vegbank.~.clean_up.sql
Aaron Marcuse-Kubitza
10:21 AM Revision 10689: inputs/VegBank/taxonobservation_/map.csv: Species and lower ranks: remapped to EQUIV#to:plantname because these contain the taxonomic name at specific ranks, but plantname contains the taxonomic name of the plant itself, which is longer and populated more often
Aaron Marcuse-Kubitza

08/19/2013

05:48 AM Revision 10688: inputs/VegBank/taxonobservation_/create.sql: also join to plantname, since plantconcept.plantname may not always be populated when plantname.plantname is
Aaron Marcuse-Kubitza
05:36 AM Revision 10687: fix: inputs/VegBank/taxonobservation_/map.csv: Species and below: remapped to _alts of scientificName, because these are actually the *full* taxonomic name at that rank, not just the epithet. Genus: documented that it includes the genus author.
Aaron Marcuse-Kubitza
05:28 AM Revision 10686: inputs/VegBank/vegbank.~.clean_up.sql: disambiguated plantconcept.plantname, plantname.reference_id to enable joining plantconcept_->plantname
Aaron Marcuse-Kubitza
05:13 AM Revision 10685: fix: inputs/VegBank/taxonobservation_/map.csv: also mapped plantname to scientificName, since int_currplantscifull is not always provided when this is. (it cannot replace int_currplantscifull, because when int_currplantscifull also provided, this often leaves out lower ranks.) this should fill in taxonomic information for taxonobservations that are currently missing it.
Aaron Marcuse-Kubitza
03:27 AM Revision 10684: bugfix: schemas/vegbien.sql: analytical_stem_view: coordinates: use the coordinates from datasource_place instead of canon_place, because canon_place's coordinates are only what the geoscrubbing output and do not contain datasource-specific information such as coordsaccuracy_m
Aaron Marcuse-Kubitza
01:53 AM Revision 10683: inputs/VegBank/taxonobservation_/map.csv: collector_id: remapped to UNUSED. removed LEFT JOIN collector_id->party since this field is never populated.
Aaron Marcuse-Kubitza
01:16 AM Revision 10682: inputs/VegBank/plot_/map.csv: area|country|territory, region|state|province (from place table): remapped to DUPLICATE, since these have the same data as, and are populated less often than, their country/stateprovince couterparts
Aaron Marcuse-Kubitza
 

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