moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

bugfix: /Makefile: install: need to run inputs/download in live mode so that the flat files are actually downloaded

fix: /Makefile: inputs/reinstall: commented out to avoid a cascade of "overriding commands for target" warnings. this will revert to the default uninstall, install sequence for this target rather than the simultaneous-reinstall optimization (which can still be invoked manually).

bugfix: /Makefile: moved inputs/reinstall to end so it overrides the corresponding subdir forwarding target

bugfix: /Makefile: inputs/install: don't run bin/reinstall_all here, because /install targets are supposed to be idempotent, forward-only actions that don't first remove existing data

bugfix: /Makefile: postgres-Darwin: don't prepend $(MAKE) to $(postgresReload-Darwin), because this is now a list of commands

bugfix: /Makefile: config: ignore errors if ~/bin/make exists

fix: /Makefile: $(macPostgresLibs): added libpq.5, which is needed by PostgreSQL 9.3

fix: /Makefile: postgres-Darwin: also need to install psycopg2

/Makefile: postgres-Linux: add the PostgreSQL 9.2 apt-src in case we ever need to downgrade to it

bugfix: /Makefile: postgres-Linux: ignore errors if `sudo apt-get update` returns a non-zero exit status due to unreachable apt sources (which are likely unrelated to PostgreSQL, and should not prevent PostgreSQL configuration from continuing)

bugfix: /Makefile: postgres-Linux: fixed command to create /etc/apt/sources.list.d/pgdg.list

/Makefile: postgres-Linux: also install postgresql-#-postgis-scripts, which is used by derived/biengeo/

Makefile, schemas/.Mac.conf: upgraded to PostgreSQL 9.3, which is needed for proper exception parsing in the auto-re-create-views functionality. this also removes the Mac 10.8 Mountain Lion quirks, such as renaming the postgres user to _postgres (which messed everything up, but is now back to normal).

/Makefile: postgres-Linux: added steps to install PostgreSQL 9.3, which is needed for proper exception parsing in the auto-re-create-views functionality

/Makefile: mk_db: config/users.sql: unset ON_ERROR_STOP so user-exists errors don't prevent further user-adds

bugfix: /Makefile: postgres-Linux: phppgadmin.conf: updated `ln -s` to /etc/apache2/conf-available/ for current name of /etc/apache2/conf.d/phppgadmin.conf, which is now just phppgadmin

/Makefile: mysql-Linux: also install mysql-workbench, for use in modifying the VegCore ERD. (note that it has to be modified on Linux, because the Linux and Mac versions of MySQL Workbench position the lines differently.)

bugfix: *Makefile: $(asAdmin) invocations of Postgres commands: need to set DB user to postgres so that it won't default to the system user _postgres

*Makefile: removed $(psqlOpts), $(psqlAsAdmin), which are now set by lib/common.Makefile

/Makefile: $(postgresReload-Darwin): also install pg_ident.Mac.conf

*Makefile: removed $(asAdmin), which is now set by lib/common.Makefile

bugfix: /Makefile: postgres-Linux: phpPgAdmin: added steps to configure it for Apache 2.4

/Makefile: new config target (part of install): install our bin/make in the user's ~/bin dir so that bin/make (with filtering of verbose messages) will always be used instead of standard make (without us needing to change every occurrence of make to bin/make!)

/Makefile: moved %/remake, %-remake to lib/common.Makefile because they are generally useful

/Makefile: moved %/reinstall to lib/common.Makefile because it is generally useful

bugfix: /Makefile: moved schemas/install from install to db so that it is also run whenever the DB is reinstalled. schemas/install is needed by the staging tables reinstallation performed by reinstall_all.

bugfix: /Makefile: apache-Linux: use the standard apt-get syntax for Makefiles (`-sudo apt-get --yes install`) instead of just `apt-get install`

/Makefile: added Apache 2.4 installation

bugfix: root Makefile: $(postgresReload-Linux): fixed the "shmat(id=...) failed: Cannot allocate memory" error by telling the user to restart PostgreSQL manually from the command line

root Makefile: $(postgresReload-Linux): don't restart Postgres twice, because this does not fix the "shmat(id=...) failed: Cannot allocate memory" error. this error is instead produced whenever PostgreSQL is restarted from within a Makefile, but not when it's run directly from the command line or /bin/sh.

root Makefile: $(postgresReload-Linux): restart Postgres twice, because the first time after the postgresql.conf has been udpated, it always produces a "shmat(id=...) failed: Cannot allocate memory" error

root Makefile: Installation: Fixed bug where need to run schemas/public/install separately because schemas/install installs only the util schemas

root Makefile: Installation: install util schemas (temp functions py_functions) before inputs, so that inputs can use util functions in their postprocess.sql or create.sql scripts. (However, they must not use util functions in views or index functions, because these would be cascadingly deleted whenever the util schemas are reinstalled before an import.)

root Makefile: Datasources: scrub: Removed no longer needed scrub-remake, which has been replaced by direct use of TNRS.ScrubbedTaxon

root Makefile: VegBIEN DB: mk_db: Added command to import arbitrary DB users from a config file

root Makefile: MySQL: mysql-Linux: Also install phpMyAdmin

root Makefile: MySQL: mysql-Linux: Split apt-get dependencies into separate commands, like for other apt-get commands, to avoid having one failed dependency prevent the following dependencies from being installed

root Makefile: MySQL: *mysql_users: Also add bien_read user

root Makefile: MySQL: Renamed *mysql_user to *mysql_users because there can be multiple users

root Makefile: misc-Linux: Added command to copy dotlockfile to the bin/ dir, so that it can be used without being SETGID mail, which would prevent it from creating lockfiles in a directory owned by the bien user and group when being run by the user

root Makefile: core: Added misc-* to install other dependencies

root Makefile: Datasources: import: Use new import_scrub instead of import (input.Makefile)

root Makefile: Datasources: Added scrub, which runs tnrs-remake and scrub-remake

root Makefile: python-Darwin: Added instructions to install dateutil for Python 3 as well as Python 2, for use in PL/Python functions

root Makefile: python-Darwin: Added note that Python 2 comes preinstalled

root Makefile: Removed $(subMake), which is now defined properly by lib/common.Makefile

Moved schemas-related commands from root Makefile to schemas/Makefile

Makefiles: Factored out common vars/functions into lib/common.Makefile

root Makefile: $(psqlNoSearchPath): Merged $(psqlAsBien) into it because it's the only place $(psqlAsBien) is used

root Makefile: $(psqlAsBien): Use psql_script_vegbien instead of psql_vegbien, which adds $(psqlOpts) itself

root Makefile: PostgreSQL: $(editPhppgadmin): Ignore errors if patch has already been applied

root Makefile: PostgreSQL: phpPgAdmin: Edit config file to allow passwordless logins. Edit login page to fill in public_ as the default username and add a message to leave the password blank for that user.

root Makefile: $(postgresReload-*): Ignore `mv -n` errors, which generally indicate that the existing *.conf was already renamed to *.conf.old

Makefile mk_db, schemas/pg_hba*.conf: Added passwordless public_ user with access to just the database schema. Note that in PostgreSQL, only users with explicit GRANT permissions on a table can read data in that table, but all DB users with a login can view all table schemas.

root Makefile: apt-get: Use --yes to allow unattended installations

root Makefile: $(postgresReload-*): Confirm the operation before continuing, since it involves changing PostgreSQL config files in nontrivial ways. Added instructions for setting kernel.shmmax to at least 4GB minus 1 byte on Linux, to work with the shared_buffers setting in postgresql.conf.

root Makefile: $(postgres-Linux): Fixed bug where need $(asAdmin) before commands to rename existing *.conf

root Makefile: $(postgres-Linux): Also install postgresql-contrib, which contains the hstore extension

root Makefile: PostgreSQL: $(postgresReload-*): Rename existing *.conf to *.conf.old

root Makefile: PostgreSQL: $(postgresReload-Linux): Try chmoding both as your user and as the bien user

root Makefile: PostgreSQL: $(postgresReload-Linux): Making schemas/*.conf world-readable: Fixed bug where need to do this as the bien user, which owns the files

root Makefile: PostgreSQL: $(postgresReload-*): Make schemas/*.conf world-readable so it's readable by the postgres user, which the .conf installation is run as

root Makefile: PostgreSQL: $(postgresReload-*): Also install pg_hba.conf

root Makefile: PostgreSQL: Added postgres_reload to reload postgresql.conf and restart the DB

root Makefile: PostgreSQL: postgres-*: Factored postgresql.conf installation out in to $(postgresReload-*)

root Makefile: VegBIEN DB: DB and users: Also create bien_read user for read-only access to the DB

root Makefile: VegBIEN DB: DB and bien user: mk_db: hstore extension: Fixed bug where need to use `CREATE EXTENSION hstore SCHEMA pg_catalog` instead of createlang, because hstore must be explicitly created in pg_catalog or else it will be created in the public schema instead, causing it to get deleted every time the public schema is reinstalled and cascading the delete to everything (including in other schemas) that uses hstore

root Makefile: PostgreSQL: postgres-Linux: Changed plpython to plpython3 in order to install plpython3u

root Makefile: Python: python-Linux: Also install python3, needed by plpython3u

root Makefile: VegBIEN DB: DB and bien user: mk_db: Also install hstore extension. Note that this is only supported by PostgreSQL 9.1+.

root Makefile: PostgreSQL: $(pg_ctl-*): Fixed bug where need to pause for a few seconds after restarting PostgreSQL, to wait for the server to be ready to accept connections

root Makefile: Installation: uninstall: Removed inputs/uninstall because the DB will be uninstalled anyway, so the inputs don't need to be individually removed first

root Makefile: PostgreSQL: postgres-Linux: Also install postgresql.conf

root Makefile: PostgreSQL: postgres-Darwin: Also install postgresql.Mac.conf

root Makefile: PostgreSQL: $(macUsePostgresLib): Factored out PostgreSQL dir to $(macPostgresDir)

root Makefile: Datasources: inputs/install: Fixed bug where need to `wait` after `. bin/reinstall_all` to wait for inputs to finish installing before installing the public schema. This is necessary because views in the public schema now have dependencies on some datasources, such as TNRS.

root Makefile: PostgreSQL: $(psqlAsAdmin): Use new $(asAdmin)

root Makefile: VegBIEN DB: Schemas: schemas/public/install: Use $(psqlNoSearchPath) instead of $(psqlAsBien) because the search_path is set by vegbien.sql

root Makefile: Datasources: Added inputs/install override which runs `. bin/reinstall_all` instead, in order to install all datasources simultaneously

root Makefile: Python: python-Darwin: Added instructions to install Python 3.2 (Python 2 comes with Mac OS X, but Python 3.2 is needed for plpython3u)

root Makefile: VegBIEN DB: DB and bien user: mk_db: Updated for PostgreSQL 9.1.6 on the Mac, which only provides plpython3u (Python 3)

root Makefile: VegBIEN DB: DB and bien user: mk_db: Updated for PostgreSQL 9.1.6, which requires the DB name to be specified on the command line instead of in the $PGDATABASE env var set by postgres_vegbien. Fixed bug where need to run createlang as postgres superuser, because plpythonu is an untrusted language (with unrestricted access to the entire DB).

root Makefile: PostgreSQL: postgres-Darwin: Updated for PostgreSQL 9.1.6, which requires some /usr/lib/ symlinks to be changed to newer versions installed in the PostgreSQL lib/ dir

root Makefile: Installation: Fixed bug where schemas/install needed to happen after inputs/install because some of the public schema's views now depend on inputs

root Makefile: VegBIEN DB: Schemas: Run all schema installs and uninstalls using no_search_path=1, so that the schemas in the automatic search_path are not required for the command to run

root Makefile: VegBIEN DB: Schemas: public: schemas/public/uninstall: Fixed bug where need to run psql_vegbien without public in the search_path because it may have already been deleted

root Makefile: VegBIEN DB: Schemas: public: schemas/public/install: Fixed bug where need to run psql_vegbien without public in the search_path because it doesn't exist, by setting public to the empty string (deleting it)

root Makefile: VegBIEN DB: DB and bien user: db: Run inputs/.TNRS/install before schemas/install because public.tnrs_input_name depends on TNRS.tnrs

root Makefile: VegBIEN DB: Schemas: schemas/rotate: Use new schemas/rename/%

root Makefile: VegBIEN DB: Schemas: Added schemas/rename/% to rename the public schema

Makefile: Moved setting of $(root) before include of lib/common.Makefile because it's used by lib/common.Makefile

Factored OS section out from Makefile, input.Makefile into lib/common.Makefile

Makefile, input.Makefile: Use new $(version), which unlike $(date) also includes the svn revision, to version log files, etc. This way, the working copy can be put back to the way it was at the time of a given import (excluding changes to nonversioned files). This also makes it easier to get all the log files for a particular import when different tables' imports started at different times.

Makefile: Added $(root) for use with $(rootRevision)

Factored $(date) out from Makefile, input.Makefile into lib/common.Makefile

root Makefile: PostgreSQL: postgres-Linux: Added postgresql-postgis apt-get

root Makefile: Maps validation: Removed no longer used $(missingMappingsCmd)

root Makefile: Maps validation: Added $(termsSubdirs) to enable generation of global unmapped_terms.csv, new_terms.csv

root Makefile, input.Makefile: Maps validation: Treat missing join mappings differently from missing non-empty join mappings, because they indicate mapping to an invalid location, which is a bug. Factored maps validation code out into new lib/mappings.Makefile.