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June 7, 2018 15:57
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| # OS X 10.13.4, Postgres 10.4 | |
| 0> curl -o bety.sql.gz http://pecan.ncsa.illinois.edu/dump/betydump.psql.gz | |
| % Total % Received % Xferd Average Speed Time Time Time Current | |
| Dload Upload Total Spent Left Speed | |
| 100 167M 100 167M 0 0 7790k 0 0:00:21 0:00:21 --:--:-- 8289k | |
| # read into a new database cluster, to avoid disturbing my local bety | |
| 0> mkdir tmp_bety chrisb@morus:~/Desktop | |
| 0> initdb -U postgres -D tmp_bety chrisb@morus:~/Desktop | |
| The files belonging to this database system will be owned by user "chrisb". | |
| This user must also own the server process. | |
| The database cluster will be initialized with locale "en_US.UTF-8". | |
| The default database encoding has accordingly been set to "UTF8". | |
| The default text search configuration will be set to "english". | |
| Data page checksums are disabled. | |
| fixing permissions on existing directory tmp_bety ... ok | |
| creating subdirectories ... ok | |
| selecting default max_connections ... 100 | |
| selecting default shared_buffers ... 128MB | |
| selecting dynamic shared memory implementation ... posix | |
| creating configuration files ... ok | |
| running bootstrap script ... ok | |
| performing post-bootstrap initialization ... ok | |
| syncing data to disk ... ok | |
| WARNING: enabling "trust" authentication for local connections | |
| You can change this by editing pg_hba.conf or using the option -A, or | |
| --auth-local and --auth-host, the next time you run initdb. | |
| Success. You can now start the database server using: | |
| pg_ctl -D tmp_bety -l logfile start | |
| 0> pg_ctl -D tmp_bety -l tmp_bety/logfile start chrisb@morus:~/Desktop | |
| waiting for server to start.... done | |
| server started | |
| # generate fresh bety as in .travis.yml | |
| # Travis version of this line has UNENCRYPTED before PASSWORD; removed when my Postgres complained | |
| 0> psql -q -o /dev/null -U postgres -c "CREATE ROLE BETY WITH LOGIN CREATEDB SUPERUSER CREATEROLE PASSWORD 'bety'"; | |
| 0> psql -q -o /dev/null -U postgres -c "CREATE DATABASE bety OWNER bety;" | |
| 0> gunzip -c bety.sql.gz | psql -q -o /dev/null -U postgres | |
| ERROR: database "betydump" does not exist | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY citations, line 1: "3 Balasko 1984 Yield and Quality of Switchgrass Grown without Soil Amendments Agronomy Journal 76 20..." | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY cultivars, line 1: "55 1477 hornum see brown2001pmg for details \N \N mghorn" | |
| ERROR: relation "pfts_species" does not exist | |
| LINE 1: SELECT EXISTS(SELECT 1 FROM pfts_species WHERE pft_id = this... | |
| ^ | |
| QUERY: SELECT EXISTS(SELECT 1 FROM pfts_species WHERE pft_id = this_pft_id) | |
| CONTEXT: PL/pgSQL function public.no_species_member(bigint) line 4 at SQL statement | |
| COPY cultivars_pfts, line 1: "137 1 2018-01-31 16:44:25.756546 2018-01-31 16:44:25.756546 1" | |
| ERROR: relation "inputs" does not exist | |
| LINE 4: inputs | |
| ^ | |
| QUERY: SELECT | |
| ARRAY_AGG(id) | |
| FROM | |
| inputs | |
| CONTEXT: PL/pgSQL function public.get_input_ids() line 5 at SQL statement | |
| COPY dbfiles, line 1: "232 mrp.clim /home/share/data/dbfiles/ 8738893b4316b11a59e50f99c04d8c2b 1 1 2 2012-07-22 22:58:45 20..." | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY entities, line 1: "1 \N Picea engelmannii collected from High elevation2013-06-05 17:22:02 2013-06-05 17:36:17" | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY formats, line 1: "21 Weekly AmeriFlux level 4 gap filled, partitioned, and flagged flux tower data. Variables descript..." | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY inputs, line 1: "5 76 2011-10-17 20:36:09 2011-10-17 20:36:09 \N \N EBI Energy farm site \N 2 2 f 10" | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY methods, line 1: "3 PM Penman-Monteith 617 2012-09-20 18:09:05 2012-09-20 18:09:05" | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY models, line 1: "13 dvmdostem git \N 2017-07-21 17:38:14.521487 2017-07-21 17:38:14.521487 4" | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY pfts, line 1: "110 Early successional hardwood for eastern temperate forest. Default pft = 9. Archetypes are poplar..." | |
| ERROR: relation "cultivars_pfts" does not exist | |
| LINE 1: SELECT EXISTS(SELECT 1 FROM cultivars_pfts WHERE pft_id = th... | |
| ^ | |
| QUERY: SELECT EXISTS(SELECT 1 FROM cultivars_pfts WHERE pft_id = this_pft_id) | |
| CONTEXT: PL/pgSQL function public.no_cultivar_member(bigint) line 4 at SQL statement | |
| COPY pfts_species, line 1: "10 938 2010-08-31 16:19:13 2010-09-01 23:05:50 1" | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY priors, line 1: "1 276 36 plants gamma 1.46999999999999997 0.0577999999999999972 \N 0 optimized to gamma with 95% CI ..." | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY sites, line 1: "668 Mount Edgecombe ZA \N \N \N elevation queried from lat lon using R geonames::GNstrm3 2011-09-..." | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY species, line 1: "30938 \N Loxosporopsis Loxosporopsis 2011-03-02 13:48:36 2011-03-02 13:48:36 LOXOS2 LOXOS2 NA L..." | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY treatments, line 1: "1 observational \N 2013-11-01 21:22:12 t \N" | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY users, line 1: "0 user0 user 0 betydb+0@gmail.com Urbana USA 1234567890abcdef BU 2018-06-07 00:04:02.366333 2018-06..." | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY variables, line 1: "605 proposed standard name for plant functional type 2016-05-18 15:44:48.424244 2016-05-18 15:44:4..." | |
| ERROR: function normalize_whitespace(text) does not exist | |
| LINE 1: SELECT string = normalize_whitespace(string) | |
| ^ | |
| HINT: No function matches the given name and argument types. You might need to add explicit type casts. | |
| QUERY: SELECT string = normalize_whitespace(string) | |
| CONTEXT: PL/pgSQL function public.is_whitespace_normalized(text) line 3 at RETURN | |
| COPY workflows, line 1: "106 /home/dlebauer/.pecan/biocrotest 2014-12-15 10:35:25 \N 2014-12-15 10:35:25 \N 154 7 localhost ..." | |
| ERROR: insert or update on table "benchmarks_ensembles" violates foreign key constraint "benchmarks_ensembles_model_id_fkey" | |
| DETAIL: Key (model_id)=(1000000002) is not present in table "models". | |
| ERROR: insert or update on table "benchmarks" violates foreign key constraint "benchmarks_input_id_fkey" | |
| DETAIL: Key (input_id)=(1000008121) is not present in table "inputs". | |
| ERROR: insert or update on table "benchmarks" violates foreign key constraint "benchmarks_site_id_fkey" | |
| DETAIL: Key (site_id)=(666) is not present in table "sites". | |
| ERROR: insert or update on table "benchmarks" violates foreign key constraint "benchmarks_variable_id_fkey" | |
| DETAIL: Key (variable_id)=(411) is not present in table "variables". | |
| ERROR: insert or update on table "citations_sites" violates foreign key constraint "fk_citations_sites_citations_1" | |
| DETAIL: Key (citation_id)=(209) is not present in table "citations". | |
| ERROR: insert or update on table "citations_sites" violates foreign key constraint "fk_citations_sites_sites_1" | |
| DETAIL: Key (site_id)=(285) is not present in table "sites". | |
| ERROR: insert or update on table "citations_treatments" violates foreign key constraint "fk_citations_treatments_citations_1" | |
| DETAIL: Key (citation_id)=(152) is not present in table "citations". | |
| ERROR: insert or update on table "citations_treatments" violates foreign key constraint "fk_citations_treatments_treatments_1" | |
| DETAIL: Key (treatment_id)=(685) is not present in table "treatments". | |
| ERROR: insert or update on table "covariates" violates foreign key constraint "fk_covariates_variables_1" | |
| DETAIL: Key (variable_id)=(191) is not present in table "variables". | |
| ERROR: insert or update on table "ensembles" violates foreign key constraint "fk_ensembles_workflows_1" | |
| DETAIL: Key (workflow_id)=(109) is not present in table "workflows". | |
| ERROR: insert or update on table "formats_variables" violates foreign key constraint "fk_formats_variables_formats_1" | |
| DETAIL: Key (format_id)=(19) is not present in table "formats". | |
| ERROR: insert or update on table "formats_variables" violates foreign key constraint "fk_formats_variables_variables_1" | |
| DETAIL: Key (variable_id)=(297) is not present in table "variables". | |
| ERROR: insert or update on table "inputs_runs" violates foreign key constraint "fk_inputs_runs_inputs_1" | |
| DETAIL: Key (input_id)=(295) is not present in table "inputs". | |
| ERROR: insert or update on table "likelihoods" violates foreign key constraint "fk_likelihoods_inputs_1" | |
| DETAIL: Key (input_id)=(1000000358) is not present in table "inputs". | |
| ERROR: insert or update on table "likelihoods" violates foreign key constraint "fk_likelihoods_variables_1" | |
| DETAIL: Key (variable_id)=(297) is not present in table "variables". | |
| ERROR: insert or update on table "managements" violates foreign key constraint "fk_managements_citations_1" | |
| DETAIL: Key (citation_id)=(42) is not present in table "citations". | |
| ERROR: insert or update on table "managements_treatments" violates foreign key constraint "fk_managements_treatments_treatments_1" | |
| DETAIL: Key (treatment_id)=(1) is not present in table "treatments". | |
| ERROR: insert or update on table "managements" violates foreign key constraint "fk_managements_users_1" | |
| DETAIL: Key (user_id)=(97) is not present in table "users". | |
| ERROR: insert or update on table "modeltypes_formats" violates foreign key constraint "fk_modeltypes_formats_formats_1" | |
| DETAIL: Key (format_id)=(24) is not present in table "formats". | |
| ERROR: insert or update on table "modeltypes" violates foreign key constraint "fk_modeltypes_users_1" | |
| DETAIL: Key (user_id)=(1000000001) is not present in table "users". | |
| ERROR: insert or update on table "posteriors" violates foreign key constraint "fk_posteriors_pfts_1" | |
| DETAIL: Key (pft_id)=(62) is not present in table "pfts". | |
| ERROR: insert or update on table "runs" violates foreign key constraint "fk_runs_models_1" | |
| DETAIL: Key (model_id)=(12) is not present in table "models". | |
| ERROR: insert or update on table "runs" violates foreign key constraint "fk_runs_sites_1" | |
| DETAIL: Key (site_id)=(1017) is not present in table "sites". | |
| ERROR: insert or update on table "sitegroups_sites" violates foreign key constraint "fk_sitegroups_sites_sites" | |
| DETAIL: Key (site_id)=(1000000030) is not present in table "sites". | |
| ERROR: insert or update on table "sitegroups" violates foreign key constraint "fk_sitegroups_users" | |
| DETAIL: Key (user_id)=(55) is not present in table "users". | |
| ERROR: insert or update on table "trait_covariate_associations" violates foreign key constraint "fk_trait_covariate_associations_variables_1" | |
| DETAIL: Key (covariate_variable_id)=(343) is not present in table "variables". | |
| ERROR: insert or update on table "trait_covariate_associations" violates foreign key constraint "fk_trait_covariate_associations_variables_2" | |
| DETAIL: Key (trait_variable_id)=(39) is not present in table "variables". | |
| ERROR: insert or update on table "yields" violates foreign key constraint "fk_yields_citations_1" | |
| DETAIL: Key (citation_id)=(808) is not present in table "citations". | |
| ERROR: insert or update on table "yields" violates foreign key constraint "fk_yields_cultivars_1" | |
| DETAIL: Key (cultivar_id)=(543) is not present in table "cultivars". | |
| ERROR: insert or update on table "yields" violates foreign key constraint "fk_yields_methods_1" | |
| DETAIL: Key (method_id)=(3) is not present in table "methods". | |
| ERROR: insert or update on table "yields" violates foreign key constraint "fk_yields_species_1" | |
| DETAIL: Key (specie_id)=(831) is not present in table "species". | |
| ERROR: insert or update on table "yields" violates foreign key constraint "fk_yields_treatments_1" | |
| DETAIL: Key (treatment_id)=(2494) is not present in table "treatments". | |
| ERROR: insert or update on table "yields" violates foreign key constraint "fk_yields_users_1" | |
| DETAIL: Key (user_id)=(2) is not present in table "users". | |
| ERROR: insert or update on table "reference_runs" violates foreign key constraint "reference_runs_model_id_fkey" | |
| DETAIL: Key (model_id)=(1000000013) is not present in table "models". | |
| 0> psql -U bety -d betydump chrisb@morus:~/Desktop | |
| psql (10.4) | |
| Type "help" for help. | |
| betydump=# select count(id) from pfts; | |
| count | |
| ------- | |
| 0 | |
| (1 row) | |
| betydump=# select count(id) from cultivars; | |
| count | |
| ------- | |
| 0 | |
| (1 row) | |
| betydump=# select count(id) from modeltypes; | |
| count | |
| ------- | |
| 16 | |
| (1 row) | |
| betydump=# select count(id) from likelihoods; | |
| count | |
| --------- | |
| 3786679 | |
| (1 row) | |
| betydump=# |
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Attempted bety load, PEcAn VM: