add first round of pgtools

.travis.yml

@@ -70,7 +70,7 @@ jobs:
 
 before_install:
   - export GALAXY_REPO=https://github.com/galaxyproject/galaxy
-  - export GALAXY_RELEASE=release_18.09
+  - export GALAXY_RELEASE=release_19.01
   - export PLANEMO_CONDA_PREFIX="$HOME/conda"
   - unset JAVA_HOME
 

tools/pg_tools/.shed.yml

@@ -0,0 +1,28 @@
+name: pgtools
+owner: bgruening
+description: tool suite for dealing with Postgresql databases from Galaxy's history
+
+long_description: |
+    The postgresql tools, are using a postgresql database in user-space.
+    Databases are packed into a tarball and stored in the user-history.
+
+    These tools are based on https://github.com/solidsnack/pglite to interact with postgresql in user-space.
+
+categories:
+    - Data Export
+    - Data Source
+remote_repository_url: https://github.com/bgruening/galaxytools/tools/pgtools
+homepage_url: https://www.postgresql.org
+
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Postgresql toolbox: {{ tool_name }}"
+suite:
+  name: "postgresql_suite"
+  description: "A suite of Galaxy tools for dealing with Postgresql databases from Galaxy's history"
+
+  long_description: |
+    The postgresql tools, are using a postgresql database in user-space.
+    Databases are packed into a tarball and stored in the user-history.
+
+    These tools are based on https://github.com/solidsnack/pglite to interact with postgresql in user-space.

tools/pg_tools/macros.xml

@@ -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>

tools/pg_tools/pg-dump.xml

@@ -0,0 +1,41 @@
+<tool id="pg_dump" name="Dump" version="@PG_VERSION@">
+    <description>postgres database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        @UNTAR_INFILE@ &&
+        @PG_START@ &&
+        pg_dump "\$(pglite url -d ./postgresql)" $no_owner -f '$outfile' &&
+        @PG_STOP@ 
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="postgresql" label="Input database" />
+        <param name="no_owner" type="boolean" truevalue="--no-owner" falsevalue="" value="--no-owner"
+            label="Do not emit owner statements"
+            help="Do not output commands to set ownership of objects to match the original database. This is turned on by default because it is expected that the pg_dump tool will be used when exporting the data for use in a system external to Galaxy. Thus the authorization statements are likely to be different so we remove this."/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param value="pg_import_result1.pg.tar.bz2" name="infile"/>
+            <output file="init-galaxy-db.sql.in" name="outfile" ftype="txt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+pg_dump
+-------
+
+This tool produces a SQL dump of the database file, compatible with import into external postgres databases.
+
+@HELP_FOOTER@
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>

tools/pg_tools/pg-import.xml

@@ -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>

tools/pg_tools/pg-query.xml

@@ -0,0 +1,55 @@
+<tool id="pg_query" name="Query" version="@PG_VERSION@">
+    <description>postgres database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+            @UNTAR_INFILE@ &&
+            @PG_START@ &&
+            ##ls -l ./postgresql &&
+            a=" with CSV HEADER DELIMITER '	';" &&
+            echo "COPY ($query) TO STDOUT"\$a | @PSQL@ -L logfile.log > '$outfile' &&
+            @PG_STOP@ 
+            &&
+            cat logfile.log
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="postgresql" label="Input database" />
+        <param name="query" type="text" area="True" size="5x50" label="The query to be issued to the database">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;" />
+                </valid>
+                <mapping initial="none">
+                    <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+                </mapping>
+            </sanitizer>
+            <validator type="expression" message="Query cannot be empty">value.strip()</validator>
+         </param>
+    </inputs>
+    <outputs>
+        <data format="txt" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="pg_import_result1.pg.tar.bz2" ftype="postgresql" />
+            <param name="query" value="select version from migrate_version" />
+            <output file="pg_query_result1.txt" name="outfile" />
+        </test>
+        <test>
+            <param name="infile" value="pg_import_result1.pg.tar.bz2" ftype="postgresql" />
+            <param name="query" value="select * from galaxy_user" />
+            <output file="pg_query_result2.txt" name="outfile" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@HELP_FOOTER@
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>