November 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 5498ff5b31ac: Allow filter to pick ID column
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285873215 -3600 # Node ID 5498ff5b31ac871c7d22df60146fd96c61b74aab # Parent ad83deba645811d8b9509a6e3c58e986ffa89e3b Allow filter to pick ID column --- a/tools/ncbi_blast_plus/blast_filter_fasta.py +++ b/tools/ncbi_blast_plus/blast_filter_fasta.py @@ -1,22 +1,26 @@ #!/usr/bin/env python -"""Filter a FASTA file using tabular BLAST output. +"""Filter a FASTA file using tabular output, e.g. from BLAST. -Takes four command line options, tabular BLAST filename, input FASTA filename, -and two output FASTA filenames (for records with and without any BLAST hits). +Takes five command line options, tabular BLAST filename, ID column number +(using one based counting), input FASTA filename, and two output FASTA +filenames (for records with and without any BLAST hits). + +In the default NCBI BLAST+ tabular output, the query sequence ID is in column +one, and the ID of the match from the database is in column two. """ -#TODO - Option to define which column to use for ID? - import sys from galaxy_utils.sequence.fasta import fastaReader, fastaWriter #Parse Command Line -blast_file, in_file, out_positive_file, out_negative_file = sys.argv[1:] +blast_file, blast_col, in_file, out_positive_file, out_negative_file = sys.argv[1:] +blast_col = int(blast_col)-1 +assert blast_col >= 0 #Read tabular BLAST file and record all queries with hit(s) ids = set() blast_handle = open(blast_file, "rU") for line in blast_handle: - ids.add(line.split("\t")[0]) + ids.add(line.split("\t")[blast_col]) blast_handle.close() #Write filtered FASTA file based on IDs from BLAST file --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ b/tools/ncbi_blast_plus/blast_filter_fasta.xml @@ -1,10 +1,13 @@ <tool id="blast_filter_fasta" name="BLAST filter FASTA file" version="0.0.1"><description>Divide a FASTA file based on BLAST hits</description><command interpreter="python"> - blast_filter_fasta.py $blast_file $in_file $out_positive_file $out_negative_file + blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file </command><inputs><param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> + <param name="blast_col" type="integer" value="1" label="Column containing FASTA identifiers"> + <validator type="in_range" min="1" /> + </param><param name="in_file" type="data" format="fasta" label="BLAST query FASTA file"/></inputs><outputs> @@ -19,8 +22,12 @@ **What it does** -Takes a multi-sequence FASTA and the tabular output of running BLAST on it, and -divides the FASTA file in two: those sequence with a BLAST hit, and those without. +Typical use would be to take a multi-sequence FASTA and the tabular output of +running BLAST on it, and divides the FASTA file in two: those sequence with a +BLAST hit, and those without. + +In the default NCBI BLAST+ tabular output, the query sequence ID is in column +one, and the ID of the match from the database is in column two. </help></tool>

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galaxy-dist commit 5176fa11ef2f: Add -strand as adv opt to blastn, blastx and tblastx wrappers
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285931141 -3600 # Node ID 5176fa11ef2f45df4a7bb0b82f2ca0871aaf2465 # Parent 6c1d520f25d44f80de926285cbd927bc35f69a6a Add -strand as adv opt to blastn, blastx and tblastx wrappers --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -7,6 +7,7 @@ -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -42,10 +43,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -6,6 +6,7 @@ -db "$database" -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -34,10 +35,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -6,6 +6,7 @@ -db "$database" -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -34,10 +35,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs>

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galaxy-dist commit 5244ad54beba: Make descriptions more concise (don't need to repeat infor from name)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285670784 -3600 # Node ID 5244ad54bebadf57e8bede36643afa49c58ac579 # Parent 6dd6224f571deb34c01c7fd0c3c4daccf948eda1 Make descriptions more concise (don't need to repeat infor from name) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -1,5 +1,5 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1"> - <description>Use NCBI BLAST+ tool to search a nucleotide database with nucleotide query sequence(s)</description> + <description>Search nucleotide database with nucleotide query sequence(s)</description><command> blastn -query "$query" --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -1,5 +1,5 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1"> - <description>Use NCBI BLAST+ tool to search a protein database with protein query sequence(s)</description> + <description>Search protein database with protein query sequence(s)</description><command> blastp -query "$query"

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galaxy-dist commit 55f909b601c4: Use the data_column type (great except on empty tabular files)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285874190 -3600 # Node ID 55f909b601c49dc0bb53f4fee538605df04d19f4 # Parent 5498ff5b31ac871c7d22df60146fd96c61b74aab Use the data_column type (great except on empty tabular files) --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ b/tools/ncbi_blast_plus/blast_filter_fasta.xml @@ -5,9 +5,7 @@ </command><inputs><param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="integer" value="1" label="Column containing FASTA identifiers"> - <validator type="in_range" min="1" /> - </param> + <param name="blast_col" type="data_column" data_ref="blast_file" numerical="true" value="1" label="Column containing FASTA identifiers" /><param name="in_file" type="data" format="fasta" label="BLAST query FASTA file"/></inputs><outputs>

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galaxy-dist commit 6c1d520f25d4: Don't default to setting seg/dust explicitly (allow BLAST+ to use its own defaults)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285930037 -3600 # Node ID 6c1d520f25d44f80de926285cbd927bc35f69a6a # Parent aa7f4bdc2eab6be57fc1311137ce423eb39750cd Don't default to setting seg/dust explicitly (allow BLAST+ to use its own defaults) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -6,7 +6,7 @@ -db "$database" -task $blast_type -evalue $evalue_cutoff - -dust $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -41,10 +41,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -6,7 +6,7 @@ -db "$database" -task $blast_type -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -38,10 +38,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs>

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galaxy-dist commit aa7f4bdc2eab: Use a select parameter for picking just column 1 or 2. Less flexible but works better for BLAST output I think
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285929247 -3600 # Node ID aa7f4bdc2eab6be57fc1311137ce423eb39750cd # Parent 55f909b601c49dc0bb53f4fee538605df04d19f4 Use a select parameter for picking just column 1 or 2. Less flexible but works better for BLAST output I think --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ b/tools/ncbi_blast_plus/blast_filter_fasta.xml @@ -1,12 +1,15 @@ -<tool id="blast_filter_fasta" name="BLAST filter FASTA file" version="0.0.1"> +<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1"><description>Divide a FASTA file based on BLAST hits</description><command interpreter="python"> blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file </command><inputs> + <param name="in_file" type="data" format="fasta" label="FASTA file to filter"/><param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="data_column" data_ref="blast_file" numerical="true" value="1" label="Column containing FASTA identifiers" /> - <param name="in_file" type="data" format="fasta" label="BLAST query FASTA file"/> + <param name="blast_col" type="select" label="Column containing FASTA identifiers"> + <option value="1">Column 1 - BLAST query ID</option> + <option value="2">Column 2 - BLAST match ID</option> + </param></inputs><outputs><data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> @@ -21,11 +24,14 @@ **What it does** Typical use would be to take a multi-sequence FASTA and the tabular output of -running BLAST on it, and divides the FASTA file in two: those sequence with a +running BLAST on it, and divide the FASTA file in two: those sequence with a BLAST hit, and those without. In the default NCBI BLAST+ tabular output, the query sequence ID is in column one, and the ID of the match from the database is in column two. +This allows you to filter the FASTA file for the subjects in the BLAST search, +rather than filtering the FASTA file for the queries in the BLAST search. + </help></tool>

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galaxy-dist commit 36086d5bd8fa: Support -db (database) or -subject (FASTA file)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285940235 -3600 # Node ID 36086d5bd8fa174ce88443eeeefec52b8fada5bd # Parent 5176fa11ef2f45df4a7bb0b82f2ca0871aaf2465 Support -db (database) or -subject (FASTA file) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -3,7 +3,11 @@ <command> blastn -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query @@ -14,12 +18,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><param name="blast_type" type="select" display="radio" label="Type of BLAST"><option value="megablast">megablast</option><option value="blastn">blastn</option> @@ -57,8 +74,7 @@ </conditional></inputs><outputs> -  - <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -3,7 +3,11 @@ <command> blastp -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <param name="database" type="select" display="radio" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + </when> + </conditional><param name="blast_type" type="select" display="radio" label="Type of BLAST"><option value="blastp">blastp</option><option value="blastp-short">blastp-short</option> @@ -47,8 +64,7 @@ </conditional></inputs><outputs> -  - <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -3,7 +3,11 @@ <command> tblastx -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query $adv_opts.strand @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option> @@ -49,8 +66,7 @@ </conditional></inputs><outputs> -  - <data name="output1" format="tabular" label="tblastx on ${database.value_label}"> + <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -3,7 +3,11 @@ <command> blastx -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query $adv_opts.strand @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein subject sequence(s)"/> + </when> + </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option> @@ -49,8 +66,7 @@ </conditional></inputs><outputs> -  - <data name="output1" format="tabular" label="blastx on ${database.value_label}"> + <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -3,7 +3,11 @@ <command> tblastn -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query -out $output1 @@ -12,12 +16,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option> @@ -43,7 +60,7 @@ </inputs><outputs> - <data name="output1" format="tabular" label="tblastn on ${database.value_label}"> + <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format>

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galaxy-dist commit 6dd6224f571d: Add basic blastp wrapper
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285670500 -3600 # Node ID 6dd6224f571deb34c01c7fd0c3c4daccf948eda1 # Parent fbc4d5d45649043ac57270cac5741ec153f6de66 Add basic blastp wrapper --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -264,6 +264,7 @@ --><section name="NCBI BLAST+" id="ncbi_blast_plus_tools"><tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /></section><section name="NGS: Mapping" id="solexa_tools"><tool file="sr_mapping/lastz_wrapper.xml" /> --- /dev/null +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -0,0 +1,111 @@ +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1"> + <description>Use NCBI BLAST+ tool to search a protein database with protein query sequence(s)</description> + <command> + blastp + -query "$query" + -db "$database" + -task $blast_type + -evalue $evalue_cutoff + -seg $adv_opts.filter_query + -out $output1 + -outfmt $out_format + -num_threads 8 + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Query sequence(s)"/> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <option value="blastp">blastp</option> + <option value="blastp-short">blastp-short</option> + </param> +  + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6">Tabular</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> +  + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"> + <param name="filter_query" type="hidden" value="yes" /> + </when> + <when value="advanced"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + </when> + </conditional> + </inputs> + <outputs> +  + <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + </change_format> + <change_format> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastn</requirement> + </requirements> + <tests> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +This runs the command line NCBI BLAST+ blastp tool. + +----- + +**Output format** + +The default Output of this tool is tabular, containing 12 columns: + +1. Id of your sequence +2. GI of the database hit +3. % identity +4. Alignment length +5. # mismatches +6. # gaps +7. Start position in your sequence +8. End position in your sequence +9. Start position in database hit +10. End position in database hit +11. E-value +12. Bit score + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + +Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. + + </help> +</tool>

1 0

galaxy-dist commit 59995b9b461b: Make the dust option a boolean (checkbox)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285335392 -3600 # Node ID 59995b9b461bfe40b48807a9ea1e81af3292d96e # Parent dc68de280ac7f2ff2ff97068694a7ecded62ee0c Make the dust option a boolean (checkbox) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -33,10 +33,7 @@ <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" /> --><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> - <param name="filter_query" type="select" label="Filter out low complexity regions (with DUST)?"> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="yes" falsevalue="no" checked="true" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option><option value="5">BLAST XML</option>

1 0

galaxy-dist commit 054e0b2c15d4: Clean up the code in the request_admin controller.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1286912182 14400 # Node ID 054e0b2c15d412c3b1d99cbbd7ccb7a653b2a637 # Parent 45fdae2622ad9f989f6f15e6b081a268430683f3 Clean up the code in the request_admin controller. --- a/test/functional/test_forms_and_requests.py +++ b/test/functional/test_forms_and_requests.py @@ -164,7 +164,7 @@ class TestFormsAndRequests( TwillTestCas str( sample_form.id ), sample_states, strings_displayed=[ 'Create a new sequencer configuration' ], - strings_displayed_after_submit=[ "Sequencer configuration <b>%s</b> has been created" % name ] ) + strings_displayed_after_submit=[ "Sequencer configuration (%s) has been created" % name ] ) global request_type1 request_type1 = get_request_type_by_name( name ) assert request_type1 is not None, 'Problem retrieving sequencer configuration named "%s" from the database' % name --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1433,7 +1433,7 @@ class TwillTestCase( unittest.TestCase ) self.check_page_for_string( check_str ) def request_type_permissions( self, request_type_id, request_type_name, role_ids_str, permissions_in, permissions_out ): # role_ids_str must be a comma-separated string of role ids - url = "requests_admin/manage_request_types?operation=permissions&id=%s&update_roles_button=Save" % ( request_type_id ) + url = "requests_admin/request_type_permissions?id=%s&update_roles_button=Save" % ( request_type_id ) for po in permissions_out: key = '%s_out' % po url ="%s&%s=%s" % ( url, key, role_ids_str ) --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -2,18 +2,15 @@ <%namespace file="/message.mako" import="render_msg" /><script type="text/javascript"> -$(document).ready(function(){ - //hide the all of the element with class msg_body - $(".msg_body").hide(); - //toggle the component with class msg_body - $(".msg_head").click(function(){ - $(this).next(".msg_body").slideToggle(450); + $(document).ready(function(){ + //hide the all of the element with class msg_body + $(".msg_body").hide(); + //toggle the component with class msg_body + $(".msg_head").click(function(){ + $(this).next(".msg_body").slideToggle(450); + }); }); -}); -</script> - -<script type="text/javascript"> function display_file_details(request_id, folder_path) { var w = document.get_data.files_list.selectedIndex; @@ -37,9 +34,7 @@ cell.html( '' ) } } -</script> -<script type="text/javascript"> function open_folder1( request_id, folder_path ) { var w = document.get_data.files_list.selectedIndex; @@ -80,25 +75,24 @@ } </style> +<br/> +<br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request.type.id ) )}">Sequencer configuration "${request.type.name}"</a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> + </li> +</ul> + %if message: ${render_msg( message, status )} %endif -<br/> -<br/> -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id( request.type.id ) )}"> - <span>Sequencer configuration "${request.type.name}"</span></a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}"> - <span>Browse this request</span></a> - </li> -</ul> -<form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', cntrller=cntrller, action='get_data', request_id=trans.security.encode_id( request.id ) )}" method="post" > - <div class="toolForm"> - <div class="toolFormTitle">Select files for transfer</div> +<div class="toolForm"> + <div class="toolFormTitle">Select files for transfer</div> + <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', cntrller=cntrller, request_id=trans.security.encode_id( request.id )}" method="post" ><div class="form-row"><label>Sample:</label> ${sample_id_select_field.get_html()} @@ -123,5 +117,5 @@ <input type="submit" name="select_show_datasets_button" value="Select & show datasets"/><input type="submit" name="select_more_button" value="Select more"/></div> - </div> -</form> + </form> +</div> --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -146,6 +146,8 @@ </div><br/><br/> +<font color="red"><b><i>A dataset can be renamed only if its status is "Not Started"</i></b></font> + <ul class="manage-table-actions"><li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li><div popupmenu="seqreq-${request.id}-popup"> @@ -157,7 +159,7 @@ %if is_admin: %if request.is_submitted: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', show_page=True, request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif %endif </div> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -106,6 +106,7 @@ class RequestsGrid( grids.Grid ): class RequestsCommon( BaseController, UsesFormDefinitionWidgets ): @web.json def sample_state_updates( self, trans, ids=None, states=None, cntrller=None ): + # TODO fix this mthod - cntrller is required in the signature. # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -114,7 +114,7 @@ </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='manage_request_types' )}" target="galaxy_main">Sequencer configurations</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='browse_request_types' )}" target="galaxy_main">Sequencer configurations</a></div><div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='browse_requests' )}" target="galaxy_main">Sequencing requests</a></div><div class="toolTitle"><a href="${h.url_for( controller='requests_common', action='find_samples', cntrller='requests_admin' )}" target="galaxy_main">Find samples</a></div></div> --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -1,12 +1,10 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -%if message: - ${render_msg( message, status )} -%endif -<h3>Rename datasets for Sample "${sample.name}"</h3> -<br/> -${render_msg('A dataset can be renamed only if its status is "Not Started"', 'ok')} +<% from galaxy.web.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> + +<br/><br/> +<font color="red"><b><i>A dataset can be renamed only if its status is "Not Started"</i></b></font><ul class="manage-table-actions"><li> @@ -17,48 +15,44 @@ </li></ul> -<form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > - <table class="grid"> - <thead> - <tr> - <th>Prepend directory name</th> - <th>Name</th> - <th>Path on Sequencer</th> - </tr> - <thead> - <tbody> - %for id in id_list: - <% - sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id) ) - import os - id = trans.security.decode_id(id) - %> - %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: - <tr> - <td> - <select name="prepend_${sample_dataset.id}" last_selected_value="2"> - <option value="None" selected></option> - %for option_index, option in enumerate(sample_dataset.file_path.split(os.sep)[:-1]): - %if option.strip(): - <option value="${option}">${option}</option> - %endif - %endfor - </select> - </td> - <td> - <input type="text" name="name_${sample_dataset.id}" value="${sample_dataset.name}" size="100"/> - </td> - <td> - ${sample_dataset.file_path} - </td> - </tr> - %endif - %endfor - </tbody> - </table> - <br/> - <div class="form-row"> - <input type="submit" name="save_button" value="Save"/> - <input type="submit" name="cancel_button" value="Close"/> +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Rename datasets for Sample "${sample.name}"</div> + <div class="toolFormBody"> + <form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > + <table class="grid"> + <thead> + <tr> + <th>Prepend directory name</th> + <th>Name</th> + <th>Path on sequencer</th> + </tr> + <thead> + <tbody> + %for sample_dataset in sample_datasets: + %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: + <tr> + <td> + <% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> + ${rename_datasets_for_sample_select_field} + </td> + <td> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id} )" value="${sample_dataset.name}" size="100"/> + </td> + <td>${sample_dataset.file_path}</td> + </tr> + %endif + %endfor + </tbody> + </table> + <br/> + <div class="form-row"> + <input type="submit" name="rename_datasets_button" value="Save"/> + <input type="submit" name="cancel_rename_datasets_button" value="Close"/> + </div> + </form></div> -</form> +</div> --- a/templates/admin/requests/create_request_type.mako +++ b/templates/admin/requests/create_request_type.mako @@ -70,7 +70,7 @@ </div><div class="form-row"><label>Add experiment name and the sample name to the dataset name?</label> - ${rename_dataset_selectbox.get_html()} + ${rename_dataset_select_field.get_html()} <div class="toolParamHelp" style="clear: both;"> The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This makes sure that dataset names remain unique in Galaxy even when they have the --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -67,9 +67,9 @@ class RequestTypeGrid( grids.Grid ): key='desc', filterable="advanced" ), RequestFormColumn( "Request Form", - link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.request_form.id ) ) ) ), + link=( lambda item: iff( item.deleted, None, dict( operation="view_form_definition", id=item.request_form.id ) ) ) ), SampleFormColumn( "Sample Form", - link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.sample_form.id ) ) ) ), + link=( lambda item: iff( item.deleted, None, dict( operation="view_form_definition", id=item.sample_form.id ) ) ) ), grids.DeletedColumn( "Deleted", key="deleted", visible=False, @@ -110,18 +110,15 @@ class DataTransferGrid( grids.Grid ): use_paging = True columns = [ NameColumn( "Name", - #key="name", link=( lambda item: dict( operation="view", id=item.id ) ), attach_popup=True, filterable="advanced" ), SizeColumn( "Size", - #key='size', filterable="advanced" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), StatusColumn( "Status", - #key='status', filterable="advanced" ), ] columns.append( grids.MulticolFilterColumn( "Search", @@ -197,15 +194,6 @@ class RequestsAdmin( BaseController, Use events={ '.ssword:*' : datatx_info[ 'password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, timeout=10 ) return unicode( output.replace( '\n', '<br/>' ) ) - @web.json - def open_folder( self, trans, id, folder_path ): - def print_ticks( d ): - pass - # Avoid caching - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) - return self.__get_files( trans, request.type, folder_path ) @web.expose @web.require_admin def reject( self, trans, **kwd ): @@ -246,29 +234,30 @@ class RequestsAdmin( BaseController, Use @web.expose @web.require_admin def manage_datasets( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() - dataset_id = kwd.get( 'id', None ) - if not dataset_id: - return invalid_id_redirect( trans, 'requests_admin', dataset_id ) - id_list = util.listify( dataset_id ) + sample_dataset_id = params.get( 'id', None ) + if not sample_dataset_id: + return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id ) + id_list = util.listify( sample_dataset_id ) if operation == "view": - sample_dataset_id = trans.security.decode_id( kwd['id'] ) - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( sample_dataset_id ) + sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) return trans.fill_template( '/admin/requests/dataset.mako', sample_dataset=sample_dataset ) elif operation == "delete": not_deleted = [] - for id in id_list: - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) + for sample_dataset_id in id_list: + sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) sample_id = sample_dataset.sample_id if sample_dataset.status == sample_dataset.sample.transfer_status.NOT_STARTED: trans.sa_session.delete( sample_dataset ) trans.sa_session.flush() else: not_deleted.append( sample_dataset.name ) - message = '%i datasets have been successfully deleted. ' % ( len( id_list ) - len( not_deleted ) ) - status = 'done' + message = '%i datasets have been deleted. ' % ( len( id_list ) - len( not_deleted ) ) if not_deleted: status = 'warning' message = message + '%s could not be deleted because their transfer status is not "Not Started". ' % str( not_deleted ) @@ -278,21 +267,21 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) ) elif operation == "rename": - sample_dataset_id = id_list[0] sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=sample_dataset.sample, id_list=id_list ) elif operation == "start transfer": - sample_dataset_id = id_list[0] sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) self.__start_datatx( trans, sample_dataset.sample, id_list ) # Render the grid view - sample_id = kwd.get( 'sample_id', None ) + sample_id = params.get( 'sample_id', None ) try: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', sample_id ) + request_id = trans.security.encode_id( sample.request.id ) + library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Datasets of sample "%s"' % sample.name self.datatx_grid.global_actions = [ grids.GridAction( "Refresh", dict( controller='requests_admin', @@ -301,24 +290,25 @@ class RequestsAdmin( BaseController, Use grids.GridAction( "Select datasets", dict( controller='requests_admin', action='get_data', - request_id=trans.security.encode_id( sample.request.id ), + request_id=request_id, folder_path=sample.request.type.datatx_info[ 'data_dir' ], - sample_id=sample_id, - show_page=True ) ), + sample_id=sample_id ) ), grids.GridAction( 'Data library "%s"' % sample.library.name, dict( controller='library_common', action='browse_library', cntrller='library_admin', - id=trans.security.encode_id( sample.library.id ) ) ), + id=library_id ) ), grids.GridAction( "Browse this request", dict( controller='requests_common', action='manage_request', cntrller='requests_admin', - id=trans.security.encode_id( sample.request.id ) ) ) ] + id=request_id ) ) ] return self.datatx_grid( trans, **kwd ) @web.expose @web.require_admin def rename_datasets( self, trans, **kwd ): + # This method is called from the DataTransferGrid when a user is renaming 1 or more + # SampleDatasets. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -327,64 +317,35 @@ class RequestsAdmin( BaseController, Use sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', sample_id ) - if params.get( 'save_button', False ): - id_list = util.listify( kwd['id_list'] ) - for id in id_list: - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) - prepend = util.restore_text( params.get( 'prepend_%i' % sample_dataset.id, '' ) ) - name = util.restore_text( params.get( 'name_%i' % sample_dataset.id, sample_dataset.name ) ) - if prepend == 'None': - sample_dataset.name = name + # id_list is list of SampleDataset ids, which is a subset of all + # of the SampleDatasets associated with the Sample. The user may + # or may not have selected all of the SampleDatasets for renaming. + id_list = util.listify( kwd.get( 'id_list', [] ) ) + # Get all of the SampleDatasets + sample_datasets = [] + for sample_dataset_id in id_list: + sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) + sample_datasets.append( sample_dataset ) + if params.get( 'rename_datasets_button', False ): + for sample_dataset in sample_datasets: + encoded_id = trans.security.encode_id( sample_dataset.id ) + selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) ) + new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) ) + if selected_option == 'none': + sample_dataset.name = new_name else: - sample_dataset.name = '%s_%s' % ( prepend, name ) + sample_dataset.name = '%s_%s' % ( selected_option, new_name ) trans.sa_session.add( sample_dataset ) trans.sa_session.flush() + message = 'Changes saved successfully.' return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=sample, - id_list=id_list, - message='Changes saved successfully.', - status='done' ) + sample_datasets=sample_datasets, + message=message, + status=status ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', sample_id=sample_id ) ) - def __get_files( self, trans, request_type, folder_path ): - # Retrieves the filenames to be transferred from the remote host. - # FIXME: sample is used in this method, but no sample obj is received... - datatx_info = request_type.datatx_info - if not datatx_info[ 'host' ] or not datatx_info[ 'username' ] or not datatx_info[ 'password' ]: - status = 'error' - message = "Error in sequencer login information." - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='view_dataset_transfer', - cntrller='requests_admin' , - sample_id=trans.security.encode_id( sample.id ), - status=status, - message=message ) ) - def print_ticks( d ): - pass - cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( datatx_info['username'], datatx_info['host'], folder_path ) - output = pexpect.run( cmd, - events={ '.ssword:*' : datatx_info['password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, - timeout=10 ) - if 'No such file or directory' in output: - status = 'error' - message = "No folder named (%s) exists on the sequencer." % folder_path - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='view_dataset_transfer', - cntrller='requests_admin' , - sample_id=trans.security.encode_id( sample.id ), - folder_path=folder_path, - status=status, - message=message ) ) - - return output.splitlines() - def __check_path( self, a_path ): - # Return a valid folder_path - if a_path and not a_path.endswith( os.sep ): - a_path += os.sep - return a_path - def __build_sample_id_select_field( self, trans, request, selected_value ): - return build_select_field( trans, request.samples, 'name', 'sample_id', selected_value=selected_value, refresh_on_change=False ) @web.expose @web.require_admin def get_data( self, trans, **kwd ): @@ -396,132 +357,129 @@ class RequestsAdmin( BaseController, Use request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', request_id ) - files_list = util.listify( params.get( 'files_list', '' ) ) + files_list = util.listify( params.get( 'files_list', [] ) ) folder_path = util.restore_text( params.get( 'folder_path', request.type.datatx_info[ 'data_dir' ] ) ) selected_value = kwd.get( 'sample_id', 'none' ) - sample_id_select_field = self.__build_sample_id_select_field( trans, request, selected_value ) - if not folder_path: - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=[], - folder_path=folder_path ) - folder_path = self.__check_path( folder_path ) - sample_id = kwd.get( 'sample_id', None ) - if params.get( 'show_page', False ): - if sample_id: + sample_id_select_field = self.__build_sample_id_select_field( request, selected_value ) + # The __get_files() method redirects here with a status of 'error' and a message if there + # was a problem retrieving the files. + if folder_path and status != 'error': + folder_path = self.__check_path( folder_path ) + sample_id = params.get( 'sample_id', None ) + try: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - if sample.datasets: - folder_path = os.path.dirname( sample.datasets[-1].file_path ) - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=[], - folder_path=folder_path, - status=status, - message=message ) - elif params.get( 'browse_button', False ): - # get the filenames from the remote host - files = self.__get_files( trans, request.type, folder_path ) - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=files, - folder_path=folder_path, - status=status, - message=message ) - elif params.get( 'folder_up', False ): - # get the filenames from the remote host - files = self.__get_files( trans, request.type, folder_path ) - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=files, - folder_path=folder_path, - status=status, - message=message ) - elif params.get( 'open_folder', False ): - if len( files_list ) == 1: - folder_path = os.path.join( folder_path, files_list[0] ) - folder_path = self.__check_path( folder_path ) - # get the filenames from the remote host - files = self.__get_files( trans, request.type, folder_path ) - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=files, - folder_path=folder_path, - status=status, - message=message ) - elif params.get( 'select_show_datasets_button', False ): - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - retval = self.__save_sample_datasets( trans, sample, files_list, folder_path ) - if retval: - message = 'The datasets %s have been selected for sample <b>%s</b>' % ( str( retval )[1:-1].replace( "'", "" ), sample.name ) - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_datasets', - sample_id=sample_id, - message=message, - status=status ) ) - elif params.get( 'select_more_button', False ): - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - retval = self.__save_sample_datasets( trans, sample, files_list, folder_path ) - if retval: - message='The datasets %s have been selected for sample <b>%s</b>' % ( str( retval )[1:-1].replace( "'", "" ), sample.name ) - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', - request_id=trans.security.encode_id( sample.request.id ), + except: + return invalid_id_redirect( trans, 'requests_admin', sample_id ) + # Get the filenames from the remote host + files = self.__get_files( trans, request, folder_path ) + if params.get( 'open_folder', False ): + if len( files_list ) == 1: + folder_path = os.path.join( folder_path, files_list[0] ) + folder_path = self.__check_path( folder_path ) + elif params.get( 'select_show_datasets_button', False ) or params.get( 'select_more_button', False ): + sample_dataset_file_names = self.__save_sample_datasets( trans, sample, files_list, folder_path ) + if sample_dataset_file_names: + message = 'Datasets (%s) have been selected for sample (%s)' % \ + ( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name ) + if params.get( 'select_show_datasets_button', False ): + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_datasets', + sample_id=sample_id, + message=message, + status=status ) ) + else: # 'select_more_button' was clicked + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='get_data', + request_id=request_id, + folder_path=folder_path, + sample_id=sample_id, + open_folder=True, + message=message, + status=status ) ) + return trans.fill_template( '/admin/requests/dataset_transfer.mako', + cntrller='requests_admin', + request=request, + sample_id_select_field=sample_id_select_field, + files=files, + folder_path=folder_path, + status=status, + message=message ) + @web.json + def open_folder( self, trans, id, folder_path ): + def print_ticks( d ): + pass + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) + return self.__get_files( trans, request, folder_path ) + def __get_files( self, trans, request, folder_path ): + # Retrieves the filenames to be transferred from the remote host. + ok = True + datatx_info = request.type.datatx_info + if not datatx_info[ 'host' ] or not datatx_info[ 'username' ] or not datatx_info[ 'password' ]: + status = 'error' + message = "Error in sequencer login information." + ok = False + def print_ticks( d ): + pass + cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( datatx_info['username'], datatx_info['host'], folder_path ) + output = pexpect.run( cmd, + events={ '.ssword:*' : datatx_info['password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, + timeout=10 ) + if 'No such file or directory' in output: + status = 'error' + message = "No folder named (%s) exists on the sequencer." % folder_path + ok = False + if ok: + return output.splitlines() + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='get_data', + request_id=trans.security.encode_id( request.id ), folder_path=folder_path, - sample_id=sample_id, - open_folder=True, - message=message, - status=status ) ) - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', - request_id=trans.security.encode_id( sample.request.id ), - folder_path=folder_path, - show_page=True ) ) + status=status, + message=message ) ) + def __check_path( self, a_path ): + # Return a valid folder_path + if a_path and not a_path.endswith( os.sep ): + a_path += os.sep + return a_path def __save_sample_datasets( self, trans, sample, files_list, folder_path ): - files = [] + sample_dataset_file_names = [] if files_list: for f in files_list: filepath = os.path.join( folder_path, f ) if f[-1] == os.sep: - # the selected item is a folder so transfer all the folder contents - # FIXME - #self.__get_files_in_dir(trans, sample, filepath) + # FIXME: The selected item is a folder so transfer all the folder contents + request_id = trans.security.ecnode_id( sample.request.id ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='get_data', - request=sample.request, + request_id=request_id, folder_path=folder_path, open_folder=True ) ) else: + name = self.__dataset_name( sample, filepath.split( '/' )[-1] ) sample_dataset = trans.model.SampleDataset( sample=sample, file_path=filepath, status=sample.transfer_status.NOT_STARTED, - name=self.__dataset_name( sample, filepath.split( '/' )[-1] ), + name=name, error_msg='', size=sample.dataset_size( filepath ) ) trans.sa_session.add( sample_dataset ) trans.sa_session.flush() - files.append( str( sample_dataset.name ) ) - return files + sample_dataset_file_names.append( str( sample_dataset.name ) ) + return sample_dataset_file_names def __dataset_name( self, sample, filepath ): name = filepath.split( '/' )[-1] options = sample.request.type.rename_dataset_options option = sample.request.type.datatx_info.get( 'rename_dataset', options.NO ) if option == options.NO: return name - elif option == options.SAMPLE_NAME: + if option == options.SAMPLE_NAME: return sample.name + '_' + name - elif option == options.EXPERIMENT_AND_SAMPLE_NAME: + if option == options.EXPERIMENT_AND_SAMPLE_NAME: return sample.request.name + '_' + sample.name + '_' + name - elif opt == options.EXPERIMENT_NAME: + if opt == options.EXPERIMENT_NAME: return sample.request.name + '_' + name def __setup_datatx_user( self, trans, library, folder ): """ @@ -625,7 +583,7 @@ class RequestsAdmin( BaseController, Use status = "error" else: self.__send_message( trans, datatx_info, sample, id_list ) - message = "%i datasets have been queued for transfer from the sequencer. Click on <b>Refresh</b> button above to get the latest transfer status." % len( id_list ) + message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to see the latest transfer status." % len( id_list ) status = "done" return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', @@ -635,91 +593,46 @@ class RequestsAdmin( BaseController, Use # Request Type Stuff @web.expose @web.require_admin - def manage_request_types( self, trans, **kwd ): + def browse_request_types( self, trans, **kwd ): if 'operation' in kwd: operation = kwd['operation'].lower() obj_id = kwd.get( 'id', None ) - if obj_id is None: - return invalid_id_redirect( trans, 'requests_admin', obj_id, action='manage_request_types' ) - if operation == "view": - return self.__view_request_type( trans, **kwd ) - elif operation == "view_form": - return self.__view_form( trans, **kwd ) - elif operation == "delete": - return self.__delete_request_type( trans, **kwd ) - elif operation == "undelete": - return self.__undelete_request_type( trans, **kwd ) - elif operation == "clone": - return self.__clone_request_type( trans, **kwd ) - elif operation == "permissions": - return self.__show_request_type_permissions( trans, **kwd ) + if operation == "view_form_definition": + return self.view_form_definition( trans, **kwd ) # Render the grid view return self.requesttype_grid( trans, **kwd ) - def __view_request_type( self, trans, **kwd ): - request_type_id = kwd.get( 'id', None ) - try: - request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='manage_request_types' ) - forms = self.get_all_forms( trans ) - rename_dataset_selectbox = self.__build_rename_dataset_select_list( trans, request_type ) - return trans.fill_template( '/admin/requests/view_request_type.mako', - request_type=request_type, - forms=forms, - rename_dataset_selectbox=rename_dataset_selectbox ) - def __view_form(self, trans, **kwd): - form_definition_id = kwd.get( 'id', None ) - try: - form_definition = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( form_definition_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', form_definition_id, action='manage_request_types' ) - return trans.fill_template( '/admin/forms/show_form_read_only.mako', - form_definition=form_definition ) @web.expose @web.require_admin def create_request_type( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + status = params.get( 'status', 'done' ) + rt_info_widgets, rt_states_widgets = self.__create_request_type_form( trans, **kwd ) + rename_dataset_select_field = self.__build_rename_dataset_select_field( trans ) if params.get( 'add_state_button', False ): - rt_info_widgets, rt_states_widgets = self.__create_request_type_form( trans, **kwd ) + # FIXME: why do we append a tuple of 2 empty strings???? rt_states_widgets.append( ( "", "" ) ) - rename_dataset_selectbox = self.__build_rename_dataset_select_list( trans ) - return trans.fill_template( '/admin/requests/create_request_type.mako', - rt_info_widgets=rt_info_widgets, - rt_states_widgets=rt_states_widgets, - rename_dataset_selectbox=rename_dataset_selectbox, - message=message, - status=status ) elif params.get( 'remove_state_button', False ): - rt_info_widgets, rt_states_widgets = self.__create_request_type_form( trans, **kwd ) index = int( params.get( 'remove_state_button', '' ).split(" ")[2] ) del rt_states_widgets[ index-1 ] - rename_dataset_selectbox = self.__build_rename_dataset_select_list( trans ) - return trans.fill_template( '/admin/requests/create_request_type.mako', - rt_info_widgets=rt_info_widgets, - rt_states_widgets=rt_states_widgets, - rename_dataset_selectbox=rename_dataset_selectbox, - message=message, - status=status ) elif params.get( 'save_request_type', False ): request_type, message = self.__save_request_type( trans, **kwd ) if not request_type: - return trans.fill_template( '/admin/requests/create_request_type.mako', - message=message, - status='error' ) - message = 'Sequencer configuration <b>%s</b> has been created' % request_type.name - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_request_types', - message=message, - status=status ) ) + status='error' + else: + message = 'Sequencer configuration (%s) has been created' % request_type.name + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='browse_request_types', + message=message, + status=status ) ) elif params.get( 'save_changes', False ): - request_type_id = kwd.get( 'rt_id', None ) + request_type_id = params.get( 'rt_id', None ) try: request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) except: - return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='manage_request_types' ) - # Data transfer info - make sure password is retrieved from kwd rathe rthan Params since Params may have munged the characters. + return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' ) + # Data transfer info - make sure password is retrieved from kwd rather + # than Params since Params may have munged the characters. request_type.datatx_info = dict( host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), password=kwd.get( 'password', '' ), @@ -731,51 +644,48 @@ class RequestsAdmin( BaseController, Use trans.sa_session.flush() message = 'Changes made to sequencer configuration <b>%s</b> has been saved' % request_type.name return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_request_types', - operation='view', + action='view_request_type', id=request_type_id, message=message, status=status ) ) - else: - rt_info_widgets, rt_states_widgets = self.__create_request_type_form( trans, **kwd ) - rename_dataset_selectbox = self.__build_rename_dataset_select_list( trans ) - return trans.fill_template( '/admin/requests/create_request_type.mako', - rt_info_widgets=rt_info_widgets, - rt_states_widgets=rt_states_widgets, - rename_dataset_selectbox=rename_dataset_selectbox, - message=message, - status=status ) + return trans.fill_template( '/admin/requests/create_request_type.mako', + rt_info_widgets=rt_info_widgets, + rt_states_widgets=rt_states_widgets, + rename_dataset_select_field=rename_dataset_select_field, + message=message, + status=status ) def __create_request_type_form( self, trans, **kwd ): - request_forms = self.get_all_forms( trans, - filter=dict( deleted=False ), - form_type=trans.model.FormDefinition.types.REQUEST ) - sample_forms = self.get_all_forms( trans, - filter=dict( deleted=False ), - form_type=trans.model.FormDefinition.types.SAMPLE ) - if not request_forms or not sample_forms: + request_form_definitionss = self.get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.model.FormDefinition.types.REQUEST ) + sample_form_definitions = self.get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.model.FormDefinition.types.SAMPLE ) + if not request_form_definitionss or not sample_form_definitions: return [],[] params = util.Params( kwd ) - rt_info_widgets = [] - rt_info_widgets.append( dict( label='Name', - widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ) ) - rt_info_widgets.append( dict( label='Description', - widget=TextField( 'desc', 40, util.restore_text( params.get( 'desc', '' ) ) ) ) ) - rf_selectbox = SelectField( 'request_form_id' ) - for fd in request_forms: - if str( fd.id ) == params.get( 'request_form_id', '' ): - rf_selectbox.add_option( fd.name, fd.id, selected=True ) - else: - rf_selectbox.add_option( fd.name, fd.id ) - rt_info_widgets.append( dict( label='Request form', - widget=rf_selectbox ) ) - sf_selectbox = SelectField( 'sample_form_id' ) - for fd in sample_forms: - if str( fd.id ) == params.get( 'sample_form_id', '' ): - sf_selectbox.add_option( fd.name, fd.id, selected=True ) - else: - sf_selectbox.add_option( fd.name, fd.id ) - rt_info_widgets.append( dict( label='Sample form', - widget=sf_selectbox ) ) + request_form_id = params.get( 'request_form_id', 'none' ) + sample_form_id = params.get( 'sample_form_id', 'none' ) + request_form_id_select_field = build_select_field( trans, + objs=request_form_definitionss, + label_attr='id', + select_field_name='request_form_id', + selected_value=request_form_id, + refresh_on_change=False ) + sample_form_id_select_field = build_select_field( trans, + objs=sample_form_definitions, + label_attr='id', + select_field_name='sample_form_id', + selected_value=sample_form_id, + refresh_on_change=False ) + rt_info_widgets = [ dict( label='Name', + widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ), + dict( label='Description', + widget=TextField( 'desc', 40, util.restore_text( params.get( 'desc', '' ) ) ) ), + dict( label='Request form', + widget=request_form_id_select_field ), + dict( label='Sample form', + widget=sample_form_id_select_field ) ] # Possible sample states rt_states = [] i=0 @@ -787,26 +697,14 @@ class RequestsAdmin( BaseController, Use else: break return rt_info_widgets, rt_states - def __build_rename_dataset_select_list( self, trans, rt=None ): - if rt: - sel_opt = rt.datatx_info.get( 'rename_dataset', trans.model.RequestType.rename_dataset_options.NO ) - else: - sel_opt = trans.model.RequestType.rename_dataset_options.NO - rename_dataset_selectbox = SelectField( 'rename_dataset' ) - for opt, opt_name in trans.model.RequestType.rename_dataset_options.items(): - if sel_opt == opt_name: - rename_dataset_selectbox.add_option( opt_name, opt_name, selected=True ) - else: - rename_dataset_selectbox.add_option( opt_name, opt_name ) - return rename_dataset_selectbox def __save_request_type(self, trans, **kwd): params = util.Params( kwd ) name = util.restore_text( params.get( 'name', '' ) ) desc = util.restore_text( params.get( 'desc', '' ) ) request_form_id = params.get( 'request_form_id', None ) - request_form = trans.sa_session.query( trans.model.FormDefinition ).get( int( request_form_id ) ) + request_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( request_form_id ) ) sample_form_id = params.get( 'sample_form_id', None ) - sample_form = trans.sa_session.query( trans.model.FormDefinition ).get( int( sample_form_id ) ) + sample_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( sample_form_id ) ) data_dir = util.restore_text( params.get( 'data_dir', '' ) ) data_dir = self.__check_path( data_dir ) # Data transfer info - Make sure password is retrieved from kwd rather than Params @@ -836,43 +734,73 @@ class RequestsAdmin( BaseController, Use i = i + 1 else: break - message = "The new sequencer configuration named '%s' with %s states has been created" % ( request_type.name, i ) + message = "The new sequencer configuration named (%s) with %s states has been created" % ( request_type.name, i ) return request_type, message - def __delete_request_type( self, trans, **kwd ): + @web.expose + @web.require_admin + def view_request_type( self, trans, **kwd ): + request_type_id = kwd.get( 'id', None ) + try: + request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' ) + forms = self.get_all_forms( trans ) + rename_dataset_select_field = self.__build_rename_dataset_select_field( trans, request_type ) + return trans.fill_template( '/admin/requests/view_request_type.mako', + request_type=request_type, + forms=forms, + rename_dataset_select_field=rename_dataset_select_field ) + @web.expose + @web.require_admin + def view_form_definition( self, trans, **kwd ): + form_definition_id = kwd.get( 'id', None ) + try: + form_definition = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( form_definition_id ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', form_definition_id, action='browse_request_types' ) + return trans.fill_template( '/admin/forms/show_form_read_only.mako', + form_definition=form_definition ) + @web.expose + @web.require_admin + def delete_request_type( self, trans, **kwd ): rt_id = kwd.get( 'id', '' ) rt_id_list = util.listify( rt_id ) for rt_id in rt_id_list: try: request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( rt_id ) ) except: - return invalid_id_redirect( trans, 'requests_admin', rt_id, action='manage_request_types' ) + return invalid_id_redirect( trans, 'requests_admin', rt_id, action='browse_request_types' ) request_type.deleted = True trans.sa_session.add( request_type ) trans.sa_session.flush() status = 'done' message = '%i sequencer configurations has been deleted' % len( rt_id_list ) return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_request_types', + action='browse_request_types', message=message, status='done' ) ) - def __undelete_request_type( self, trans, **kwd ): + @web.expose + @web.require_admin + def undelete_request_type( self, trans, **kwd ): rt_id = kwd.get( 'id', '' ) rt_id_list = util.listify( rt_id ) for rt_id in rt_id_list: try: request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( rt_id ) ) except: - return invalid_id_redirect( trans, 'requests_admin', rt_id, action='manage_request_types' ) + return invalid_id_redirect( trans, 'requests_admin', rt_id, action='browse_request_types' ) request_type.deleted = False trans.sa_session.add( request_type ) trans.sa_session.flush() status = 'done' message = '%i sequencer configurations have been undeleted' % len( rt_id_list ) return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_request_types', + action='browse_request_types', message=message, status=status ) ) - def __show_request_type_permissions( self, trans, **kwd ): + @web.expose + @web.require_admin + def request_type_permissions( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -880,7 +808,7 @@ class RequestsAdmin( BaseController, Use try: request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) except: - return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='manage_request_types' ) + return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' ) roles = trans.sa_session.query( trans.model.Role ) \ .filter( trans.model.Role.table.c.deleted==False ) \ .order_by( trans.model.Role.table.c.name ) @@ -897,3 +825,30 @@ class RequestsAdmin( BaseController, Use roles=roles, status=status, message=message ) + # ===== Methods for building SelectFields used on various admin_requests forms + def __build_sample_id_select_field( self, request, selected_value ): + return build_select_field( trans, request.samples, 'name', 'sample_id', selected_value=selected_value, refresh_on_change=False ) + def __build_rename_dataset_select_field( self, trans, request_type=None ): + if request_type: + selected_value = request_type.datatx_info.get( 'rename_dataset', trans.model.RequestType.rename_dataset_options.NO ) + else: + selected_value = trans.model.RequestType.rename_dataset_options.NO + return build_select_field( trans, + objs=[ v for k, v in trans.model.RequestType.rename_dataset_options.items() ], + label_attr='self', + select_field_name='rename_dataset', + selected_value=selected_value, + refresh_on_change=False ) +# ===== Methods for building SelectFields used on various admin_requests forms - used outside this controller ===== +def build_rename_datasets_for_sample_select_field( trans, sample_dataset, selected_value='none' ): + options = [] + for option_index, option in enumerate( sample_dataset.file_path.split( os.sep )[ :-1 ] ): + option = option.strip() + if option: + options.append( option ) + return build_select_field( trans, + objs=options, + label_attr='self', + select_field_name='rename_datasets_for_sample_%s' % trans.security.encode_id( sample_dataset.id ), + selected_value=selected_value, + refresh_on_change=False ) --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -64,7 +64,7 @@ </div><div class="form-row"><label>Add experiment name and the sample name to the dataset name?</label> - ${rename_dataset_selectbox.get_html()} + ${rename_dataset_select_field.get_html()} <div class="toolParamHelp" style="clear: both;"> The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This makes sure that dataset names remain unique in Galaxy even when they have the --- a/templates/admin/requests/request_type_permissions.mako +++ b/templates/admin/requests/request_type_permissions.mako @@ -32,7 +32,7 @@ <div class="toolForm"><div class="toolFormTitle">Manage permissions on "${request_type.name}"</div><div class="toolFormBody"> - <form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='requests_admin', action='manage_request_types', operation="permissions", id=trans.security.encode_id( request_type.id ) )}" method="post"> + <form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='requests_admin', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"><% obj_name = request_type.name --- a/templates/admin/requests/dataset.mako +++ b/templates/admin/requests/dataset.mako @@ -19,51 +19,51 @@ <div class="toolForm"><div class="toolFormTitle">Dataset Information</div><div class="toolFormBody"> - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} - </div> - <div style="clear: both"></div> + <div class="form-row"> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.name} </div> - <div class="form-row"> - <label>File on the Sequencer:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.file_path} - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>File on the Sequencer:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.file_path} </div> - <div class="form-row"> - <label>Size:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.size} - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Size:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.size} </div> - <div class="form-row"> - <label>Created on:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.create_time} - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Created on:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.create_time} </div> - <div class="form-row"> - <label>Updated on:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.update_time} - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Updated on:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.update_time} </div> - <div class="form-row"> - <label>Transfer status:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.status} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Transfer status:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.status} + %if sample_dataset.status == sample.transfer_status.ERROR: <br/> - %if sample_dataset.status == sample.transfer_status.ERROR: - ${sample_dataset.error_msg} - %endif - </div> - <div style="clear: both"></div> + ${sample_dataset.error_msg} + %endif </div> + <div style="clear: both"></div> + </div></div></div>

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