- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 13 new changesets
by commits-noreply＠bitbucket.org 08 Apr '13

08 Apr '13

13 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b6306be4e4c/ Changeset: 5b6306be4e4c User: jmchilton Date: 2013-03-22 06:41:08 Summary: Refactor tool loading and macro preprocessing stuff into its own module, implement unit tests for basic functionality. Affected #: 2 files diff -r 14ab08c0fbfe3e9735e94f4e399aeabc870fe4b2 -r 5b6306be4e4c7f20b6b4e473449cbe7a02ebe921 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -29,7 +29,6 @@ from mako.template import Template from paste import httpexceptions from sqlalchemy import and_ -from copy import deepcopy from galaxy import jobs, model from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper @@ -58,6 +57,7 @@ from galaxy.web import url_for from galaxy.web.form_builder import SelectField from tool_shed.util import shed_util_common +from .loader import load_tool log = logging.getLogger( __name__ ) @@ -577,7 +577,7 @@ def load_tool( self, config_file, guid=None, **kwds ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element - tree = self._load_and_preprocess_tool_xml( config_file ) + tree = load_tool( config_file ) root = tree.getroot() # Allow specifying a different tool subclass to instantiate if root.find( "type" ) is not None: @@ -762,102 +762,6 @@ return rval - def _load_and_preprocess_tool_xml(self, config_file): - tree = parse_xml(config_file) - root = tree.getroot() - macros_el = root.find('macros') - if not macros_el: - return tree - tool_dir = os.path.dirname(config_file) - macros = self._load_macros(macros_el, tool_dir) - - self._expand_macros([root], macros) - return tree - - def _expand_macros(self, elements, macros): - for element in elements: - # HACK for elementtree, newer implementations (etree/lxml) won't - # require this parent_map data structure but elementtree does not - # track parents or recongnize .find('..'). - parent_map = dict((c, p) for p in element.getiterator() for c in p) - for expand_el in element.findall('.//expand'): - macro_name = expand_el.get('macro') - macro_def = deepcopy(macros[macro_name]) # deepcopy needed? - - yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')] - - expand_el_children = expand_el.getchildren() - macro_def_parent_map = \ - dict((c, p) for macro_def_el in macro_def for p in macro_def_el.getiterator() for c in p) - - for yield_el in yield_els: - self._xml_replace(yield_el, expand_el_children, macro_def_parent_map) - - # Recursively expand contained macros. - self._expand_macros(macro_def, macros) - self._xml_replace(expand_el, macro_def, parent_map) - - def _load_macros(self, macros_el, tool_dir): - macros = {} - # Import macros from external files. - macros.update(self._load_imported_macros(macros_el, tool_dir)) - # Load all directly defined macros. - macros.update(self._load_embedded_macros(macros_el, tool_dir)) - return macros - - def _load_embedded_macros(self, macros_el, tool_dir): - macros = {} - - macro_els = [] - if macros_el: - macro_els = macros_el.findall("macro") - for macro in macro_els: - macro_name = macro.get("name") - macros[macro_name] = self._load_macro_def(macro) - - return macros - - def _load_imported_macros(self, macros_el, tool_dir): - macros = {} - - macro_import_els = [] - if macros_el: - macro_import_els = macros_el.findall("import") - for macro_import_el in macro_import_els: - raw_import_path = macro_import_el.text - tool_relative_import_path = \ - os.path.basename(raw_import_path) # Sanitize this - import_path = \ - os.path.join(tool_dir, tool_relative_import_path) - file_macros = self._load_macro_file(import_path, tool_dir) - macros.update(file_macros) - - return macros - - def _load_macro_file(self, path, tool_dir): - tree = parse_xml(path) - root = tree.getroot() - return self._load_macros(root, tool_dir) - - def _load_macro_def(self, macro): - return list(macro.getchildren()) - - def _xml_replace(self, query, targets, parent_map): - #parent_el = query.find('..') ## Something like this would be better with newer xml library - parent_el = parent_map[query] - matching_index = -1 - #for index, el in enumerate(parent_el.iter('.')): ## Something like this for newer implementation - for index, el in enumerate(parent_el.getchildren()): - if el == query: - matching_index = index - break - assert matching_index >= 0 - current_index = matching_index - for target in targets: - current_index += 1 - parent_el.insert(current_index, deepcopy(target)) - parent_el.remove(query) - class ToolSection( object ): """ diff -r 14ab08c0fbfe3e9735e94f4e399aeabc870fe4b2 -r 5b6306be4e4c7f20b6b4e473449cbe7a02ebe921 lib/galaxy/tools/loader.py --- /dev/null +++ b/lib/galaxy/tools/loader.py @@ -0,0 +1,223 @@ +from __future__ import with_statement + +from copy import deepcopy +import os + +from galaxy.util import parse_xml + + +def load_tool(path): + """ + Loads tool from file system and preprocesses tool macros. + """ + tree = parse_xml(path) + root = tree.getroot() + macros_el = root.find('macros') + if not macros_el: + return tree + tool_dir = os.path.dirname(path) + macros = _load_macros(macros_el, tool_dir) + + _expand_macros([root], macros) + return tree + + +def _expand_macros(elements, macros): + for element in elements: + # HACK for elementtree, newer implementations (etree/lxml) won't + # require this parent_map data structure but elementtree does not + # track parents or recongnize .find('..'). + parent_map = dict((c, p) for p in element.getiterator() for c in p) + for expand_el in element.findall('.//expand'): + macro_name = expand_el.get('macro') + macro_def = deepcopy(macros[macro_name]) # deepcopy needed? + + yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')] + + expand_el_children = expand_el.getchildren() + macro_def_parent_map = \ + dict((c, p) for macro_def_el in macro_def for p in macro_def_el.getiterator() for c in p) + + for yield_el in yield_els: + _xml_replace(yield_el, expand_el_children, macro_def_parent_map) + + # Recursively expand contained macros. + _expand_macros(macro_def, macros) + _xml_replace(expand_el, macro_def, parent_map) + + +def _load_macros(macros_el, tool_dir): + macros = {} + # Import macros from external files. + macros.update(_load_imported_macros(macros_el, tool_dir)) + # Load all directly defined macros. + macros.update(_load_embedded_macros(macros_el, tool_dir)) + return macros + + +def _load_embedded_macros(macros_el, tool_dir): + macros = {} + + macro_els = [] + if macros_el: + macro_els = macros_el.findall("macro") + for macro in macro_els: + macro_name = macro.get("name") + macros[macro_name] = _load_macro_def(macro) + + return macros + + +def _load_imported_macros(macros_el, tool_dir): + macros = {} + + macro_import_els = [] + if macros_el: + macro_import_els = macros_el.findall("import") + for macro_import_el in macro_import_els: + raw_import_path = macro_import_el.text + tool_relative_import_path = \ + os.path.basename(raw_import_path) # Sanitize this + import_path = \ + os.path.join(tool_dir, tool_relative_import_path) + file_macros = _load_macro_file(import_path, tool_dir) + macros.update(file_macros) + + return macros + + +def _load_macro_file(path, tool_dir): + tree = parse_xml(path) + root = tree.getroot() + return _load_macros(root, tool_dir) + + +def _load_macro_def(macro): + return list(macro.getchildren()) + + +def _xml_replace(query, targets, parent_map): + #parent_el = query.find('..') ## Something like this would be better with newer xml library + parent_el = parent_map[query] + matching_index = -1 + #for index, el in enumerate(parent_el.iter('.')): ## Something like this for newer implementation + for index, el in enumerate(parent_el.getchildren()): + if el == query: + matching_index = index + break + assert matching_index >= 0 + current_index = matching_index + for target in targets: + current_index += 1 + parent_el.insert(current_index, deepcopy(target)) + parent_el.remove(query) + + +def test_loader(): + """ + Function to test this module. Galaxy doesn't seem to have a + place to put unit tests that are not doctests. These tests can + be run with nosetests via the following command: + + % nosetests --with-doctest lib/galaxy/tools/loader.py + + """ + from tempfile import mkdtemp + from shutil import rmtree + + class TestToolDirectory(object): + def __init__(self): + self.temp_directory = mkdtemp() + + def __enter__(self): + return self + + def __exit__(self, type, value, tb): + rmtree(self.temp_directory) + + def write(self, contents, name="tool.xml"): + open(os.path.join(self.temp_directory, name), "w").write(contents) + + def load(self, name="tool.xml", preprocess=True): + if preprocess: + loader = load_tool + else: + loader = parse_xml + return loader(os.path.join(self.temp_directory, name)) + + ## Test simple macro replacement. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <macro name="inputs"> + <inputs /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load(preprocess=False) + assert xml.find("inputs") is None + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None + + # Test importing macros from external files + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <import>external.xml</import> + </macros> +</tool>''') + + tool_dir.write(''' +<macros> + <macro name="inputs"> + <inputs /> + </macro> +</macros>''', name="external.xml") + xml = tool_dir.load(preprocess=False) + assert xml.find("inputs") is None + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None + + # Test macros with unnamed yield statements. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").find("input").get("name") == "first_input" + + # Test recursive macro applications. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + <expand macro="second" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + <macro name="second"> + <input name="second_input" /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").findall("input")[1].get("name") == "second_input" https://bitbucket.org/galaxy/galaxy-central/commits/8400b75d0a68/ Changeset: 8400b75d0a68 User: jmchilton Date: 2013-03-22 06:41:08 Summary: Refactor macro stuff to allow multiple macro types (default type is xml, <xml> will be short for <macro type="xml"), improves ordering of interleaving imports and embedded macros. Affected #: 1 file diff -r 5b6306be4e4c7f20b6b4e473449cbe7a02ebe921 -r 8400b75d0a688ec4a6a07e2e5aa98ef9dcbb193c lib/galaxy/tools/loader.py --- a/lib/galaxy/tools/loader.py +++ b/lib/galaxy/tools/loader.py @@ -13,12 +13,17 @@ tree = parse_xml(path) root = tree.getroot() macros_el = root.find('macros') - if not macros_el: - return tree tool_dir = os.path.dirname(path) - macros = _load_macros(macros_el, tool_dir) - _expand_macros([root], macros) + if macros_el: + macro_els = _load_macros(macros_el, tool_dir) + _xml_set_children(macros_el, macro_els) + + macro_dict = dict([(macro_el.get("name"), list(macro_el.getchildren())) \ + for macro_el in macro_els \ + if macro_el.get('type') == 'xml']) + _expand_macros([root], macro_dict) + return tree @@ -30,6 +35,7 @@ parent_map = dict((c, p) for p in element.getiterator() for c in p) for expand_el in element.findall('.//expand'): macro_name = expand_el.get('macro') + print macros.keys() macro_def = deepcopy(macros[macro_name]) # deepcopy needed? yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')] @@ -47,29 +53,43 @@ def _load_macros(macros_el, tool_dir): - macros = {} + macros = [] # Import macros from external files. - macros.update(_load_imported_macros(macros_el, tool_dir)) + macros.extend(_load_imported_macros(macros_el, tool_dir)) # Load all directly defined macros. - macros.update(_load_embedded_macros(macros_el, tool_dir)) + macros.extend(_load_embedded_macros(macros_el, tool_dir)) return macros def _load_embedded_macros(macros_el, tool_dir): - macros = {} + macros = [] macro_els = [] + # attribute typed macro if macros_el: macro_els = macros_el.findall("macro") for macro in macro_els: - macro_name = macro.get("name") - macros[macro_name] = _load_macro_def(macro) + if 'type' not in macro.attrib: + macro.attrib['type'] = 'xml' + macros.append(macro) + + # type shortcuts (<xml> is a shortcut for <macro type="xml", + # likewise for <template>. + typed_tag = ['xml'] + for tag in typed_tag: + macro_els = [] + if macros_el: + macro_els = macros_el.findall(tag) + for macro_el in macro_els: + macro_el.attrib['type'] = tag + macro_el.tag = 'macro' + macros.append(macro_el) return macros def _load_imported_macros(macros_el, tool_dir): - macros = {} + macros = [] macro_import_els = [] if macros_el: @@ -81,7 +101,7 @@ import_path = \ os.path.join(tool_dir, tool_relative_import_path) file_macros = _load_macro_file(import_path, tool_dir) - macros.update(file_macros) + macros.extend(file_macros) return macros @@ -96,6 +116,13 @@ return list(macro.getchildren()) +def _xml_set_children(element, new_children): + for old_child in element.getchildren(): + element.remove(old_child) + for i, new_child in enumerate(new_children): + element.insert(i, new_child) + + def _xml_replace(query, targets, parent_map): #parent_el = query.find('..') ## Something like this would be better with newer xml library parent_el = parent_map[query] @@ -119,7 +146,7 @@ place to put unit tests that are not doctests. These tests can be run with nosetests via the following command: - % nosetests --with-doctest lib/galaxy/tools/loader.py + % nosetests lib/galaxy/tools/loader.py """ from tempfile import mkdtemp @@ -221,3 +248,17 @@ </tool>''') xml = tool_dir.load() assert xml.find("inputs").findall("input")[1].get("name") == "second_input" + + # Test <xml> is shortcut for macro type="xml" + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <xml name="inputs"> + <inputs /> + </xml> + </macros> +</tool>''') + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None https://bitbucket.org/galaxy/galaxy-central/commits/96aae9b33613/ Changeset: 96aae9b33613 User: jmchilton Date: 2013-03-22 06:41:08 Summary: Implement 'template' macros that define variables which are made available to cheetah templates. Affected #: 2 files diff -r 8400b75d0a688ec4a6a07e2e5aa98ef9dcbb193c -r 96aae9b336130398250524311b4b69c432a44966 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -57,7 +57,7 @@ from galaxy.web import url_for from galaxy.web.form_builder import SelectField from tool_shed.util import shed_util_common -from .loader import load_tool +from .loader import load_tool, template_macro_params log = logging.getLogger( __name__ ) @@ -1246,6 +1246,7 @@ # thus hardcoded) FIXME: hidden parameters aren't # parameters at all really, and should be passed in a different # way, making this check easier. + self.template_macro_params = template_macro_params(root) for param in self.inputs.values(): if not isinstance( param, ( HiddenToolParameter, BaseURLToolParameter ) ): self.input_required = True @@ -2367,7 +2368,7 @@ `to_param_dict_string` method of the associated input. """ param_dict = dict() - + param_dict.update(self.template_macro_params) # All parameters go into the param_dict param_dict.update( incoming ) diff -r 8400b75d0a688ec4a6a07e2e5aa98ef9dcbb193c -r 96aae9b336130398250524311b4b69c432a44966 lib/galaxy/tools/loader.py --- a/lib/galaxy/tools/loader.py +++ b/lib/galaxy/tools/loader.py @@ -12,22 +12,51 @@ """ tree = parse_xml(path) root = tree.getroot() + + _import_macros(root, path) + + # Expand xml macros + macro_dict = _macros_of_type(root, 'xml', lambda el: list(el.getchildren())) + _expand_macros([root], macro_dict) + + return tree + + +def template_macro_params(root): + """ + Look for template macros and populate param_dict (for cheetah) + with these. + """ + param_dict = {} + macro_dict = _macros_of_type(root, 'template', lambda el: el.text) + for key, value in macro_dict.iteritems(): + param_dict[key] = value + return param_dict + + +def _import_macros(root, path): + tool_dir = os.path.dirname(path) macros_el = root.find('macros') - tool_dir = os.path.dirname(path) - if macros_el: macro_els = _load_macros(macros_el, tool_dir) _xml_set_children(macros_el, macro_els) - macro_dict = dict([(macro_el.get("name"), list(macro_el.getchildren())) \ + +def _macros_of_type(root, type, el_func): + macros_el = root.find('macros') + macro_dict = {} + if macros_el: + macro_els = macros_el.findall('macro') + macro_dict = dict([(macro_el.get("name"), el_func(macro_el)) \ for macro_el in macro_els \ - if macro_el.get('type') == 'xml']) - _expand_macros([root], macro_dict) - - return tree + if macro_el.get('type') == type]) + return macro_dict def _expand_macros(elements, macros): + if not macros: + return + for element in elements: # HACK for elementtree, newer implementations (etree/lxml) won't # require this parent_map data structure but elementtree does not @@ -35,7 +64,6 @@ parent_map = dict((c, p) for p in element.getiterator() for c in p) for expand_el in element.findall('.//expand'): macro_name = expand_el.get('macro') - print macros.keys() macro_def = deepcopy(macros[macro_name]) # deepcopy needed? yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')] @@ -75,7 +103,7 @@ # type shortcuts (<xml> is a shortcut for <macro type="xml", # likewise for <template>. - typed_tag = ['xml'] + typed_tag = ['template', 'xml'] for tag in typed_tag: macro_els = [] if macros_el: @@ -260,5 +288,20 @@ </xml></macros></tool>''') - xml = tool_dir.load(preprocess=True) + xml = tool_dir.load() assert xml.find("inputs") is not None + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <command interpreter="python">tool_wrapper.py + #include source=$tool_params + </command> + <macros> + <template name="tool_params">-a 1 -b 2</template> + </macros> +</tool> +''') + xml = tool_dir.load() + params_dict = template_macro_params(xml.getroot()) + assert params_dict['tool_params'] == "-a 1 -b 2" https://bitbucket.org/galaxy/galaxy-central/commits/dd8e910f6d30/ Changeset: dd8e910f6d30 User: jmchilton Date: 2013-03-22 06:41:08 Summary: Add GATK macros file and import in each wrapper. Affected #: 17 files diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/analyze_covariates.xml --- a/tools/gatk/analyze_covariates.xml +++ b/tools/gatk/analyze_covariates.xml @@ -3,6 +3,9 @@ <requirements><requirement type="package" version="1.4">gatk</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -4,6 +4,9 @@ <requirement type="package" version="1.4">gatk</requirement><requirement type="package">samtools</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -4,6 +4,9 @@ <requirement type="package" version="1.4">gatk</requirement><requirement type="package">samtools</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/gatk_macros.xml --- /dev/null +++ b/tools/gatk/gatk_macros.xml @@ -0,0 +1,2 @@ +<macros> +</macros> \ No newline at end of file diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -4,6 +4,9 @@ <requirement type="package" version="1.4">gatk</requirement><requirement type="package">samtools</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -4,6 +4,9 @@ <requirement type="package" version="1.4">gatk</requirement><requirement type="package">samtools</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -4,6 +4,9 @@ <requirement type="package" version="1.3">gatk</requirement><requirement type="package">samtools</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -4,6 +4,9 @@ <requirement type="package" version="1.4">gatk</requirement><requirement type="package">samtools</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -4,6 +4,9 @@ <requirement type="package" version="1.4">gatk</requirement><requirement type="package">samtools</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -4,6 +4,9 @@ <requirement type="package" version="1.4">gatk</requirement><requirement type="package">samtools</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -3,6 +3,9 @@ <requirements><requirement type="package" version="1.4">gatk</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -3,6 +3,9 @@ <requirements><requirement type="package" version="1.4">gatk</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -3,6 +3,9 @@ <requirements><requirement type="package" version="1.4">gatk</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py #from binascii import hexlify --max_jvm_heap_fraction "1" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -3,6 +3,9 @@ <requirements><requirement type="package" version="1.4">gatk</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py #from binascii import hexlify --max_jvm_heap_fraction "1" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -3,6 +3,9 @@ <requirements><requirement type="package" version="1.4">gatk</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -3,6 +3,9 @@ <requirements><requirement type="package" version="1.4">gatk</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py #from binascii import hexlify --max_jvm_heap_fraction "1" diff -r 96aae9b336130398250524311b4b69c432a44966 -r dd8e910f6d30086bb8fcacdc400fe2ee2305d991 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -3,6 +3,9 @@ <requirements><requirement type="package" version="1.4">gatk</requirement></requirements> + <macros> + <import>gatk_macros.xml</import> + </macros><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" https://bitbucket.org/galaxy/galaxy-central/commits/1857f97b6772/ Changeset: 1857f97b6772 User: jmchilton Date: 2013-03-22 06:41:08 Summary: Create shared cheetah template variable for gatk standard options. Affected #: 16 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/0be733a1029e/ Changeset: 0be733a1029e User: jmchilton Date: 2013-03-22 06:41:08 Summary: Refactor big GATK parameter type conditional into shared macro for 15 GATK tools. Affected #: 16 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/83ff3052f4b6/ Changeset: 83ff3052f4b6 User: jmchilton Date: 2013-03-22 06:41:08 Summary: Implement another macro type (token) that performs direct string substition on element text. Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/6ec03dde4504/ Changeset: 6ec03dde4504 User: jmchilton Date: 2013-03-22 06:41:08 Summary: Extend token macro expansion to include XML attributes. Optimize expansion performance slightly. Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/ca5333e3daaf/ Changeset: ca5333e3daaf User: jmchilton Date: 2013-03-22 06:41:08 Summary: Refactor GATK wrappers to use token macros to eliminate duplication in citation section. Affected #: 17 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/c28e4c6eced2/ Changeset: c28e4c6eced2 User: jmchilton Date: 2013-03-22 06:41:08 Summary: Covert more duplicated GATK wrapper code to macros. Affected #: 16 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/71caf4b3d201/ Changeset: 71caf4b3d201 User: jmchilton Date: 2013-03-22 06:41:08 Summary: Remove unused code in lib/galaxy/tools/loader.py Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/2c39e7cb976f/ Changeset: 2c39e7cb976f User: jmchilton Date: 2013-03-31 19:39:20 Summary: Tool Macros: Added test case for doubly recursive macros. Implement bug fix and refactor to simplify things and make problem/fix more obvious. Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/8fc56b85e0a5/ Changeset: 8fc56b85e0a5 User: jgoecks Date: 2013-04-08 23:10:21 Summary: Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #140) Improvements to Tool XML Macroing System Affected #: 19 files Diff not available. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 08 Apr '13

08 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d7f37a2fe690/ Changeset: d7f37a2fe690 Branch: stable User: natefoo Date: 2013-04-08 18:28:46 Summary: Added tag security_2013.04.08 for changeset 2cc8d10988e0 Affected #: 1 file diff -r 04c85ce163d3fb330c80fe61db4755cc446dd244 -r d7f37a2fe69089c97c4d121287736c5c15f37795 .hgtags --- a/.hgtags +++ b/.hgtags @@ -1,3 +1,4 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 +2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 https://bitbucket.org/galaxy/galaxy-central/commits/788cd3d06541/ Changeset: 788cd3d06541 User: natefoo Date: 2013-04-08 18:30:08 Summary: Merged stable. Affected #: 1 file diff -r 19f6e62bd372dc44e0d6b906fa2817122a5a57e4 -r 788cd3d065413b2611d82375a5d0d562775ea529 .hgtags --- a/.hgtags +++ b/.hgtags @@ -1,3 +1,4 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 +2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Add Reports runtime files to .hgignore
by commits-noreply＠bitbucket.org 08 Apr '13

08 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/19f6e62bd372/ Changeset: 19f6e62bd372 User: dannon Date: 2013-04-08 16:56:26 Summary: Add Reports runtime files to .hgignore Affected #: 1 file diff -r b12b245510bea4d59f485dbfdd663a47c5443d5c -r 19f6e62bd372dc44e0d6b906fa2817122a5a57e4 .hgignore --- a/.hgignore +++ b/.hgignore @@ -35,6 +35,11 @@ tool_shed_webapp.pid hgweb.config* +# Reports Runtime Files +reports_webapp.lock +reports_webapp.log +reports_webapp.pid + # Config files universe_wsgi.ini reports_wsgi.ini Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Inserted a button for trackster visualization into the BED-file data display viewer.
by commits-noreply＠bitbucket.org 08 Apr '13

08 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b12b245510be/ Changeset: b12b245510be User: guerler Date: 2013-04-08 16:19:37 Summary: Inserted a button for trackster visualization into the BED-file data display viewer. Affected #: 4 files diff -r cb25513c63cd7aa2ebd472e91109c96276ed6d9d -r b12b245510bea4d59f485dbfdd663a47c5443d5c lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -696,6 +696,11 @@ # Get dataset to add. new_dataset_id = kwargs.get( "dataset_id", None ) + + # Get gene region + new_chrom = kwargs.get( "chrom", None ) + new_start = kwargs.get( "start", 0 ) + new_end = kwargs.get( "end", 0 ) # Set up new browser if no id provided. if not id: @@ -706,7 +711,7 @@ if dbkey == '?': dbkey = kwargs.get( "dbkey", None ) - return trans.fill_template( "tracks/browser.mako", config={}, + return trans.fill_template( "tracks/browser.mako", viewport_config={"chrom" : new_chrom, "start" : int(new_start), "end" : int(new_end)}, add_dataset=new_dataset_id, default_dbkey=dbkey ) diff -r cb25513c63cd7aa2ebd472e91109c96276ed6d9d -r b12b245510bea4d59f485dbfdd663a47c5443d5c static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -20,7 +20,7 @@ }, initialize: function() { - // -- Create and initialize metadata. -- + // -- Create and initialize metadata. -- var metadata = new DatasetMetadata(); @@ -111,10 +111,8 @@ initialize: function(options) {}, - render: function() { - // Add loading indicator div. - this.$el.append( $('<div/>').attr('id', 'loading_indicator') ); - + render: function() + { // Add data table and header. var data_table = $('<table/>').attr({ id: 'content_table', @@ -223,6 +221,121 @@ } }); +/** + * Provides table-based, dynamic view of a bed dataset. + * NOTE: view's el must be in DOM already and provided when + * creating the view so that scrolling event can be attached + * to the correct container. + */ +var BedDatasetChunkedView = TabularDatasetChunkedView.extend( +{ + // gene region columns + col: { + chrom : null, + start : null, + end : null, + }, + + // url for trackster + url_viz : null, + + // dataset id + dataset_id : null, + + // backbone initialize + initialize: function (options) + { + // verify that metadata exists + var metadata = options.model.attributes.metadata.attributes; + if (typeof metadata.chromCol === "undefined" || typeof metadata.startCol === "undefined" || typeof metadata.endCol === "undefined") + console.log("BedDatasetChunkedView:initialize() : Metadata for column identification is missing."); + else + { + // read in columns + this.col.chrom = metadata.chromCol - 1; + this.col.start = metadata.startCol - 1; + this.col.end = metadata.endCol - 1; + } + + // get dataset id + if (typeof options.model.attributes.id === "undefined") + console.log("BedDatasetChunkedView:initialize() : Dataset identification is missing."); + else + this.dataset_id = options.model.attributes.id; + + // get url + if (typeof options.model.attributes.url_viz === "undefined") + console.log("BedDatasetChunkedView:initialize() : Url for visualization controller is missing."); + else + this.url_viz = options.model.attributes.url_viz; + }, + + // backbone events + events: + { + 'mouseover tr' : 'btn_viz_show', + 'mouseleave' : 'btn_viz_hide' + }, + + // show button + btn_viz_show: function (e) + { + // get selected data line + var row = $(e.target).parent(); + + // get target gene region + var btn_viz_pars = { + dataset_id : this.dataset_id, + chrom : row.children().eq(this.col.chrom).html(), + start : row.children().eq(this.col.start).html(), + end : row.children().eq(this.col.end).html() + }; + + // verify that location has been found + if (btn_viz_pars.chrom != "") + { + // get button position + var offset = row.offset(); + var left = offset.left - 10; + var top = offset.top; + + // update css + $('#btn_viz').css({'position': 'fixed', 'top': top + 'px', 'left': left + 'px'}); + $('#btn_viz').attr('href', "javascript:window.parent.location.href = '" + this.url_viz + "/trackster?" + $.param(btn_viz_pars) + "';"); + + // show the button + $('#btn_viz').show(); + } + }, + + // hide button + btn_viz_hide: function (e) + { + // hide button from screen + $('#btn_viz').hide(); + }, + + // render frame + render: function() + { + // render the icon from template + var btn_viz = new IconButtonView({ model : new IconButton({ + title : 'Visualize', + icon_class : 'chart_curve', + id : 'btn_viz' + })}); + + // add it to the screen + this.$el.append(btn_viz.render().$el); + + // hide the button + $('#btn_viz').hide(); + + // call parent render + TabularDatasetChunkedView.prototype.render.call(this); + } +}); + // -- Utility functions. -- /** @@ -252,10 +365,19 @@ var view_div = $('<div/>').appendTo(parent_elt); // Create view with model, render, and return. - return new TabularDatasetChunkedView({ - el: view_div, - model: new TabularDataset(dataset_config) - }).render(); + if (dataset_config.data_type == 'bed') + // bed datatype viewer + return new BedDatasetChunkedView({ + el: view_div, + model: new TabularDataset(dataset_config) + }).render(); + else + // default viewer + return new TabularDatasetChunkedView({ + el: view_div, + model: new TabularDataset(dataset_config) + }).render(); + }; return { @@ -263,6 +385,7 @@ TabularDataset: TabularDataset, DatasetCollection: DatasetCollection, TabularDatasetChunkedView: TabularDatasetChunkedView, + BedDatasetChunkedView: BedDatasetChunkedView, createTabularDatasetChunkedView: createTabularDatasetChunkedView }; diff -r cb25513c63cd7aa2ebd472e91109c96276ed6d9d -r b12b245510bea4d59f485dbfdd663a47c5443d5c templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -6,6 +6,8 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js( "libs/require" )} + ${h.templates("helpers-common-templates")} + <script type="text/javascript"> require.config({ baseUrl: "${h.url_for('/static/scripts')}", @@ -19,7 +21,8 @@ data.createTabularDatasetChunkedView( _.extend( ${h.to_json_string( trans.security.encode_dict_ids( dataset.get_api_value() ) )}, { - chunk_url: "${h.url_for( controller='/dataset', action='display', + url_viz: "${h.url_for( controller='/visualization')}", + chunk_url: "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}", first_data_chunk: ${chunk} } diff -r cb25513c63cd7aa2ebd472e91109c96276ed6d9d -r b12b245510bea4d59f485dbfdd663a47c5443d5c templates/webapps/galaxy/tracks/browser.mako --- a/templates/webapps/galaxy/tracks/browser.mako +++ b/templates/webapps/galaxy/tracks/browser.mako @@ -89,7 +89,7 @@ container: $("#browser-container"), name: $("#new-title").val(), dbkey: $("#new-dbkey").val() - } ); + }, JSON.parse('${ h.to_json_string( viewport_config ) }')); view.editor = true; init_editor(); set_up_router({view: view}); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Fixes logout with remote_user=True (almost, logout.mako still uses the wrong template -- bug introduced in 56de0ee7932f)
by commits-noreply＠bitbucket.org 05 Apr '13

05 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/04c85ce163d3/ Changeset: 04c85ce163d3 Branch: stable User: dannon Date: 2013-04-04 16:19:17 Summary: Fixes logout with remote_user=True (almost, logout.mako still uses the wrong template -- bug introduced in 56de0ee7932f) Affected #: 1 file diff -r df5bad7a86dfd7af48a57a593028a1520c18a69b -r 04c85ce163d3fb330c80fe61db4755cc446dd244 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -157,10 +157,7 @@ else: menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - if app.config.require_login: - logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout' ) - else: - logout_url = h.url_for( controller='/user', action='logout' ) + logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 9 new changesets
by commits-noreply＠bitbucket.org 05 Apr '13

05 Apr '13

9 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/52351e7d6433/ Changeset: 52351e7d6433 User: jmchilton Date: 2013-03-26 16:30:46 Summary: Fix typo related to lwr in job_conf.xml.sample_advanced. Affected #: 1 file diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r 52351e7d6433973cac61a9822f20559560e10491 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -7,7 +7,7 @@ <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/><plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/><plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> - <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr.LwrJobRunner" /> + <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner" /><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /></plugins> https://bitbucket.org/galaxy/galaxy-central/commits/7aba79e8068c/ Changeset: 7aba79e8068c User: jmchilton Date: 2013-03-26 17:16:30 Summary: Fix returning destination id from dynamic job runners, JobMapper was using self.app.job_config but it didn't have access to app, now JobWrapper is passing job_config into JobMapper which in turn is storing it. Affected #: 2 files diff -r 52351e7d6433973cac61a9822f20559560e10491 -r 7aba79e8068c658fe7a1a7f412f999ac276c1940 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -580,7 +580,7 @@ self.tool_provided_job_metadata = None # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) - self.job_runner_mapper = JobRunnerMapper( self, queue.dispatcher.url_to_destination ) + self.job_runner_mapper = JobRunnerMapper( self, queue.dispatcher.url_to_destination, self.app.job_config ) self.params = None if job.params: self.params = from_json_string( job.params ) diff -r 52351e7d6433973cac61a9822f20559560e10491 -r 7aba79e8068c658fe7a1a7f412f999ac276c1940 lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -21,9 +21,10 @@ (in the form of job_wrappers) to job runner url strings. """ - def __init__( self, job_wrapper, url_to_destination ): + def __init__( self, job_wrapper, url_to_destination, job_config ): self.job_wrapper = job_wrapper self.url_to_destination = url_to_destination + self.job_config = job_config self.rule_modules = self.__get_rule_modules( ) def __get_rule_modules( self ): @@ -135,7 +136,7 @@ if '://' in rval: return self.__convert_url_to_destination(rval) else: - return self.app.job_config.get_destination(rval) + return self.job_config.get_destination(rval) elif isinstance(rval, galaxy.jobs.JobDestination): # If the function generated a JobDestination, we'll use that # destination directly. However, for advanced job limiting, a https://bitbucket.org/galaxy/galaxy-central/commits/150660f80ca1/ Changeset: 150660f80ca1 User: jmchilton Date: 2013-03-26 17:18:36 Summary: Slight optimization in JobMapper, no need to prefetch rules modules and hit the disk for every job mapper if 99.9% of them are never going to use rules. Affected #: 1 file diff -r 7aba79e8068c658fe7a1a7f412f999ac276c1940 -r 150660f80ca10c1d31b0d60ca2e9ae3f9fa8dbee lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -25,7 +25,6 @@ self.job_wrapper = job_wrapper self.url_to_destination = url_to_destination self.job_config = job_config - self.rule_modules = self.__get_rule_modules( ) def __get_rule_modules( self ): unsorted_module_names = self.__get_rule_module_names( ) @@ -119,7 +118,7 @@ def __last_rule_module_with_function( self, function_name ): # self.rule_modules is sorted in reverse order, so find first # wiht function - for rule_module in self.rule_modules: + for rule_module in self.__get_rule_modules( ): if hasattr( rule_module, function_name ): return rule_module return None https://bitbucket.org/galaxy/galaxy-central/commits/9bc03c707d69/ Changeset: 9bc03c707d69 User: jmchilton Date: 2013-03-26 17:29:23 Summary: Cleanup/reworking of logic in JobMapper for handling multiple possible output types coming from dynamic rules. This is a little more pythonic in that it is making fewer assumptions about types. This is also slightly less code, reduces the number of return statements, etc.... Also removed the the #TODO: Test extensively, this has now been done. Affected #: 1 file diff -r 150660f80ca10c1d31b0d60ca2e9ae3f9fa8dbee -r 9bc03c707d69c165b07dcdc07ea9d60efd11d74a lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -128,27 +128,14 @@ if expand_type == "python": expand_function_name = self.__determine_expand_function_name( destination ) expand_function = self.__get_expand_function( expand_function_name ) - rval = self.__invoke_expand_function( expand_function ) - # TODO: test me extensively - if isinstance(rval, basestring): - # If the function returned a string, check if it's a URL, convert if necessary - if '://' in rval: - return self.__convert_url_to_destination(rval) + job_destination = self.__invoke_expand_function( expand_function ) + if not isinstance(job_destination, galaxy.jobs.JobDestination): + job_destination_rep = str(job_destination) # Should be either id or url + if '://' in job_destination_rep: + job_destination = self.__convert_url_to_destination(job_destination_rep) else: - return self.job_config.get_destination(rval) - elif isinstance(rval, galaxy.jobs.JobDestination): - # If the function generated a JobDestination, we'll use that - # destination directly. However, for advanced job limiting, a - # function may want to set the JobDestination's 'tags' - # attribute so that limiting can be done on a destination tag. - #id_or_tag = rval.get('id') - #if rval.get('tags', None): - # # functions that are generating destinations should only define one tag - # id_or_tag = rval.get('tags')[0] - #return id_or_tag, rval - return rval - else: - raise Exception( 'Dynamic function returned a value that could not be understood: %s' % rval ) + job_destination = self.job_config.get_destination(job_destination_rep) + return job_destination elif expand_type is None: raise Exception( 'Dynamic function type not specified (hint: add <param id="type">python</param> to your <destination>)' ) else: https://bitbucket.org/galaxy/galaxy-central/commits/7cf608b34231/ Changeset: 7cf608b34231 User: jmchilton Date: 2013-03-26 19:14:50 Summary: Dynamic job runner will take id of the tool as the python function if one is not specified. This extends that logic to handle newer tools (i.e. tool shed tools) that may have multiple ids. The most specific id with a corresponding function name will be used. Affected #: 2 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/14a5aecf14cf/ Changeset: 14a5aecf14cf User: jmchilton Date: 2013-03-26 21:24:25 Summary: Specify `python` as default dynamic job runner type - simplifies configuration and documentation and other types cheetah, XML, etc... do not seem to be on the roadmap. Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/bdc4af97dbed/ Changeset: bdc4af97dbed User: jmchilton Date: 2013-03-27 21:19:57 Summary: Bug fix for recent changes to the LWR server's handling of config files. Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/f63846588983/ Changeset: f63846588983 User: jmchilton Date: 2013-03-27 21:27:38 Summary: Small documentation update to reflect changes in 14a5aec. Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/cb25513c63cd/ Changeset: cb25513c63cd User: natefoo Date: 2013-04-05 23:05:41 Summary: Merged in jmchilton/galaxy-central-multi-input-tool-fixes-2 (pull request #143) Affected #: 5 files Diff not available. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: controllers/root.default: have default return the same message as a 404 (HTTPNotFound)
by commits-noreply＠bitbucket.org 05 Apr '13

05 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e061edf06175/ Changeset: e061edf06175 User: carlfeberhard Date: 2013-04-05 23:02:07 Summary: controllers/root.default: have default return the same message as a 404 (HTTPNotFound) Affected #: 1 file diff -r 438028ac0148d64f4b3f26e0137d443ac2df41f2 -r e061edf06175b8e2557f8dd286ff97f8e2e59d02 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -5,6 +5,8 @@ import urllib import cgi +from paste.httpexceptions import HTTPNotFound + from galaxy.web.base.controller import BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin from galaxy.model.item_attrs import UsesAnnotations from galaxy import util, web @@ -21,7 +23,7 @@ def default(self, trans, target1=None, target2=None, **kwd): """Called on any url that does not match a controller method. """ - return 'This link may not be followed from within Galaxy.' + raise HTTPNotFound( 'This link may not be followed from within Galaxy.' ) @web.expose def index(self, trans, id=None, tool_id=None, mode=None, workflow_id=None, m_c=None, m_a=None, **kwd): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Relocate TracksterConfig import in tools package to avoid circular import w/ visual_analytics that was preventing the reports app from functioning.
by commits-noreply＠bitbucket.org 05 Apr '13

05 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/438028ac0148/ Changeset: 438028ac0148 User: dannon Date: 2013-04-05 21:58:31 Summary: Relocate TracksterConfig import in tools package to avoid circular import w/ visual_analytics that was preventing the reports app from functioning. Affected #: 1 file diff -r b84e39f2b4db6d5e6a147b5cf66ca864d9491de8 -r 438028ac0148d64f4b3f26e0137d443ac2df41f2 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -54,7 +54,6 @@ from galaxy.util.none_like import NoneDataset from galaxy.util.odict import odict from galaxy.util.template import fill_template -from galaxy.visualization.genome.visual_analytics import TracksterConfig from galaxy.web import url_for from galaxy.web.form_builder import SelectField from tool_shed.util import shed_util_common @@ -1289,6 +1288,7 @@ # Trackster configuration. trackster_conf = root.find( "trackster_conf" ) if trackster_conf is not None: + from galaxy.visualization.genome.visual_analytics import TracksterConfig self.trackster_conf = TracksterConfig.parse( trackster_conf ) else: self.trackster_conf = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Relocate TracksterConfig import in tools package to avoid circular import w/ visual_analytics that was preventing the reports app from functioning.
by commits-noreply＠bitbucket.org 05 Apr '13

05 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/df5bad7a86df/ Changeset: df5bad7a86df Branch: stable User: dannon Date: 2013-04-05 21:58:31 Summary: Relocate TracksterConfig import in tools package to avoid circular import w/ visual_analytics that was preventing the reports app from functioning. Affected #: 1 file diff -r 2cc8d10988e03257dc7b97f8bb332c7df745d1dd -r df5bad7a86dfd7af48a57a593028a1520c18a69b lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -54,7 +54,6 @@ from galaxy.util.none_like import NoneDataset from galaxy.util.odict import odict from galaxy.util.template import fill_template -from galaxy.visualization.genome.visual_analytics import TracksterConfig from galaxy.web import url_for from galaxy.web.form_builder import SelectField from tool_shed.util import shed_util_common @@ -1289,6 +1288,7 @@ # Trackster configuration. trackster_conf = root.find( "trackster_conf" ) if trackster_conf is not None: + from galaxy.visualization.genome.visual_analytics import TracksterConfig self.trackster_conf = TracksterConfig.parse( trackster_conf ) else: self.trackster_conf = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: history panel: do not fetch display apps if there are no hdas yet
by commits-noreply＠bitbucket.org 05 Apr '13

05 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b84e39f2b4db/ Changeset: b84e39f2b4db User: carlfeberhard Date: 2013-04-05 20:01:59 Summary: history panel: do not fetch display apps if there are no hdas yet Affected #: 2 files diff -r ac4f3e90b6e39b3329eb3f59fa9cce8534e0505a -r b84e39f2b4db6d5e6a147b5cf66ca864d9491de8 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -60,7 +60,9 @@ this.hdas.reset( initialHdas ); this.checkForUpdates(); //TODO: don't call if force_history_refresh - this.updateDisplayApplications(); + if( this.hdas.length > 0 ){ + this.updateDisplayApplications(); + } // handle errors in initialHdas //TODO: errors from the api shouldn't be plain strings... diff -r ac4f3e90b6e39b3329eb3f59fa9cce8534e0505a -r b84e39f2b4db6d5e6a147b5cf66ca864d9491de8 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates();this.updateDisplayApplications()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}this.hdas.bind("state:ready",function(d,f,c){if(d.get("force_history_refresh")){var e=this;setTimeout(function(){e.stateUpdater()},History.UPDATE_DELAY)}},this)},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server:")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(e,d,f){c.hdas.set(e)},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){var f="Error fetching display applications, "+a+":"+(g.responseText||e);Galaxy.show_modal("History panel error",f,{Ok:function(){Galaxy.hide_modal()}});this.log(f)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}this.hdas.bind("state:ready",function(d,f,c){if(d.get("force_history_refresh")){var e=this;setTimeout(function(){e.stateUpdater()},History.UPDATE_DELAY)}},this)},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server:")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(e,d,f){c.hdas.set(e)},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){var f="Error fetching display applications, "+a+":"+(g.responseText||e);Galaxy.show_modal("History panel error",f,{Ok:function(){Galaxy.hide_modal()}});this.log(f)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0