1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ccfcca670dfa/ changeset: ccfcca670dfa user: dannon date: 2012-06-15 23:01:05 summary: Updates to tabular dataset display. Ship first data chunk with the page, and use metadata or datatype column_names as a table header row if available. affected #: 4 files
diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r ccfcca670dfa5303d09a178473b663c15e5dc80a lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -19,7 +19,7 @@
class Tabular( data.Text ): """Tab delimited data""" - CHUNK_SIZE = 20000 + CHUNK_SIZE = 50000
"""Add metadata elements""" MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 ) @@ -246,26 +246,40 @@ raise Exception, "Can't create peek rows %s" % str( exc ) return "".join( out )
+ def get_chunk(self, trans, dataset, chunk): + ck_index = int(chunk) + f = open(dataset.file_name) + f.seek(ck_index * self.CHUNK_SIZE) + # If we aren't at the start of the file, seek to next newline. Do this better eventually. + if f.tell() != 0: + cursor = f.read(1) + while cursor and cursor != '\n': + cursor = f.read(1) + ck_data = f.read(self.CHUNK_SIZE) + cursor = f.read(1) + while cursor and ck_data[-1] != '\n': + ck_data += cursor + cursor = f.read(1) + return to_json_string({'ck_data': ck_data, 'ck_index': ck_index+1}) + def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None): #TODO Prevent failure when displaying extremely long > 50kb lines. if to_ext: return self._serve_raw(trans, dataset, to_ext) if chunk: - ck_index = int(chunk) - f = open(dataset.file_name) - f.seek(ck_index * self.CHUNK_SIZE) - # If we aren't at the start of the file, seek to next newline. Do this better eventually. - if f.tell() != 0: - cursor = f.read(1) - while cursor and cursor != '\n': - cursor = f.read(1) - ck_data = f.read(self.CHUNK_SIZE) - cursor = f.read(1) - while cursor and ck_data[-1] != '\n': - ck_data += cursor - cursor = f.read(1) - return to_json_string({'ck_data': ck_data, 'ck_index': ck_index+1}) - return trans.fill_template( "/dataset/tabular_chunked.mako",dataset = dataset) + return self.get_chunk(trans, dataset, chunk) + else: + column_names = 'null' + if dataset.metadata.column_names: + column_names = dataset.metadata.column_names + elif hasattr(dataset.datatype, 'column_names'): + column_names = dataset.datatype.column_names + return trans.fill_template( "/dataset/tabular_chunked.mako", + dataset = dataset, + chunk = self.get_chunk(trans, dataset, 0), + column_number = dataset.metadata.columns, + column_names = column_names, + column_types = dataset.metadata.column_types)
def set_peek( self, dataset, line_count=None, is_multi_byte=False): super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte)
diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r ccfcca670dfa5303d09a178473b663c15e5dc80a static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1713,6 +1713,7 @@ top:10px; height:32px; width:32px; + display:none; background:url(largespinner.gif); }
diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r ccfcca670dfa5303d09a178473b663c15e5dc80a static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -724,7 +724,7 @@ div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} div.toolTitleNoSection{padding-bottom:5px;font-weight:bold;} #tool-search{padding-top:5px;padding-bottom:10px;position:relative;} -#loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;background:url(largespinner.gif);} +#loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;display:none;background:url(largespinner.gif);} #content_table td{text-align:right;white-space:nowrap;padding:2px 10px;} #content_table td.stringalign{text-align:left;} .toolMenuAndView .toolForm{float:left;background-color:white;margin:10px;}
diff -r 0bd0c35351c4eb9c7103b6d737543317abc54ac0 -r ccfcca670dfa5303d09a178473b663c15e5dc80a templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ b/templates/dataset/tabular_chunked.mako @@ -6,18 +6,19 @@ <%def name="javascripts()"> ${parent.javascripts()} <script type="text/javascript"> + var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; + var COLUMN_NUMBER = ${column_number}; + var COLUMN_TYPES = ${column_types}; + var COLUMN_NAMES = ${column_names};
- var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; - var DATASET_COLS = ${dataset.metadata.columns}; - var DATASET_TYPES = ${dataset.metadata.column_types}; - + var chunk = ${chunk}; var current_chunk = 0;
function renderCell(cell_contents, index, colspan){ if (colspan !== undefined){ return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } - else if (DATASET_TYPES[index] == 'str'){ + else if (COLUMN_TYPES[index] == 'str'){ /* Left align all str columns, right align the rest */ return $('<td>').addClass('stringalign').text(cell_contents);; } @@ -30,19 +31,19 @@ /* Check length of cells to ensure this is a complete row. */ var cells = line.split('\t'); var row = $('<tr>'); - if (cells.length == DATASET_COLS){ + if (cells.length == COLUMN_NUMBER){ $.each(cells, function(index, cell_contents){ row.append(renderCell(cell_contents, index)); }); } - else if(cells.length > DATASET_COLS){ + else if(cells.length > COLUMN_NUMBER){ /* SAM file or like format with optional metadata included */ - $.each(cells.slice(0, DATASET_COLS -1), function(index, cell_contents){ + $.each(cells.slice(0, COLUMN_NUMBER -1), function(index, cell_contents){ row.append(renderCell(cell_contents, index)); }); - row.append(renderCell(cells.slice(DATASET_COLS -1).join('\t'), DATASET_COLS-1)); + row.append(renderCell(cells.slice(COLUMN_NUMBER -1).join('\t'), COLUMN_NUMBER-1)); } - else if(DATASET_COLS > 5 && cells.length == DATASET_COLS - 1 ){ + else if(COLUMN_NUMBER > 5 && cells.length == COLUMN_NUMBER - 1 ){ /* SAM file or like format with optional metadata missing */ $.each(cells, function(index, cell_contents){ row.append(renderCell(cell_contents, index)); @@ -51,41 +52,44 @@ } else{ /* Comment line, just return the one cell*/ - row.append(renderCell(line, 0, DATASET_COLS)); + row.append(renderCell(line, 0, COLUMN_NUMBER)); } return row; }
- function fillTable(){ - if (current_chunk !== -1){ - var table = $('#content_table'); - $.getJSON(DATASET_URL, {chunk: current_chunk}, function (result) { - if (result.ck_data !== ""){ - var lines = result.ck_data.split('\n'); - $.each(lines, function(index, line){ - table.append(renderRow(line)); - }); - current_chunk = result.ck_index; - } - else { - current_chunk = -1; - } + function renderChunk(chunk){ + var table = $('#content_table'); + if (chunk.ck_data == ""){ + current_chunk = -1; + } + else if(chunk.ck_index === current_chunk + 1){ + if (current_chunk === 0 && COLUMN_NAMES){ + table.append('<tr><th>' + COLUMN_NAMES.join('</th><th>') + '</th></tr>'); + } + var lines = chunk.ck_data.split('\n'); + $.each(lines, function(index, line){ + table.append(renderRow(line)); }); + current_chunk = chunk.ck_index; } }
$(document).ready(function(){ - fillTable(); + renderChunk(chunk); $(window).scroll(function(){ if ($(window).scrollTop() == $(document).height() - $(window).height()){ - fillTable(); + if (current_chunk !== -1){ + $.getJSON(DATASET_URL, + {chunk: current_chunk}, + function(result){renderChunk(result)}); + } } }); - $('#loading_indicator').ajaxStart(function(){ - $(this).show(); - }).ajaxStop(function(){ - $(this).hide(); - }); + $('#loading_indicator').ajaxStart(function(){ + $(this).show(); + }).ajaxStop(function(){ + $(this).hide(); + }); }); </script></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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