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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272 |
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added:
macros.xml pg-import.xml test-data/init-galaxy-db.sql.in test-data/pg_import_result1.pg.tar.bz2 test-data/pg_query_result1.txt test-data/pg_query_result2.txt |
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| diff -r 000000000000 -r 2c43bac3579f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 24 06:11:25 2019 -0400 |
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| @@ -0,0 +1,76 @@ +<?xml version="1.0"?> +<macros> + <xml name="inputs_outputs"> + <inputs> + <param format="tabular" help="" label="Input tabular dataset" name="in_file" type="data" /> + <yield /> + </inputs> + <outputs> + <data format="tabular" name="out_file" label="${tool.name} on ${on_string}" /> + </outputs> + </xml> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@PG_VERSION@">postgresql</requirement> + <requirement type="package" version="0.1">pglite</requirement> + </requirements> + </xml> + + <token name="@PG_VERSION@">11.2</token> + + <token name="@HELP_FOOTER@"> + The postgresql tools, are using a postgresql database in user-space. Databases are packed into a tarball and stored in the user-history. + </token> + + <token name="@UNTAR_INFILE@"><![CDATA[ + tar -xjvf '$infile' && + export PWD=`pwd` && + sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '\$PWD/postgresql/'|" ./postgresql/db/postgresql.conf + ]]> + </token> + + <token name="@PG_SETUP@"><![CDATA[ + pglite setup -d ./postgresql && + @PG_START@ + ]]> + </token> + + <token name="@PSQL@"><![CDATA[ + psql "\$(pglite url -d ./postgresql)" + ]]> + </token> + + <token name="@STATUS_RUNNING@"><![CDATA[ + timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "server is running"; do sleep 1; done' && + pglite status -d ./postgresql && + timeout 60 bash -c 'until ls -la ./postgresql | grep -F -q ".s.PGSQL.5432"; do sleep 1; done' + && pglite status -d ./postgresql + ]]> + </token> + + <token name="@STOPPED@"><![CDATA[ + timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' + ]]> + </token> + + <token name="@PG_START@"><![CDATA[ + pglite start -d ./postgresql && + @STATUS_RUNNING@ + ]]> + </token> + + <token name="@PG_STOP@"><![CDATA[ + pglite stop -d ./postgresql && + @STOPPED@ + ]]> + </token> + + <token name="@ARCHIVE_DATABASE@"><![CDATA[ + tar -cvjf postgresql_out.tar.bz2 postgresql + ]]> + </token> + <xml name="citations"> + <citations></citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 2c43bac3579f pg-import.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pg-import.xml Wed Apr 24 06:11:25 2019 -0400 |
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| @@ -0,0 +1,36 @@ +<tool id="pg_import" name="Postgresql" version="@PG_VERSION@"> + <description>import sql dump</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + @PG_SETUP@ && + ls -l ./postgresql && + @PSQL@ -f '$infile' -L logfile.log && + @PG_STOP@ && + @ARCHIVE_DATABASE@ && + cat logfile.log + ]]> + </command> + <inputs> + <param format="txt" name="infile" type="data" label="Input SQL dump" /> + </inputs> + <outputs> + <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" /> + </outputs> + <tests> + <test> + <param name="infile" value="init-galaxy-db.sql.in" ftype="txt" /> + <output file="pg_import_result1.pg.tar.bz2" name="outfile" ftype="postgresql" compare="sim_size" delta="200000" /> + </test> + </tests> + <help> +<![CDATA[ + +@HELP_FOOTER@ + +]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 2c43bac3579f test-data/init-galaxy-db.sql.in --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/init-galaxy-db.sql.in Wed Apr 24 06:11:25 2019 -0400 |
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| b"@@ -0,0 +1,16059 @@\n+--\n+-- PostgreSQL database dump\n+--\n+\n+-- Dumped from database version 11.2\n+-- Dumped by pg_dump version 11.2\n+\n+SET statement_timeout = 0;\n+SET lock_timeout = 0;\n+SET idle_in_transaction_session_timeout = 0;\n+SET client_encoding = 'UTF8';\n+SET standard_conforming_strings = on;\n+SELECT pg_catalog.set_config('search_path', '', false);\n+SET check_function_bodies = false;\n+SET client_min_messages = warning;\n+SET row_security = off;\n+\n+SET default_tablespace = '';\n+\n+SET default_with_oids = false;\n+\n+--\n+-- Name: api_keys; Type: TABLE; Schema: public; Owner: lite\n+--\n+\n+CREATE TABLE public.api_keys (\n+ id integer NOT NULL,\n+ create_time timestamp without time zone,\n+ user_id integer,\n+ key character varying(32)\n+);\n+\n+\n+ALTER TABLE public.api_keys OWNER TO lite;\n+\n+--\n+-- Name: api_keys_id_seq; Type: SEQUENCE; Schema: public; Owner: lite\n+--\n+\n+CREATE SEQUENCE public.api_keys_id_seq\n+ START WITH 1\n+ INCREMENT BY 1\n+ NO MINVALUE\n+ NO MAXVALUE\n+ CACHE 1;\n+\n+\n+ALTER TABLE public.api_keys_id_seq OWNER TO lite;\n+\n+--\n+-- Name: api_keys_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: lite\n+--\n+\n+ALTER SEQUENCE public.api_keys_id_seq OWNED BY public.api_keys.id;\n+\n+\n+--\n+-- Name: cleanup_event; Type: TABLE; Schema: public; Owner: lite\n+--\n+\n+CREATE TABLE public.cleanup_event (\n+ id integer NOT NULL,\n+ create_time timestamp without time zone,\n+ message character varying(1024)\n+);\n+\n+\n+ALTER TABLE public.cleanup_event OWNER TO lite;\n+\n+--\n+-- Name: cleanup_event_dataset_association; Type: TABLE; Schema: public; Owner: lite\n+--\n+\n+CREATE TABLE public.cleanup_event_dataset_association (\n+ id integer NOT NULL,\n+ create_time timestamp without time zone,\n+ cleanup_event_id integer,\n+ dataset_id integer\n+);\n+\n+\n+ALTER TABLE public.cleanup_event_dataset_association OWNER TO lite;\n+\n+--\n+-- Name: cleanup_event_dataset_association_id_seq; Type: SEQUENCE; Schema: public; Owner: lite\n+--\n+\n+CREATE SEQUENCE public.cleanup_event_dataset_association_id_seq\n+ START WITH 1\n+ INCREMENT BY 1\n+ NO MINVALUE\n+ NO MAXVALUE\n+ CACHE 1;\n+\n+\n+ALTER TABLE public.cleanup_event_dataset_association_id_seq OWNER TO lite;\n+\n+--\n+-- Name: cleanup_event_dataset_association_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: lite\n+--\n+\n+ALTER SEQUENCE public.cleanup_event_dataset_association_id_seq OWNED BY public.cleanup_event_dataset_association.id;\n+\n+\n+--\n+-- Name: cleanup_event_hda_association; Type: TABLE; Schema: public; Owner: lite\n+--\n+\n+CREATE TABLE public.cleanup_event_hda_association (\n+ id integer NOT NULL,\n+ create_time timestamp without time zone,\n+ cleanup_event_id integer,\n+ hda_id integer\n+);\n+\n+\n+ALTER TABLE public.cleanup_event_hda_association OWNER TO lite;\n+\n+--\n+-- Name: cleanup_event_hda_association_id_seq; Type: SEQUENCE; Schema: public; Owner: lite\n+--\n+\n+CREATE SEQUENCE public.cleanup_event_hda_association_id_seq\n+ START WITH 1\n+ INCREMENT BY 1\n+ NO MINVALUE\n+ NO MAXVALUE\n+ CACHE 1;\n+\n+\n+ALTER TABLE public.cleanup_event_hda_association_id_seq OWNER TO lite;\n+\n+--\n+-- Name: cleanup_event_hda_association_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: lite\n+--\n+\n+ALTER SEQUENCE public.cleanup_event_hda_association_id_seq OWNED BY public.cleanup_event_hda_association.id;\n+\n+\n+--\n+-- Name: cleanup_event_history_association; Type: TABLE; Schema: public; Owner: lite\n+--\n+\n+CREATE TABLE public.cleanup_event_history_association (\n+ id integer NOT NULL,\n+ create_time timestamp without time zone,\n+ cleanup_event_id integer,\n+ history_id integer\n+);\n+\n+\n+ALTER TABLE public.cleanup_event_history_association OWNER TO lite;\n+\n+--\n+-- Name: cleanup_event_history_association_id_seq; Type: SEQUENCE; Schema: public; Owner: lite\n+--\n+\n+CREATE SEQUENCE public.cleanup_event_history_association_id_seq\n+ START WITH 1\n+ INCREMENT BY 1\n+ NO MINVALUE\n+ NO MAXVALUE\n+ CACHE 1;\n+\n+\n+ALTER TABLE public.cleanup_event_his"..b' public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step_annotation_association\n+ ADD CONSTRAINT workflow_step_annotation_association_workflow_step_id_fkey FOREIGN KEY (workflow_step_id) REFERENCES public.workflow_step(id);\n+\n+\n+--\n+-- Name: workflow_step_connection workflow_step_connection_input_step_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step_connection\n+ ADD CONSTRAINT workflow_step_connection_input_step_id_fkey FOREIGN KEY (input_step_id) REFERENCES public.workflow_step(id);\n+\n+\n+--\n+-- Name: workflow_step_connection workflow_step_connection_input_subworkflow_step_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step_connection\n+ ADD CONSTRAINT workflow_step_connection_input_subworkflow_step_id_fkey FOREIGN KEY (input_subworkflow_step_id) REFERENCES public.workflow_step(id);\n+\n+\n+--\n+-- Name: workflow_step_connection workflow_step_connection_output_step_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step_connection\n+ ADD CONSTRAINT workflow_step_connection_output_step_id_fkey FOREIGN KEY (output_step_id) REFERENCES public.workflow_step(id);\n+\n+\n+--\n+-- Name: workflow_step workflow_step_subworkflow_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step\n+ ADD CONSTRAINT workflow_step_subworkflow_id_fkey FOREIGN KEY (subworkflow_id) REFERENCES public.workflow(id);\n+\n+\n+--\n+-- Name: workflow_step_tag_association workflow_step_tag_association_tag_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step_tag_association\n+ ADD CONSTRAINT workflow_step_tag_association_tag_id_fkey FOREIGN KEY (tag_id) REFERENCES public.tag(id);\n+\n+\n+--\n+-- Name: workflow_step_tag_association workflow_step_tag_association_user_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step_tag_association\n+ ADD CONSTRAINT workflow_step_tag_association_user_id_fkey FOREIGN KEY (user_id) REFERENCES public.galaxy_user(id);\n+\n+\n+--\n+-- Name: workflow_step_tag_association workflow_step_tag_association_workflow_step_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step_tag_association\n+ ADD CONSTRAINT workflow_step_tag_association_workflow_step_id_fkey FOREIGN KEY (workflow_step_id) REFERENCES public.workflow_step(id);\n+\n+\n+--\n+-- Name: workflow_step workflow_step_workflow_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_step\n+ ADD CONSTRAINT workflow_step_workflow_id_fkey FOREIGN KEY (workflow_id) REFERENCES public.workflow(id);\n+\n+\n+--\n+-- Name: workflow workflow_stored_workflow_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow\n+ ADD CONSTRAINT workflow_stored_workflow_id_fkey FOREIGN KEY (stored_workflow_id) REFERENCES public.stored_workflow(id);\n+\n+\n+--\n+-- Name: workflow_tag_association workflow_tag_association_tag_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_tag_association\n+ ADD CONSTRAINT workflow_tag_association_tag_id_fkey FOREIGN KEY (tag_id) REFERENCES public.tag(id);\n+\n+\n+--\n+-- Name: workflow_tag_association workflow_tag_association_user_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_tag_association\n+ ADD CONSTRAINT workflow_tag_association_user_id_fkey FOREIGN KEY (user_id) REFERENCES public.galaxy_user(id);\n+\n+\n+--\n+-- Name: workflow_tag_association workflow_tag_association_workflow_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: lite\n+--\n+\n+ALTER TABLE ONLY public.workflow_tag_association\n+ ADD CONSTRAINT workflow_tag_association_workflow_id_fkey FOREIGN KEY (workflow_id) REFERENCES public.workflow(id);\n+\n+\n+--\n+-- PostgreSQL database dump complete\n+--\n+\n' |
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| diff -r 000000000000 -r 2c43bac3579f test-data/pg_import_result1.pg.tar.bz2 |
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| Binary file test-data/pg_import_result1.pg.tar.bz2 has changed |
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| diff -r 000000000000 -r 2c43bac3579f test-data/pg_query_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pg_query_result1.txt Wed Apr 24 06:11:25 2019 -0400 |
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| @@ -0,0 +1,2 @@ +version +135 |
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| diff -r 000000000000 -r 2c43bac3579f test-data/pg_query_result2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pg_query_result2.txt Wed Apr 24 06:11:25 2019 -0400 |
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| @@ -0,0 +1,1 @@ +id create_time update_time email password external deleted purged username form_values_id disk_usage activation_token active last_password_change |