November 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2941: Fixed the functional test to create new user a...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c81a9407c7a8 changeset: 2941:c81a9407c7a8 user: rc date: Mon Nov 02 16:12:31 2009 -0500 description: Fixed the functional test to create new user as admin diffstat: test/base/twilltestcase.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r cd0596754ff1 -r c81a9407c7a8 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Nov 02 13:30:17 2009 -0500 +++ b/test/base/twilltestcase.py Mon Nov 02 16:12:31 2009 -0500 @@ -922,7 +922,7 @@ def create_new_account_as_admin( self, email='test4(a)bx.psu.edu', password='testuser' ): """Create a new account for another user""" self.home() - self.visit_url( "%s/admin/create_new_user?email=%s&password=%s&confirm=%s&user_create_button=Create&subscribe=False" \ + self.visit_url( "%s/user/create?admin_view=True&email=%s&password=%s&confirm=%s&create_user_button=Submit&subscribe=False" \ % ( self.url, email, password, password ) ) try: self.check_page_for_string( "Created new user account" )

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[hg] galaxy 2942: Remove old encode import tools
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/67dce52402fd changeset: 2942:67dce52402fd user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Nov 02 16:21:28 2009 -0500 description: Remove old encode import tools diffstat: tools/data_source/encode_import.py | 82 ---------- tools/data_source/encode_import_all_latest_datasets.xml | 65 -------- tools/data_source/encode_import_chromatin_and_chromosomes.xml | 64 -------- tools/data_source/encode_import_code.py | 54 ------ tools/data_source/encode_import_gencode.xml | 67 -------- tools/data_source/encode_import_genes_and_transcripts.xml | 64 -------- tools/data_source/encode_import_multi-species_sequence_analysis.xml | 66 -------- tools/data_source/encode_import_transcription_regulation.xml | 65 -------- 8 files changed, 0 insertions(+), 527 deletions(-) diffs (565 lines): diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import.py --- a/tools/data_source/encode_import.py Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -#!/usr/bin/env python - -""" -Script that imports locally stored data as a new dataset for the user -Usage: import id outputfile -""" -import sys, os -from shutil import copyfile - -assert sys.version_info[:2] >= ( 2, 4 ) - -BUFFER = 1048576 - -def stop_err( msg ): - sys.stderr.write( msg ) - sys.exit() - -def main(): - uids = sys.argv[1].split(",") - out_file1 = sys.argv[2] - file_name = "%s/encode_datasets.loc" % sys.argv[3] - - #remove NONE from uids - have_none = True - while have_none: - try: - uids.remove('None') - except: - have_none = False - - #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files - available_files = {} - try: - for i, line in enumerate( file ( file_name ) ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - fields = line.split( '\t' ) - try: - encode_group = fields[0].strip() - build = fields[1].strip() - description = fields[2].strip() - uid = fields[3].strip() - path = fields[4].strip() - try: - file_type = fields[5].strip() - except: - file_type = "bed" - except: - continue - available_files[uid] = ( description, path, build, file_type ) - except: - stop_err( "It appears that the configuration file for this tool is missing." ) - - #create list of tuples of ( displayName, FileName, build ) for desired files - desired_files = [] - for uid in uids: - try: - desired_files.append( available_files[uid] ) - except: - continue - - #copy first file to contents of given output file - file1_copied = False - while not file1_copied: - try: - first_file = desired_files.pop(0) - except: - stop_err( "There were no valid files requested." ) - file1_desc, file1_path, file1_build, file1_type = first_file - try: - copyfile( file1_path, out_file1 ) - print "#File1\t" + file1_desc + "\t" + file1_build + "\t" + file1_type - file1_copied = True - except: - stop_err( "The file '%s' is missing." %str( file1_path ) ) - - #Tell post-process filter where remaining files reside - for extra_output in desired_files: - file_desc, file_path, file_build, file_type = extra_output - print "#NewFile\t" + file_desc + "\t" + file_build + "\t" + file_path + "\t" + file_type - -if __name__ == "__main__": main() diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_all_latest_datasets.xml --- a/tools/data_source/encode_import_all_latest_datasets.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -<tool id="encode_import_all_latest_datasets1" name="Combined Datasets"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="ALD" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="ALD" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A… - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - - </help> -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_chromatin_and_chromosomes.xml --- a/tools/data_source/encode_import_chromatin_and_chromosomes.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -<tool id="encode_import_chromatin_and_chromosomes1" name="Chromatin and Chromosomes"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="CC" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="CC" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A… - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - </help> -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_code.py --- a/tools/data_source/encode_import_code.py Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -import os, sys - -from galaxy import datatypes, config, jobs -from shutil import copyfile - -#post processing, set build for data and add additional data to history -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - base_dataset = out_data.items()[0][1] - history = base_dataset.history - if history == None: - print "unknown history!" - return - new_stdout = "" - split_stdout = stdout.split("\n") - basic_name = "" - for line in split_stdout: - fields = line.split("\t") - if fields[0] == "#File1": - description = fields[1] - dbkey = fields[2] - file_type = fields[3] - name, data = out_data.items()[0] - data.set_size() - basic_name = data.name - data.name = data.name + " (" + description + ")" - data.dbkey = dbkey - data.info = data.name - data = app.datatypes_registry.change_datatype( data, file_type ) - data.init_meta() - data.set_peek() - app.model.flush() - elif fields[0] == "#NewFile": - description = fields[1] - dbkey = fields[2] - filepath = fields[3] - file_type = fields[4] - newdata = app.model.HistoryDatasetAssociation( create_dataset = True ) #This import should become a library - newdata.set_size() - newdata.extension = file_type - newdata.name = basic_name + " (" + description + ")" - history.add_dataset( newdata ) - app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) - app.model.flush() - try: - copyfile(filepath,newdata.file_name) - newdata.info = newdata.name - newdata.state = jobs.JOB_OK - except: - newdata.info = "The requested file is missing from the system." - newdata.state = jobs.JOB_ERROR - newdata.dbkey = dbkey - newdata.set_meta() - newdata.set_peek() - app.model.flush() diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_gencode.xml --- a/tools/data_source/encode_import_gencode.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -<tool id="encode_import_gencode1" name="Gencode Datasets"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="GENCODE" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="GENCODE" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -These are the datasets used for partitioning files. - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A… - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - </help> - -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_genes_and_transcripts.xml --- a/tools/data_source/encode_import_genes_and_transcripts.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -<tool id="encode_import_genes_and_transcripts1" name="Genes and Transcripts"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="GT" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="GT" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A… - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - </help> -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_multi-species_sequence_analysis.xml --- a/tools/data_source/encode_import_multi-species_sequence_analysis.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -<tool id="encode_import_multi-species_sequence_analysis1" name="Multi-species Sequence Analysis"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="MSA" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="MSA" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A… - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - - - </help> -</tool> diff -r c81a9407c7a8 -r 67dce52402fd tools/data_source/encode_import_transcription_regulation.xml --- a/tools/data_source/encode_import_transcription_regulation.xml Mon Nov 02 16:12:31 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -<tool id="encode_import_transcription_regulation1" name="Transcription Regulation"> - <command interpreter="python">encode_import.py $hg17,$hg16 $output ${GALAXY_DATA_INDEX_DIR}</command> - <inputs> - <display> - <p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p> - <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p> - </display> - <param name="hg17" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="TR" column="0"/> - <filter type="static_value" name="dbkey" value="hg17" column="1"/> - </options> - </param> - <param name="hg16" type="select" display="checkboxes" multiple="true"> - <options from_file="encode_datasets.loc"> - <column name="name" index="2"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <column name="encode_group" index="0"/> - <column name="uid" index="3"/> - <filter type="static_value" name="encode_group" value="TR" column="0"/> - <filter type="static_value" name="dbkey" value="hg16" column="1"/> - </options> - </param> - </inputs> - <outputs> - <data format="bed" name="output"/> - </outputs> - <code file="encode_import_code.py"/> - <help> - -.. class:: warningmark - -The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data. - -.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960 - -For detailed information about data deposition and partitioning, click here_. - -.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A… - -*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: - -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: - 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) - 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) - 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) - 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. - 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. - 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. - 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. - ------ - -.. class:: infomark - -**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. - - </help> - -</tool>

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[hg] galaxy 2943: Update rg test data sample outputs to match th...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6e657b4aa837 changeset: 2943:6e657b4aa837 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Nov 02 16:52:32 2009 -0500 description: Update rg test data sample outputs to match the new versions Ross uploaded diffstat: test-data/rgenetics.bed | 2 +- test-data/rgenetics.bim | 35 ++++++++--- test-data/rgenetics.fam | 130 +++++++++++++------------------------------ test-data/rgenetics.map | 35 ++++++++--- test-data/rgenetics.ped | 130 +++++++++++++------------------------------ 5 files changed, 131 insertions(+), 201 deletions(-) diffs (354 lines): diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.bed --- a/test-data/rgenetics.bed Mon Nov 02 16:21:28 2009 -0500 +++ b/test-data/rgenetics.bed Mon Nov 02 16:52:32 2009 -0500 @@ -1,1 +1,1 @@ -lÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿï¾î¸ÿÿüþ¿ÿ¿ûú¿¿ï/ÿÿþÿï¯ê¸ëê°®¾î®ãê¸;ì/âïú¯ï¯Îê¼ïâ°¯þÏªã¯ø+ì?âÿú¯ïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïÿÿÿÿÿºÿÿþ¯þï¿ÿ»ÿÿþÿÿÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿÿÿÿÿþïÿÿÿþÿÿÿÿûÿûÿÿÿ»ÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïëÿê¾ÿºúïþ¯îë¿þ;¯>âïþ» \ No newline at end of file +lÿëþ¿¾+êóª¿ü £ïªîþ¨êÿïªûÿÿÿÿÿÿþï®¨ª"ëú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿þ¿ÿëþ¿¾+êóª¿ºûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ ú¢ª±«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü( \ No newline at end of file diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.bim --- a/test-data/rgenetics.bim Mon Nov 02 16:21:28 2009 -0500 +++ b/test-data/rgenetics.bim Mon Nov 02 16:52:32 2009 -0500 @@ -1,10 +1,25 @@ -22 rs5992809 16.5965 16596539 0 C -22 rs12168131 16.6573 16657262 G A -22 rs390041 16.6629 16662916 T C -22 rs437633 16.6697 16669684 A G -22 rs450960 16.6909 16690858 T C -22 rs450975 16.6909 16690887 T C -22 rs451740 16.6912 16691174 T C -22 rs8139723 16.6917 16691696 T C -22 rs405490 16.6922 16692175 G A -22 rs415170 16.6935 16693517 G C +22 rs2283802 0 21784722 4 2 +22 rs2267000 0 21785366 4 2 +22 rs16997606 0 21794754 1 3 +22 rs4820537 0 21794810 1 3 +22 rs3788347 0 21797804 3 1 +22 rs756632 0 21799918 4 2 +22 rs4820539 0 21807970 1 3 +22 rs2283804 0 21820335 1 2 +22 rs2267006 0 21820990 3 1 +22 rs4822363 0 21821000 4 2 +22 rs5751592 0 21827674 4 2 +22 rs5759608 0 21832708 2 4 +22 rs5759612 0 21833170 3 1 +22 rs2267009 0 21860168 3 4 +22 rs2267010 0 21864366 3 1 +22 rs5759636 0 21868698 4 2 +22 rs2071436 0 21871488 4 2 +22 rs2267013 0 21875879 3 1 +22 rs6003566 0 21889806 3 1 +22 rs2256725 0 21892891 2 1 +22 rs12160770 0 21892925 1 3 +22 rs5751611 0 21896019 2 4 +22 rs762601 0 21898858 1 3 +22 rs2156921 0 21899063 3 1 +22 rs4822375 0 21905642 1 3 diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.fam --- a/test-data/rgenetics.fam Mon Nov 02 16:21:28 2009 -0500 +++ b/test-data/rgenetics.fam Mon Nov 02 16:52:32 2009 -0500 @@ -1,90 +1,40 @@ -CH18526 NA18526 0 0 2 1 -CH18524 NA18524 0 0 1 1 -CH18529 NA18529 0 0 2 1 -CH18558 NA18558 0 0 1 1 -CH18532 NA18532 0 0 2 1 -CH18561 NA18561 0 0 1 1 -CH18562 NA18562 0 0 1 1 -CH18537 NA18537 0 0 2 2 -CH18603 NA18603 0 0 1 2 -CH18540 NA18540 0 0 2 1 -CH18605 NA18605 0 0 1 1 -CH18542 NA18542 0 0 2 1 -CH18545 NA18545 0 0 2 1 -CH18572 NA18572 0 0 1 2 -CH18547 NA18547 0 0 2 2 -CH18609 NA18609 0 0 1 1 -CH18550 NA18550 0 0 2 1 -CH18608 NA18608 0 0 1 1 -CH18552 NA18552 0 0 2 1 -CH18611 NA18611 0 0 1 1 -CH18555 NA18555 0 0 2 1 -CH18564 NA18564 0 0 2 2 -CH18566 NA18566 0 0 2 1 -CH18563 NA18563 0 0 1 1 -CH18570 NA18570 0 0 2 1 -CH18612 NA18612 0 0 1 2 -CH18571 NA18571 0 0 2 1 -CH18620 NA18620 0 0 1 1 -CH18621 NA18621 0 0 1 1 -CH18594 NA18594 0 0 2 1 -CH18622 NA18622 0 0 1 2 -CH18573 NA18573 0 0 2 2 -CH18623 NA18623 0 0 1 1 -CH18576 NA18576 0 0 2 1 -CH18577 NA18577 0 0 2 1 -CH18624 NA18624 0 0 1 1 -CH18579 NA18579 0 0 2 1 -CH18632 NA18632 0 0 1 2 -CH18582 NA18582 0 0 2 1 -CH18633 NA18633 0 0 1 1 -CH18635 NA18635 0 0 1 2 -CH18592 NA18592 0 0 2 1 -CH18636 NA18636 0 0 1 1 -CH18593 NA18593 0 0 2 2 -CH18637 NA18637 0 0 1 1 -JA18942 NA18942 0 0 2 2 -JA18940 NA18940 0 0 1 2 -JA18951 NA18951 0 0 2 2 -JA18943 NA18943 0 0 1 2 -JA18947 NA18947 0 0 2 2 -JA18944 NA18944 0 0 1 2 -JA18945 NA18945 0 0 1 2 -JA18949 NA18949 0 0 2 2 -JA18948 NA18948 0 0 1 2 -JA18952 NA18952 0 0 1 2 -JA18956 NA18956 0 0 2 2 -JA18964 NA18964 0 0 2 2 -JA18953 NA18953 0 0 1 1 -JA18968 NA18968 0 0 2 2 -JA18959 NA18959 0 0 1 2 -JA18969 NA18969 0 0 2 1 -JA18960 NA18960 0 0 1 2 -JA18961 NA18961 0 0 1 2 -JA18972 NA18972 0 0 2 2 -JA18965 NA18965 0 0 1 2 -JA18973 NA18973 0 0 2 2 -JA18966 NA18966 0 0 1 2 -JA18975 NA18975 0 0 2 2 -JA18967 NA18967 0 0 1 2 -JA18976 NA18976 0 0 2 1 -JA18978 NA18978 0 0 2 2 -JA18970 NA18970 0 0 1 1 -JA18980 NA18980 0 0 2 2 -JA18995 NA18995 0 0 1 1 -JA18981 NA18981 0 0 2 2 -JA18971 NA18971 0 0 1 2 -JA18974 NA18974 0 0 1 1 -JA18987 NA18987 0 0 2 2 -JA18990 NA18990 0 0 1 1 -JA18991 NA18991 0 0 2 2 -JA18994 NA18994 0 0 1 2 -JA18992 NA18992 0 0 2 2 -JA18997 NA18997 0 0 2 2 -JA18998 NA18998 0 0 2 2 -JA19000 NA19000 0 0 1 2 -JA19005 NA19005 0 0 1 2 -JA18999 NA18999 0 0 2 2 -JA19007 NA19007 0 0 1 2 -JA19003 NA19003 0 0 2 2 -JA19012 NA19012 0 0 1 2 +101 1 3 2 2 2 +101 2 0 0 2 1 +101 3 0 0 1 1 +105 1 3 2 2 2 +105 2 0 0 2 1 +105 3 0 0 1 1 +112 1 3 2 1 2 +112 2 0 0 2 1 +112 3 0 0 1 1 +117 1 3 2 2 2 +117 2 0 0 2 1 +117 3 0 0 1 1 +12 1 3 2 1 2 +12 2 0 0 2 1 +12 3 0 0 1 1 +13 1 3 2 1 2 +13 2 0 0 2 1 +13 3 0 0 1 1 +1334 1 10 11 1 2 +1334 10 0 0 1 1 +1334 11 0 0 2 1 +1334 12 0 0 1 1 +1334 13 0 0 2 1 +1334 2 12 13 2 2 +1340 1 9 10 1 2 +1340 10 0 0 2 1 +1340 11 0 0 1 1 +1340 12 0 0 2 1 +1340 2 11 12 2 2 +1340 9 0 0 1 1 +1341 1 11 12 1 1 +1341 11 0 0 1 1 +1341 12 0 0 2 1 +1341 13 0 0 1 1 +1341 14 0 0 2 1 +1341 2 13 14 2 1 +1344 1 12 13 1 1 +1344 12 0 0 1 1 +1344 13 0 0 2 1 +1345 12 0 0 1 1 diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.map --- a/test-data/rgenetics.map Mon Nov 02 16:21:28 2009 -0500 +++ b/test-data/rgenetics.map Mon Nov 02 16:52:32 2009 -0500 @@ -1,10 +1,25 @@ -22 rs5992809 16.5965 16596539 -22 rs12168131 16.6573 16657262 -22 rs390041 16.6629 16662916 -22 rs437633 16.6697 16669684 -22 rs450960 16.6909 16690858 -22 rs450975 16.6909 16690887 -22 rs451740 16.6912 16691174 -22 rs8139723 16.6917 16691696 -22 rs405490 16.6922 16692175 -22 rs415170 16.6935 16693517 +22 rs2283802 0 21784722 +22 rs2267000 0 21785366 +22 rs16997606 0 21794754 +22 rs4820537 0 21794810 +22 rs3788347 0 21797804 +22 rs756632 0 21799918 +22 rs4820539 0 21807970 +22 rs2283804 0 21820335 +22 rs2267006 0 21820990 +22 rs4822363 0 21821000 +22 rs5751592 0 21827674 +22 rs5759608 0 21832708 +22 rs5759612 0 21833170 +22 rs2267009 0 21860168 +22 rs2267010 0 21864366 +22 rs5759636 0 21868698 +22 rs2071436 0 21871488 +22 rs2267013 0 21875879 +22 rs6003566 0 21889806 +22 rs2256725 0 21892891 +22 rs12160770 0 21892925 +22 rs5751611 0 21896019 +22 rs762601 0 21898858 +22 rs2156921 0 21899063 +22 rs4822375 0 21905642 diff -r 67dce52402fd -r 6e657b4aa837 test-data/rgenetics.ped --- a/test-data/rgenetics.ped Mon Nov 02 16:21:28 2009 -0500 +++ b/test-data/rgenetics.ped Mon Nov 02 16:52:32 2009 -0500 @@ -1,90 +1,40 @@ -CH18526 NA18526 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18524 NA18524 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18529 NA18529 0 0 2 1 C C A A T C A G T C T C T C C C G A G C -CH18558 NA18558 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18532 NA18532 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18561 NA18561 0 0 1 1 C C A A C C G G T C C C T C C C G A G C -CH18562 NA18562 0 0 1 1 C C G A T C A G T C C C T C C C G A G C -CH18537 NA18537 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -CH18603 NA18603 0 0 1 2 C C G A T C A G C C C C C C C C A A C C -CH18540 NA18540 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18605 NA18605 0 0 1 1 C C A A T T A A C C C C C C C C A A C C -CH18542 NA18542 0 0 2 1 C C G A T C G G C C C C C C C C A A C C -CH18545 NA18545 0 0 2 1 C C G A T C A G T C C C T C C C G A G C -CH18572 NA18572 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -CH18547 NA18547 0 0 2 2 C C G A T C A G T C C C T C C C G A G C -CH18609 NA18609 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18550 NA18550 0 0 2 1 C C G G T T A A T C C C T C T C G A G C -CH18608 NA18608 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18552 NA18552 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18611 NA18611 0 0 1 1 C C G A T C A G T C C C T C C C G A G C -CH18555 NA18555 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18564 NA18564 0 0 2 2 C C A A T C G G C C C C C C C C A A C C -CH18566 NA18566 0 0 2 1 C C A A T C A G C C C C C C T C A A C C -CH18563 NA18563 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18570 NA18570 0 0 2 1 C C A A T C A G T C T C T C C C G A G C -CH18612 NA18612 0 0 1 2 C C A A T C A A T C T C T C C C G A G C -CH18571 NA18571 0 0 2 1 C C A A T C A G C C C C C C C C A A C C -CH18620 NA18620 0 0 1 1 C C A A C C G G T C T C T C C C G A G C -CH18621 NA18621 0 0 1 1 C C G G T T A A T C C C T C C C G A G C -CH18594 NA18594 0 0 2 1 C C A A T T A A C C C C C C C C A A G C -CH18622 NA18622 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -CH18573 NA18573 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -CH18623 NA18623 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18576 NA18576 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18577 NA18577 0 0 2 1 C C A A T C A G C C C C C C C C A A G C -CH18624 NA18624 0 0 1 1 C C A A T C A G C C C C C C C C A A C C -CH18579 NA18579 0 0 2 1 C C A A T C A G T C T C T C T C G A G C -CH18632 NA18632 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -CH18582 NA18582 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18633 NA18633 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18635 NA18635 0 0 1 2 C C A A T C G G C C C C C C C C A A C C -CH18592 NA18592 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18636 NA18636 0 0 1 1 C C A A T C A A T C T C T C C C G A G C -CH18593 NA18593 0 0 2 2 C C A A C C G G T C T C T C C C G A G C -CH18637 NA18637 0 0 1 1 C C A A T C A G T C T C T C C C G A G C -JA18942 NA18942 0 0 2 2 C C A A C C A G C C C C C C C C A A C C -JA18940 NA18940 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -JA18951 NA18951 0 0 2 2 C C G A T C A G C C C C C C C C A A C C -JA18943 NA18943 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18947 NA18947 0 0 2 2 C C G A T T A A C C C C C C C C A A G C -JA18944 NA18944 0 0 1 2 C C A A T C A G T C T C T C C C G A G C -JA18945 NA18945 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18949 NA18949 0 0 2 2 C C G A T C G G C C C C C C C C A A C C -JA18948 NA18948 0 0 1 2 C C G A T C G G C C C C C C C C A A C C -JA18952 NA18952 0 0 1 2 C C A A T C A G C C C C C C C C A A C C -JA18956 NA18956 0 0 2 2 C C A A C C A G T C T C T C C C G A G C -JA18964 NA18964 0 0 2 2 C C A A T T A A C C C C C C C C A A G C -JA18953 NA18953 0 0 1 1 C C A A T C A G C C C C C C T C A A C C -JA18968 NA18968 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18959 NA18959 0 0 1 2 C C G A T C G G C C C C C C C C A A C C -JA18969 NA18969 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -JA18960 NA18960 0 0 1 2 C C A A T C A G T C T C T C C C G A G C -JA18961 NA18961 0 0 1 2 C C A A C C A G C C C C C C C C A A C C -JA18972 NA18972 0 0 2 2 C C G A T T A A T T T C T T C C G G G G -JA18965 NA18965 0 0 1 2 C C A A T T A A C C C C C C C C A A C C -JA18973 NA18973 0 0 2 2 C C A A C C G G C C C C C C T C A A C C -JA18966 NA18966 0 0 1 2 C C G A T C A G T C C C T C C C G A G C -JA18975 NA18975 0 0 2 2 C C A A C C G G C C C C C C C C A A G C -JA18967 NA18967 0 0 1 2 C C A A C C G G C C C C C C C C A A G C -JA18976 NA18976 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -JA18978 NA18978 0 0 2 2 C C G A T C G G C C C C C C C C A A C C -JA18970 NA18970 0 0 1 1 C C G G T T A A T T C C T T C C G G G G -JA18980 NA18980 0 0 2 2 C C A A T C A G T C T C T C C C G A G C -JA18995 NA18995 0 0 1 1 C C A A T T A A C C C C C C C C A A G G -JA18981 NA18981 0 0 2 2 C C A A T C A G C C C C C C C C A A G C -JA18971 NA18971 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18974 NA18974 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -JA18987 NA18987 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18990 NA18990 0 0 1 1 C C A A T C G G C C C C C C C C A A G C -JA18991 NA18991 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18994 NA18994 0 0 1 2 C C G A T C A G C C C C C C C C A A G C -JA18992 NA18992 0 0 2 2 C C A A T C A G C C C C C C T C A A C C -JA18997 NA18997 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18998 NA18998 0 0 2 2 C C A A C C G G C C C C C C T C A A C C -JA19000 NA19000 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA19005 NA19005 0 0 1 2 C C A A C C G G C C C C C C C C A A G C -JA18999 NA18999 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -JA19007 NA19007 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -JA19003 NA19003 0 0 2 2 C C A A T C G G C C C C C C C C A A C C -JA19012 NA19012 0 0 1 2 C C A A 0 0 G G C C C C C C 0 0 A A C C +101 1 3 2 2 2 2 2 4 2 1 3 3 3 3 3 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 3 1 3 1 2 1 0 0 2 2 1 3 3 1 1 3 +101 2 0 0 2 1 2 2 4 2 1 3 3 3 3 3 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 3 1 3 1 2 1 3 3 2 2 1 3 3 1 1 3 +101 3 0 0 1 1 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 1 3 2 4 3 3 1 1 3 3 +105 1 3 2 2 2 2 2 4 2 3 3 3 3 3 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 3 1 1 1 2 1 0 0 2 2 1 1 3 3 1 1 +105 2 0 0 2 1 2 2 4 4 3 3 3 3 3 1 2 2 1 3 1 2 3 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +105 3 0 0 1 1 4 2 2 2 3 3 3 3 3 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +112 1 3 2 1 2 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +112 2 0 0 2 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +112 3 0 0 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0 0 0 3 3 1 1 3 3 +13 3 0 0 1 1 2 2 4 4 1 3 3 3 3 3 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 3 1 2 2 2 2 1 1 3 1 1 1 3 3 2 2 3 3 1 1 3 3 +1334 1 10 11 1 2 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1334 10 0 0 1 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1334 11 0 0 2 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1334 12 0 0 1 1 4 2 2 2 3 3 1 3 1 1 2 2 3 3 2 2 1 1 2 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1334 13 0 0 2 1 4 2 4 2 3 3 1 3 3 1 4 2 1 3 2 2 1 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1334 2 12 13 2 2 4 4 2 2 3 3 1 3 1 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 3 1 1 2 2 4 4 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1340 1 9 10 1 2 4 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 3 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1340 10 0 0 2 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 3 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1340 11 0 0 1 1 4 2 4 2 3 3 1 3 3 1 4 2 1 3 2 2 1 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 12 0 0 2 1 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 4 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 2 11 12 2 2 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 9 0 0 1 1 4 4 2 2 3 3 1 1 1 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 3 1 1 2 2 4 4 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 1 11 12 1 1 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 0 0 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1 +1341 11 0 0 1 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 4 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1341 12 0 0 2 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 4 2 4 2 3 1 1 1 2 1 3 3 2 2 1 1 3 3 1 1 +1341 13 0 0 1 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 14 0 0 2 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 2 13 14 2 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1344 1 12 13 1 1 2 2 4 4 3 3 3 3 3 3 4 4 1 1 2 2 1 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1 +1344 12 0 0 1 1 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1344 13 0 0 2 1 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1345 12 0 0 1 1 4 2 4 2 3 3 3 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 4 2 4 2 3 1 1 1 2 1 3 3 2 2 1 1 3 3 1 1

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[hg] galaxy 2935: Add contributed Debian init script and OS X La...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/da1a03642283 changeset: 2935:da1a03642283 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Oct 30 12:41:17 2009 -0400 description: Add contributed Debian init script and OS X LaunchDaemon plist from James Casbon, and my Solaris SMF manifest. diffstat: contrib/README | 19 ++++++ contrib/edu.psu.galaxy.GalaxyServer.plist | 22 +++++++ contrib/galaxy.debian-init | 55 ++++++++++++++++++ contrib/galaxy.solaris-smf.xml | 75 +++++++++++++++++++++++++ 4 files changed, 171 insertions(+), 0 deletions(-) diffs (187 lines): diff -r 979534de254d -r da1a03642283 contrib/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/contrib/README Fri Oct 30 12:41:17 2009 -0400 @@ -0,0 +1,19 @@ +CONTENTS +-------- + +edu.psu.galaxy.GalaxyServer.plist: + + LaunchDaemon definition for OS X (pre-Snow Leopard?). Modify paths and + load with `launchctl load edu.psu.galaxy.GalaxyServer.plist`. Written and + submitted by James Casbon. + +galaxy.debian-init: + + init script for Debian/Ubuntu Linux. Copy to /etc/init.d/galaxy, modify + paths, and configure for start at boot with `update-rc.d galaxy defaults`. + Also written and submitted by James Casbon. + +galaxy.solaris-smf.xml: + + SMF Manifest for Solaris 10 and OpenSolaris. Import with `svccfg import + galaxy.solaris-smf.xml`. diff -r 979534de254d -r da1a03642283 contrib/edu.psu.galaxy.GalaxyServer.plist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/contrib/edu.psu.galaxy.GalaxyServer.plist Fri Oct 30 12:41:17 2009 -0400 @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> +<plist version="1.0"> +<dict> + <key>Label</key> + <string>edu.psu.galaxy.GalaxyServer</string> + <key>OnDemand</key> + <false/> + <key>Program</key> + <string>galaxy_dist/run.sh<string> + <key>RunAtLoad</key> + <true/> + <key>ServiceDescription</key> + <string>Galaxy</string> + <key>StandardErrorPath</key> + <string>galaxy_dist/log/galaxy.stderr</string> + <key>StandardOutPath</key> + <string>galaxy_dist/log/galaxy.stdout</string> + <key>UserName</key> + <string>galaxy</string> +</dict> +</plist> diff -r 979534de254d -r da1a03642283 contrib/galaxy.debian-init --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/contrib/galaxy.debian-init Fri Oct 30 12:41:17 2009 -0400 @@ -0,0 +1,55 @@ +#!/bin/bash + +# Author: James Casbon, 2009 + +### BEGIN INIT INFO +# Provides: galaxy +# Required-Start: $network $local_fs $mysql +# Required-Stop: +# Default-Start: 2 3 4 5 +# Default-Stop: 0 1 6 +# Short-Description: Galaxy +### END INIT INFO + +. /lib/lsb/init-functions + +USER="galaxy" +GROUP="nogroup" +DIR="/home/galaxy/galaxy_dist/" +PYTHON="/usr/bin/python" +OPTS="-ES ./scripts/paster.py serve --log-file /home/galaxy/galaxy.log universe_wsgi.ini" +PIDFILE="/var/run/galaxy.pid" + +case "${1:-''}" in + 'start') + log_daemon_msg "Starting Galaxy" + if start-stop-daemon --chuid $USER --group $GROUP --start --make-pidfile \ + --pidfile $PIDFILE --background --chdir $DIR --exec $PYTHON -- $OPTS; then + log_end_msg 0 + else + log_end_msg 1 + fi + + ;; + 'stop') + log_daemon_msg "Stopping Galaxy" + if start-stop-daemon --stop --pidfile $PIDFILE; then + log_end_msg 0 + else + log_end_msg 1 + fi + ;; + 'restart') + # restart commands here + $0 stop + $0 start + + ;; + *) # no parameter specified + echo "Usage: $SELF start|stop|restart|reload|force-reload|status" + exit 1 + ;; +esac + + + diff -r 979534de254d -r da1a03642283 contrib/galaxy.solaris-smf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/contrib/galaxy.solaris-smf.xml Fri Oct 30 12:41:17 2009 -0400 @@ -0,0 +1,75 @@ +<?xml version="1.0"?> +<!DOCTYPE service_bundle SYSTEM "/usr/share/lib/xml/dtd/service_bundle.dtd.1"> + +<service_bundle type='manifest' name='nginx'> + +<service name='application/galaxy' type='service' version='0'> + + <dependency name='net' + grouping='require_all' + restart_on='none' + type='service'> + <service_fmri + value='svc:/network/loopback'/> + </dependency> + + <dependency name='filesystem-local' + grouping='require_all' + restart_on='none' + type='service'> + <service_fmri + value='svc:/system/filesystem/local:default'/> + </dependency> + + <instance name='main' enabled='false'> + + <exec_method name='start' + type='method' + exec='python -ES ./scripts/paster.py serve universe_wsgi.webapp.ini --log-file=log/main.log --daemon' + timeout_seconds='60'> + <method_context + working_directory='/galaxy'> + <method_credential user='galaxy' group='galaxy' /> + <method_environment> + <envvar name="PATH" value="/opt/local/bin:/bin:/usr/bin" /> + <envvar name="TEMP" value="/galaxy/database/tmp" /> + </method_environment> + </method_context> + + </exec_method> + + <exec_method name='stop' + type='method' + exec=':kill' + timeout_seconds='60'> + <method_context> + <method_credential user='galaxy' group='galaxy' /> + </method_context> + </exec_method> + + <property_group name='general' type='framework'> + <propval name='action_authorization' type='astring' + value='solaris.smf.manage.galaxy' /> + <propval name='value_authorization' type='astring' + value='solaris.smf.manage.galaxy' /> + </property_group> + + </instance> + + <stability value='Evolving' /> + + <template> + <common_name> + <loctext xml:lang='C'> + Galaxy + </loctext> + </common_name> + <documentation> + <doc_link name='galaxyproject.org' + uri='http://galaxyproject.org' /> + </documentation> + </template> + +</service> + +</service_bundle>

1 0

[hg] galaxy 2937: Fix a bug in file staging
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dac542cca894 changeset: 2937:dac542cca894 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Oct 30 14:27:48 2009 -0400 description: Fix a bug in file staging diffstat: lib/galaxy/jobs/runners/pbs.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 583fab0515a0 -r dac542cca894 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Fri Oct 30 12:51:07 2009 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Fri Oct 30 14:27:48 2009 -0400 @@ -217,7 +217,7 @@ # write the job script if self.app.config.pbs_stage_path != '': - script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_fnames), self.app.config.pbs_stage_path, exec_dir, command_line) + script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_files), self.app.config.pbs_stage_path, exec_dir, command_line) else: if self.app.config.set_metadata_externally: external_metadata_script = job_wrapper.setup_external_metadata( exec_dir = exec_dir, tmp_dir = self.app.config.new_file_path, dataset_files_path = self.app.model.Dataset.file_path, output_fnames = output_fnames, kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior

1 0

[hg] galaxy 2936: Try block around the stat for setting permissi...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/583fab0515a0 changeset: 2936:583fab0515a0 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Oct 30 12:51:07 2009 -0400 description: Try block around the stat for setting permissions and groups diffstat: lib/galaxy/util/__init__.py | 6 +++++- 1 files changed, 5 insertions(+), 1 deletions(-) diffs (16 lines): diff -r da1a03642283 -r 583fab0515a0 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Fri Oct 30 12:41:17 2009 -0400 +++ b/lib/galaxy/util/__init__.py Fri Oct 30 12:51:07 2009 -0400 @@ -488,7 +488,11 @@ umask-friendly permissions fixing """ perms = unmasked_perms & ~umask - st = os.stat( path ) + try: + st = os.stat( path ) + except OSError, e: + log.exception( 'Unable to set permissions or group on %s' % path ) + return # fix modes if stat.S_IMODE( st.st_mode ) != perms: try:

1 0

[hg] galaxy 2928: Specify color for feature tracks in one place ...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fabb2f6abc45 changeset: 2928:fabb2f6abc45 user: James Taylor <james(a)jamestaylor.org> date: Wed Oct 28 15:09:05 2009 -0400 description: Specify color for feature tracks in one place (eventually should be configurable) diffstat: static/scripts/trackster.js | 11 ++++++----- 1 files changed, 6 insertions(+), 5 deletions(-) diffs (51 lines): diff -r edb48f2816b5 -r fabb2f6abc45 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Oct 27 22:34:30 2009 -0400 +++ b/static/scripts/trackster.js Wed Oct 28 15:09:05 2009 -0400 @@ -240,10 +240,10 @@ var min_label = $("<div class='yaxislabel'>" + track.min_value + "</div>"); var max_label = $("<div class='yaxislabel'>" + track.max_value + "</div>"); - max_label.css({ position: "relative", top: "20px" }); + max_label.css({ position: "relative", top: "35px" }); max_label.prependTo(track.container_div) - min_label.css({ position: "relative", top: track.height_px + 50 + "px", }); + min_label.css({ position: "relative", top: track.height_px + 32 + "px", }); min_label.prependTo(track.container_div); track.draw(); @@ -324,6 +324,7 @@ this.show_labels_scale = 0.001; this.showing_labels = false; this.vertical_gap = 10; + this.base_color = "#2C3143"; }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { @@ -427,7 +428,7 @@ new_canvas.get(0).height = height; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = new_canvas.get(0).getContext("2d"); - ctx.fillStyle = "#000"; + ctx.fillStyle = this.base_color; ctx.font = "10px monospace"; ctx.textAlign = "right"; @@ -462,7 +463,7 @@ ctx.fillStyle = LEFT_STRAND; } ctx.fillRect(f_start, y_center, f_end - f_start, 10); - ctx.fillStyle = "#000"; + ctx.fillStyle = this.base_color; } for (var k = 0, k_len = blocks.length; k < k_len; k++) { @@ -497,7 +498,7 @@ ctx.fillStyle = LEFT_STRAND_INV; } ctx.fillRect(f_start, y_center, f_end - f_start, 10); - ctx.fillStyle = "#000"; + ctx.fillStyle = this.base_color; } } }

1 0

[hg] galaxy 2930: Fix for Nate's get_platform monkey patch.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1aafea08f0e8 changeset: 2930:1aafea08f0e8 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Oct 29 09:25:52 2009 -0400 description: Fix for Nate's get_platform monkey patch. diffstat: lib/galaxy/__init__.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r a9426ddbe468 -r 1aafea08f0e8 lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py Wed Oct 28 15:09:10 2009 -0400 +++ b/lib/galaxy/__init__.py Thu Oct 29 09:25:52 2009 -0400 @@ -12,7 +12,7 @@ import os, sys from distutils.sysconfig import get_config_vars -if ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and sys.prefix.startswith( '/System' ) ) or \ +if ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ): # Has to be before anything imports pkg_resources def _get_platform_monkeypatch():

1 0

[hg] galaxy 2929: Pages can now be deleted. Pages have a 'publis...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a9426ddbe468 changeset: 2929:a9426ddbe468 user: James Taylor <james(a)jamestaylor.org> date: Wed Oct 28 15:09:10 2009 -0400 description: Pages can now be deleted. Pages have a 'published' attribute that determines whether they are publicly accessible. There is now a list of all published pages from all users diffstat: lib/galaxy/model/mapping.py | 2 + lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py | 35 ++ lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py | 34 ++ lib/galaxy/web/controllers/page.py | 141 +++++++- lib/galaxy/web/framework/helpers/grids.py | 2 +- templates/base_panels.mako | 3 + 6 files changed, 194 insertions(+), 23 deletions(-) diffs (332 lines): diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Oct 28 15:09:05 2009 -0400 +++ b/lib/galaxy/model/mapping.py Wed Oct 28 15:09:10 2009 -0400 @@ -545,6 +545,8 @@ ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), Column( "title", TEXT ), Column( "slug", TEXT, unique=True, index=True ), + Column( "published", Boolean, index=True, default=False ), + Column( "deleted", Boolean, index=True, default=False ), ) PageRevision.table = Table( "page_revision", metadata, diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py Wed Oct 28 15:09:10 2009 -0400 @@ -0,0 +1,35 @@ +""" +Migration script to add columns for tracking whether pages are deleted and +publicly accessible. +""" + +from sqlalchemy import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def upgrade(): + + print __doc__ + metadata.reflect() + + Page_table = Table( "page", metadata, autoload=True ) + + c = Column( "published", Boolean, index=True, default=False ) + c.create( Page_table ) + assert c is Page_table.c.published + + c = Column( "deleted", Boolean, index=True, default=False ) + c.create( Page_table ) + assert c is Page_table.c.deleted + +def downgrade(): + metadata.reflect() + + Page_table = Table( "page", metadata, autoload=True ) + Page_table.c.published.drop() + Page_table.c.deleted.drop() diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py Wed Oct 28 15:09:10 2009 -0400 @@ -0,0 +1,34 @@ +""" +Remove unique constraint from page slugs to allow creating a page with +the same slug as a deleted page. +""" + +from sqlalchemy import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def upgrade(): + print __doc__ + metadata.reflect() + + Page_table = Table( "page", metadata, autoload=True ) + + i = Index( "ix_page_slug", Page_table.c.slug ) + i.drop() + + i = Index( "ix_page_slug", Page_table.c.slug, unique=False ) + i.create() + + +def downgrade(): + metadata.reflect() + #Page_table = Table( "page", metadata, autoload=True ) + #Page_table.c.slug.alter( unique=True ) diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Wed Oct 28 15:09:05 2009 -0400 +++ b/lib/galaxy/web/controllers/page.py Wed Oct 28 15:09:10 2009 -0400 @@ -6,16 +6,27 @@ VALID_SLUG_RE = re.compile( "^[a-z0-9\-]+$" ) +def format_bool( b ): + if b: + return "yes" + else: + return "" + +class PublicURLColumn( grids.GridColumn ): + def get_value( self, trans, grid, item ): + username = trans.user.username or "???" + return username + "/" + item.slug + def get_link( self, trans, grid, item ): + if trans.user.username: + return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) + else: + return None + +class OwnerColumn( grids.GridColumn ): + def get_value( self, trans, grid, item ): + return item.user.username + class PageListGrid( grids.Grid ): - class URLColumn( grids.GridColumn ): - def get_value( self, trans, grid, item ): - username = trans.user.username or "???" - return username + "/" + item.slug - def get_link( self, trans, grid, item ): - if trans.user.username: - return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) - else: - return None # Grid definition use_panels = True title = "Your pages" @@ -23,7 +34,8 @@ default_sort_key = "-create_time" columns = [ grids.GridColumn( "Title", key="title", attach_popup=True ), - URLColumn( "Public URL" ), + PublicURLColumn( "Public URL" ), + grids.GridColumn( "Published", key="published", format=format_bool ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -32,25 +44,67 @@ ] operations = [ grids.GridOperation( "View", allow_multiple=False, url_args=dict( action='display') ), - grids.GridOperation( "Edit", allow_multiple=False, url_args=dict( action='edit') ) + grids.GridOperation( "Edit name/id", allow_multiple=False, url_args=dict( action='edit') ), + grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ), + grids.GridOperation( "Delete" ), + grids.GridOperation( "Publish", condition=( lambda item: not item.published ) ), + grids.GridOperation( "Unpublish", condition=( lambda item: item.published ) ), ] def apply_default_filter( self, trans, query, **kwargs ): - return query.filter_by( user=trans.user ) + return query.filter_by( user=trans.user, deleted=False ) + +class PageAllPublishedGrid( grids.Grid ): + # Grid definition + use_panels = True + title = "Published pages from all users" + model_class = model.Page + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Title", key="title" ), + PublicURLColumn( "Public URL" ), + OwnerColumn( "Published by" ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + ] + def apply_default_filter( self, trans, query, **kwargs ): + return query.filter_by( deleted=False, published=True ) class PageController( BaseController ): - list = PageListGrid() + _page_list = PageListGrid() + _all_published_list = PageAllPublishedGrid() @web.expose - @web.require_admin + @web.require_login() def index( self, trans, *args, **kwargs ): + # Handle operation + if 'operation' in kwargs and 'id' in kwargs: + session = trans.sa_session + operation = kwargs['operation'] + ids = util.listify( kwargs['id'] ) + for id in ids: + item = session.query( model.Page ).get( trans.security.decode_id( id ) ) + if operation == "Delete": + item.deleted = True + elif operation == "Publish": + item.published = True + elif operation == "Unpublish": + item.published = False + session.flush() # Build grid - grid = self.list( trans, *args, **kwargs ) + grid = self._page_list( trans, *args, **kwargs ) # Render grid wrapped in panels return trans.fill_template( "page/index.mako", grid=grid ) @web.expose - @web.require_admin + @web.require_login() + def list_published( self, trans, *args, **kwargs ): + grid = self._all_published_list( trans, *args, **kwargs ) + # Render grid wrapped in panels + return trans.fill_template( "page/index.mako", grid=grid ) + + + @web.expose @web.require_login( "create pages" ) def create( self, trans, page_title="", page_slug="" ): """ @@ -65,7 +119,7 @@ page_slug_err = "Page id is required" elif not VALID_SLUG_RE.match( page_slug ): page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" - elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug ).first(): + elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): page_slug_err = "Page id must be unique" else: # Create the new stored workflow @@ -98,9 +152,50 @@ template="page/create.mako" ) @web.expose - @web.require_admin + @web.require_login( "create pages" ) + def edit( self, trans, id, page_title="", page_slug="" ): + """ + Create a new page + """ + encoded_id = id + id = trans.security.decode_id( id ) + session = trans.sa_session + page = session.query( model.Page ).get( id ) + user = trans.user + assert page.user == user + page_title_err = page_slug_err = "" + if trans.request.method == "POST": + if not page_title: + page_title_err = "Page name is required" + elif not page_slug: + page_slug_err = "Page id is required" + elif not VALID_SLUG_RE.match( page_slug ): + page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character" + elif page_slug == page.slug or trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): + page_slug_err = "Page id must be unique" + else: + page.title = page_title + page.slug = page_slug + session.flush() + # Display the management page + return trans.response.send_redirect( web.url_for( action='index' ) ) + else: + page_title = page.title + page_slug = page.slug + return trans.show_form( + web.FormBuilder( web.url_for( id=encoded_id ), "Edit page attributes", submit_text="Submit" ) + .add_text( "page_title", "Page title", value=page_title, error=page_title_err ) + .add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err, + help="""A unique identifier that will be used for + public links to this page. A default is generated + from the page title, but can be edited. This field + must contain only lowercase letters, numbers, and + the '-' character.""" ), + template="page/create.mako" ) + + @web.expose @web.require_login( "edit pages" ) - def edit( self, trans, id ): + def edit_content( self, trans, id ): """ Render the main page editor interface. """ @@ -110,7 +205,7 @@ return trans.fill_template( "page/editor.mako", page=page ) @web.expose - @web.require_admin + @web.require_login() def save( self, trans, id, content ): id = trans.security.decode_id( id ) page = trans.sa_session.query( model.Page ).get( id ) @@ -126,10 +221,12 @@ trans.sa_session.flush() @web.expose - @web.require_admin + @web.require_login() def display( self, trans, id ): id = trans.security.decode_id( id ) page = trans.sa_session.query( model.Page ).get( id ) + if page.user is not trans.user: + error( "Page is not owned by current user" ) return trans.fill_template( "page/display.mako", page=page ) @web.expose @@ -138,7 +235,7 @@ user = session.query( model.User ).filter_by( username=username ).first() if user is None: raise web.httpexceptions.HTTPNotFound() - page = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug ).first() + page = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug, deleted=False, published=True ).first() if page is None: raise web.httpexceptions.HTTPNotFound() return trans.fill_template( "page/display.mako", page=page ) diff -r fabb2f6abc45 -r a9426ddbe468 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Wed Oct 28 15:09:05 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Wed Oct 28 15:09:10 2009 -0400 @@ -279,7 +279,7 @@ temp['id'] = item.id return temp else: - return dict( operation=operation.label, id=item.id ) + return dict( operation=self.label, id=item.id ) def allowed( self, item ): if self.condition: diff -r fabb2f6abc45 -r a9426ddbe468 templates/base_panels.mako --- a/templates/base_panels.mako Wed Oct 28 15:09:05 2009 -0400 +++ b/templates/base_panels.mako Wed Oct 28 15:09:10 2009 -0400 @@ -243,6 +243,9 @@ <li><hr style="color: inherit; background-color: gray"/></li> <li><a target="galaxy_main" href="${h.url_for( controller='history', action='list' )}">Histories</a></li> <li><a target="galaxy_main" href="${h.url_for( controller='dataset', action='list' )}">Datasets</a></li> + %if app.config.get_bool( 'enable_pages', False ): + <li><a href="${h.url_for( controller='page' )}">Pages</a></li> + %endif %endif </ul> </div>

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[hg] galaxy 2931: Fix page migration for mysql
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/86cc0b2b9e09 changeset: 2931:86cc0b2b9e09 user: James Taylor <james(a)jamestaylor.org> date: Thu Oct 29 10:06:11 2009 -0400 description: Fix page migration for mysql diffstat: lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py | 17 ++++++-- 1 files changed, 13 insertions(+), 4 deletions(-) diffs (29 lines): diff -r 1aafea08f0e8 -r 86cc0b2b9e09 lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py --- a/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py Thu Oct 29 09:25:52 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py Thu Oct 29 10:06:11 2009 -0400 @@ -21,12 +21,21 @@ Page_table = Table( "page", metadata, autoload=True ) - i = Index( "ix_page_slug", Page_table.c.slug ) - i.drop() + try: + + # Sqlite doesn't support .alter, so we need to drop an recreate - i = Index( "ix_page_slug", Page_table.c.slug, unique=False ) - i.create() + i = Index( "ix_page_slug", Page_table.c.slug ) + i.drop() + + i = Index( "ix_page_slug", Page_table.c.slug, unique=False ) + i.create() + except: + + # Mysql doesn't have a named index, but alter should work + + Page_table.c.slug.alter( unique=False ) def downgrade(): metadata.reflect()

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