galaxy-dev August 2009

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156 discussions

[hg] galaxy 2620: Message for page change script
by Nate Coraor 25 Aug '09

25 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/899a830754a3 changeset: 2620:899a830754a3 user: James Taylor <james(a)jamestaylor.org> date: Mon Aug 24 16:38:24 2009 -0400 description: Message for page change script 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0014_pages.py diffs (21 lines): diff -r 3ca815c4be07 -r 899a830754a3 lib/galaxy/model/migrate/versions/0014_pages.py --- a/lib/galaxy/model/migrate/versions/0014_pages.py Mon Aug 24 15:55:39 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0014_pages.py Mon Aug 24 16:38:24 2009 -0400 @@ -1,3 +1,9 @@ +""" +Migration script to add support for "Pages". + 1) Creates Page and PageRevision tables + 2) Adds username column to User table +""" + from sqlalchemy import * from migrate import * from migrate.changeset import * @@ -31,6 +37,7 @@ ) def upgrade(): + print __doc__ metadata.reflect() try: Page_table.create()

1 0

[hg] galaxy 2616: Cache defeat for css/js
by Nate Coraor 25 Aug '09

25 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4ff4be2f436f changeset: 2616:4ff4be2f436f user: James Taylor <james(a)jamestaylor.org> date: Mon Aug 24 15:27:27 2009 -0400 description: Cache defeat for css/js 3 file(s) affected in this change: lib/galaxy/web/framework/helpers/__init__.py templates/base.mako templates/workflow/editor.mako diffs (70 lines): diff -r 168a6ef6a99a -r 4ff4be2f436f lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py Sun Aug 23 17:13:04 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/__init__.py Mon Aug 24 15:27:27 2009 -0400 @@ -27,14 +27,17 @@ Take a list of stylesheet names (no extension) and return appropriate string of link tags. - TODO: This has a hardcoded "?v=1" to defeat caching. This should be done + TODO: This has a hardcoded "?v=2" to defeat caching. This should be done in a better way. """ - return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=1" ) for name in args ] ) + return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=2" ) for name in args ] ) def js( *args ): """ Take a list of javascript names (no extension) and return appropriate string of script tags. + + TODO: This has a hardcoded "?v=2" to defeat caching. This should be done + in a better way. """ - return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js" ) for name in args ] ) \ No newline at end of file + return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=2" ) for name in args ] ) diff -r 168a6ef6a99a -r 4ff4be2f436f templates/base.mako --- a/templates/base.mako Sun Aug 23 17:13:04 2009 -0400 +++ b/templates/base.mako Mon Aug 24 15:27:27 2009 -0400 @@ -27,9 +27,6 @@ ##  - <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script> - <script type="text/javascript" src="${h.url_for('/static/scripts/galaxy.base.js')}"></script> - - + ${h.js( "jquery", "galaxy.base" )} </%def> diff -r 168a6ef6a99a -r 4ff4be2f436f templates/workflow/editor.mako --- a/templates/workflow/editor.mako Sun Aug 23 17:13:04 2009 -0400 +++ b/templates/workflow/editor.mako Mon Aug 24 15:27:27 2009 -0400 @@ -25,17 +25,17 @@  - <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.drag.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.drop.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.hover.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.form.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.jstore-all.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/json2.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.base.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.workflow_editor.canvas.js')}"> </script> - + ${h.js( "jquery", + "jquery.event.drag", + "jquery.event.drop", + "jquery.event.hover", + "jquery.form", + "jquery.jstore-all", + "json2", + "galaxy.base", + "galaxy.workflow_editor.canvas" )} + <!--[if lt IE 7]> <script type='text/javascript'> window.lt_ie_7 = true;

1 0

[hg] galaxy 2617: Support for user defined pages. Page content i...
by Nate Coraor 25 Aug '09

25 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9c325f3656b5 changeset: 2617:9c325f3656b5 user: James Taylor <james(a)jamestaylor.org> date: Mon Aug 24 15:53:17 2009 -0400 description: Support for user defined pages. Page content is stripped down XHTML. Pages can be edited using a WYM editor, and have stable public urls. This is VERY PRELIMINARY, but functional 67 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0014_pages.py lib/galaxy/util/sanitize_html.py lib/galaxy/web/__init__.py lib/galaxy/web/buildapp.py lib/galaxy/web/controllers/page.py lib/galaxy/web/controllers/user.py lib/galaxy/web/framework/helpers/grids.py static/scripts/jquery.wymeditor.js static/wymeditor/iframe/default/lbl-blockquote.png static/wymeditor/iframe/default/lbl-h1.png static/wymeditor/iframe/default/lbl-h2.png static/wymeditor/iframe/default/lbl-h3.png static/wymeditor/iframe/default/lbl-h4.png static/wymeditor/iframe/default/lbl-h5.png static/wymeditor/iframe/default/lbl-h6.png static/wymeditor/iframe/default/lbl-p.png static/wymeditor/iframe/default/lbl-pre.png static/wymeditor/iframe/default/wymiframe.css static/wymeditor/iframe/default/wymiframe.html static/wymeditor/iframe/galaxy/lbl-blockquote.png static/wymeditor/iframe/galaxy/lbl-h1.png static/wymeditor/iframe/galaxy/lbl-h2.png static/wymeditor/iframe/galaxy/lbl-h3.png static/wymeditor/iframe/galaxy/lbl-h4.png static/wymeditor/iframe/galaxy/lbl-h5.png static/wymeditor/iframe/galaxy/lbl-h6.png static/wymeditor/iframe/galaxy/lbl-p.png static/wymeditor/iframe/galaxy/lbl-pre.png static/wymeditor/iframe/galaxy/wymiframe.css static/wymeditor/iframe/galaxy/wymiframe.html static/wymeditor/lang/bg.js static/wymeditor/lang/ca.js static/wymeditor/lang/cs.js static/wymeditor/lang/de.js static/wymeditor/lang/en.js static/wymeditor/lang/es.js static/wymeditor/lang/fa.js static/wymeditor/lang/fi.js static/wymeditor/lang/fr.js static/wymeditor/lang/he.js static/wymeditor/lang/hr.js static/wymeditor/lang/hu.js static/wymeditor/lang/it.js static/wymeditor/lang/nb.js static/wymeditor/lang/nl.js static/wymeditor/lang/nn.js static/wymeditor/lang/pl.js static/wymeditor/lang/pt-br.js static/wymeditor/lang/pt.js static/wymeditor/lang/ru.js static/wymeditor/lang/sv.js static/wymeditor/lang/tr.js static/wymeditor/lang/zh_cn.js static/wymeditor/skins/default/icons.png static/wymeditor/skins/default/skin.css static/wymeditor/skins/default/skin.js static/wymeditor/skins/galaxy/icons.png static/wymeditor/skins/galaxy/skin.css static/wymeditor/skins/galaxy/skin.js templates/grid.mako templates/page/create.mako templates/page/display.mako templates/page/editor.mako templates/page/index.mako templates/user/index.mako diffs (truncated from 7896 to 3000 lines): diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Aug 24 15:27:27 2009 -0400 +++ b/lib/galaxy/model/__init__.py Mon Aug 24 15:53:17 2009 -0400 @@ -33,6 +33,7 @@ self.external = False self.deleted = False self.purged = False + self.username = None # Relationships self.histories = [] @@ -1118,7 +1119,20 @@ self.country+'<br/>'+ \ 'Phone: '+self.phone +class Page( object ): + def __init__( self ): + self.id = None + self.user = None + self.title = None + self.slug = None + self.latest_revision_id = None + self.revisions = [] +class PageRevision( object ): + def __init__( self ): + self.user = None + self.title = None + self.content = None diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Aug 24 15:27:27 2009 -0400 +++ b/lib/galaxy/model/mapping.py Mon Aug 24 15:53:17 2009 -0400 @@ -42,6 +42,7 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "email", TrimmedString( 255 ), nullable=False ), + Column( "username", TrimmedString( 255 ), index=True, unique=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ), @@ -523,6 +524,26 @@ Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), Column( "comment", TEXT ) ) +Page.table = Table( "page", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + 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 ), + ) + +PageRevision.table = Table( "page_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "content", TEXT ) + ) + # With the tables defined we can define the mappers and setup the # relationships between the model objects. @@ -905,6 +926,18 @@ assign_mapper( context, MetadataFile, MetadataFile.table, properties=dict( history_dataset=relation( HistoryDatasetAssociation ), library_dataset=relation( LibraryDatasetDatasetAssociation ) ) ) +assign_mapper( context, PageRevision, PageRevision.table ) + +assign_mapper( context, Page, Page.table, + properties=dict( user=relation( User ), + revisions=relation( PageRevision, backref='page', + cascade="all, delete-orphan", + primaryjoin=( Page.table.c.id == PageRevision.table.c.page_id ) ), + latest_revision=relation( PageRevision, post_update=True, + primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), + lazy=False ) + ) ) + def db_next_hid( self ): """ Override __next_hid to generate from the database in a concurrency diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/model/migrate/versions/0014_pages.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0014_pages.py Mon Aug 24 15:53:17 2009 -0400 @@ -0,0 +1,55 @@ +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 ) + +Page_table = Table( "page", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + 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 ), + ) + +PageRevision_table = Table( "page_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "content", TEXT ) + ) + +def upgrade(): + metadata.reflect() + try: + Page_table.create() + except: + log.debug( "Could not create page table" ) + try: + PageRevision_table.create() + except: + log.debug( "Could not create page_revision table" ) + + # Add 1 column to the user table + User_table = Table( "galaxy_user", metadata, autoload=True ) + col = Column( 'username', String(255), index=True, unique=True, default=False ) + col.create( User_table ) + assert col is User_table.c.username + +def downgrade(): + metadata.reflect() + Page_table.drop() + PageRevision_table.drop() + User_table = Table( "galaxy_user", metadata, autoload=True ) + User_table.c.username.drop() diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/util/sanitize_html.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/util/sanitize_html.py Mon Aug 24 15:53:17 2009 -0400 @@ -0,0 +1,439 @@ +""" +HTML Sanitizer (ripped from feedparser) +""" + +import re, sgmllib + +# reversable htmlentitydefs mappings for Python 2.2 +try: + from htmlentitydefs import name2codepoint, codepoint2name +except: + import htmlentitydefs + name2codepoint={} + codepoint2name={} + for (name,codepoint) in htmlentitydefs.entitydefs.iteritems(): + if codepoint.startswith('&#'): codepoint=unichr(int(codepoint[2:-1])) + name2codepoint[name]=ord(codepoint) + codepoint2name[ord(codepoint)]=name + +_cp1252 = { + unichr(128): unichr(8364), # euro sign + unichr(130): unichr(8218), # single low-9 quotation mark + unichr(131): unichr( 402), # latin small letter f with hook + unichr(132): unichr(8222), # double low-9 quotation mark + unichr(133): unichr(8230), # horizontal ellipsis + unichr(134): unichr(8224), # dagger + unichr(135): unichr(8225), # double dagger + unichr(136): unichr( 710), # modifier letter circumflex accent + unichr(137): unichr(8240), # per mille sign + unichr(138): unichr( 352), # latin capital letter s with caron + unichr(139): unichr(8249), # single left-pointing angle quotation mark + unichr(140): unichr( 338), # latin capital ligature oe + unichr(142): unichr( 381), # latin capital letter z with caron + unichr(145): unichr(8216), # left single quotation mark + unichr(146): unichr(8217), # right single quotation mark + unichr(147): unichr(8220), # left double quotation mark + unichr(148): unichr(8221), # right double quotation mark + unichr(149): unichr(8226), # bullet + unichr(150): unichr(8211), # en dash + unichr(151): unichr(8212), # em dash + unichr(152): unichr( 732), # small tilde + unichr(153): unichr(8482), # trade mark sign + unichr(154): unichr( 353), # latin small letter s with caron + unichr(155): unichr(8250), # single right-pointing angle quotation mark + unichr(156): unichr( 339), # latin small ligature oe + unichr(158): unichr( 382), # latin small letter z with caron + unichr(159): unichr( 376)} # latin capital letter y with diaeresis + +class _BaseHTMLProcessor(sgmllib.SGMLParser): + special = re.compile('''[<>'"]''') + bare_ampersand = re.compile("&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)") + elements_no_end_tag = ['area', 'base', 'basefont', 'br', 'col', 'frame', 'hr', + 'img', 'input', 'isindex', 'link', 'meta', 'param'] + + def __init__(self, encoding, type): + self.encoding = encoding + self.type = type + ## if _debug: sys.stderr.write('entering BaseHTMLProcessor, encoding=%s\n' % self.encoding) + sgmllib.SGMLParser.__init__(self) + + def reset(self): + self.pieces = [] + sgmllib.SGMLParser.reset(self) + + def _shorttag_replace(self, match): + tag = match.group(1) + if tag in self.elements_no_end_tag: + return '<' + tag + ' />' + else: + return '<' + tag + '></' + tag + '>' + + def parse_starttag(self,i): + j=sgmllib.SGMLParser.parse_starttag(self, i) + if self.type == 'application/xhtml+xml': + if j>2 and self.rawdata[j-2:j]=='/>': + self.unknown_endtag(self.lasttag) + return j + + def feed(self, data): + data = re.compile(r'<!((?!DOCTYPE|--|\[))', re.IGNORECASE).sub(r'<!\1', data) + #data = re.sub(r'<(\S+?)\s*?/>', self._shorttag_replace, data) # bug [ 1399464 ] Bad regexp for _shorttag_replace + data = re.sub(r'<([^<>\s]+?)\s*/>', self._shorttag_replace, data) + data = data.replace(''', "'") + data = data.replace('"', '"') + if self.encoding and type(data) == type(u''): + data = data.encode(self.encoding) + sgmllib.SGMLParser.feed(self, data) + sgmllib.SGMLParser.close(self) + + def normalize_attrs(self, attrs): + if not attrs: return attrs + # utility method to be called by descendants + attrs = dict([(k.lower(), v) for k, v in attrs]).items() + attrs = [(k, k in ('rel', 'type') and v.lower() or v) for k, v in attrs] + attrs.sort() + return attrs + + def unknown_starttag(self, tag, attrs): + # called for each start tag + # attrs is a list of (attr, value) tuples + # e.g. for <pre class='screen'>, tag='pre', attrs=[('class', 'screen')] + ## if _debug: sys.stderr.write('_BaseHTMLProcessor, unknown_starttag, tag=%s\n' % tag) + uattrs = [] + strattrs='' + if attrs: + for key, value in attrs: + value=value.replace('>','>').replace('<','<').replace('"','"') + value = self.bare_ampersand.sub("&", value) + # thanks to Kevin Marks for this breathtaking hack to deal with (valid) high-bit attribute values in UTF-8 feeds + if type(value) != type(u''): + try: + value = unicode(value, self.encoding) + except: + value = unicode(value, 'iso-8859-1') + uattrs.append((unicode(key, self.encoding), value)) + strattrs = u''.join([u' %s="%s"' % (key, value) for key, value in uattrs]) + if self.encoding: + try: + strattrs=strattrs.encode(self.encoding) + except: + pass + if tag in self.elements_no_end_tag: + self.pieces.append('<%(tag)s%(strattrs)s />' % locals()) + else: + self.pieces.append('<%(tag)s%(strattrs)s>' % locals()) + + def unknown_endtag(self, tag): + # called for each end tag, e.g. for </pre>, tag will be 'pre' + # Reconstruct the original end tag. + if tag not in self.elements_no_end_tag: + self.pieces.append("</%(tag)s>" % locals()) + + def handle_charref(self, ref): + # called for each character reference, e.g. for ' ', ref will be '160' + # Reconstruct the original character reference. + if ref.startswith('x'): + value = unichr(int(ref[1:],16)) + else: + value = unichr(int(ref)) + + if value in _cp1252.keys(): + self.pieces.append('&#%s;' % hex(ord(_cp1252[value]))[1:]) + else: + self.pieces.append('&#%(ref)s;' % locals()) + + def handle_entityref(self, ref): + # called for each entity reference, e.g. for '©', ref will be 'copy' + # Reconstruct the original entity reference. + if name2codepoint.has_key(ref): + self.pieces.append('&%(ref)s;' % locals()) + else: + self.pieces.append('&%(ref)s' % locals()) + + def handle_data(self, text): + # called for each block of plain text, i.e. outside of any tag and + # not containing any character or entity references + # Store the original text verbatim. + ## if _debug: sys.stderr.write('_BaseHTMLProcessor, handle_text, text=%s\n' % text) + self.pieces.append(text) + + def handle_comment(self, text): + # called for each HTML comment, e.g.  + # Reconstruct the original comment. + self.pieces.append('' % locals()) + + def handle_pi(self, text): + # called for each processing instruction, e.g. <?instruction> + # Reconstruct original processing instruction. + self.pieces.append('<?%(text)s>' % locals()) + + def handle_decl(self, text): + # called for the DOCTYPE, if present, e.g. + # <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" + # "http://www.w3.org/TR/html4/loose.dtd"> + # Reconstruct original DOCTYPE + self.pieces.append('<!%(text)s>' % locals()) + + _new_declname_match = re.compile(r'[a-zA-Z][-_.a-zA-Z0-9:]*\s*').match + def _scan_name(self, i, declstartpos): + rawdata = self.rawdata + n = len(rawdata) + if i == n: + return None, -1 + m = self._new_declname_match(rawdata, i) + if m: + s = m.group() + name = s.strip() + if (i + len(s)) == n: + return None, -1 # end of buffer + return name.lower(), m.end() + else: + self.handle_data(rawdata) +# self.updatepos(declstartpos, i) + return None, -1 + + def convert_charref(self, name): + return '&#%s;' % name + + def convert_entityref(self, name): + return '&%s;' % name + + def output(self): + '''Return processed HTML as a single string''' + return ''.join([str(p) for p in self.pieces]) + +class _HTMLSanitizer(_BaseHTMLProcessor): + acceptable_elements = ['a', 'abbr', 'acronym', 'address', 'area', 'article', + 'aside', 'audio', 'b', 'big', 'blockquote', 'br', 'button', 'canvas', + 'caption', 'center', 'cite', 'code', 'col', 'colgroup', 'command', + 'datagrid', 'datalist', 'dd', 'del', 'details', 'dfn', 'dialog', 'dir', + 'div', 'dl', 'dt', 'em', 'event-source', 'fieldset', 'figure', 'footer', + 'font', 'form', 'header', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6', 'hr', 'i', + 'img', 'input', 'ins', 'keygen', 'kbd', 'label', 'legend', 'li', 'm', 'map', + 'menu', 'meter', 'multicol', 'nav', 'nextid', 'ol', 'output', 'optgroup', + 'option', 'p', 'pre', 'progress', 'q', 's', 'samp', 'section', 'select', + 'small', 'sound', 'source', 'spacer', 'span', 'strike', 'strong', 'sub', + 'sup', 'table', 'tbody', 'td', 'textarea', 'time', 'tfoot', 'th', 'thead', + 'tr', 'tt', 'u', 'ul', 'var', 'video', 'noscript'] + + acceptable_attributes = ['abbr', 'accept', 'accept-charset', 'accesskey', + 'action', 'align', 'alt', 'autocomplete', 'autofocus', 'axis', + 'background', 'balance', 'bgcolor', 'bgproperties', 'border', + 'bordercolor', 'bordercolordark', 'bordercolorlight', 'bottompadding', + 'cellpadding', 'cellspacing', 'ch', 'challenge', 'char', 'charoff', + 'choff', 'charset', 'checked', 'cite', 'class', 'clear', 'color', 'cols', + 'colspan', 'compact', 'contenteditable', 'controls', 'coords', 'data', + 'datafld', 'datapagesize', 'datasrc', 'datetime', 'default', 'delay', + 'dir', 'disabled', 'draggable', 'dynsrc', 'enctype', 'end', 'face', 'for', + 'form', 'frame', 'galleryimg', 'gutter', 'headers', 'height', 'hidefocus', + 'hidden', 'high', 'href', 'hreflang', 'hspace', 'icon', 'id', 'inputmode', + 'ismap', 'keytype', 'label', 'leftspacing', 'lang', 'list', 'longdesc', + 'loop', 'loopcount', 'loopend', 'loopstart', 'low', 'lowsrc', 'max', + 'maxlength', 'media', 'method', 'min', 'multiple', 'name', 'nohref', + 'noshade', 'nowrap', 'open', 'optimum', 'pattern', 'ping', 'point-size', + 'prompt', 'pqg', 'radiogroup', 'readonly', 'rel', 'repeat-max', + 'repeat-min', 'replace', 'required', 'rev', 'rightspacing', 'rows', + 'rowspan', 'rules', 'scope', 'selected', 'shape', 'size', 'span', 'src', + 'start', 'step', 'summary', 'suppress', 'tabindex', 'target', 'template', + 'title', 'toppadding', 'type', 'unselectable', 'usemap', 'urn', 'valign', + 'value', 'variable', 'volume', 'vspace', 'vrml', 'width', 'wrap', + 'xml:lang'] + + unacceptable_elements_with_end_tag = ['script', 'applet', 'style'] + + acceptable_css_properties = ['azimuth', 'background-color', + 'border-bottom-color', 'border-collapse', 'border-color', + 'border-left-color', 'border-right-color', 'border-top-color', 'clear', + 'color', 'cursor', 'direction', 'display', 'elevation', 'float', 'font', + 'font-family', 'font-size', 'font-style', 'font-variant', 'font-weight', + 'height', 'letter-spacing', 'line-height', 'overflow', 'pause', + 'pause-after', 'pause-before', 'pitch', 'pitch-range', 'richness', + 'speak', 'speak-header', 'speak-numeral', 'speak-punctuation', + 'speech-rate', 'stress', 'text-align', 'text-decoration', 'text-indent', + 'unicode-bidi', 'vertical-align', 'voice-family', 'volume', + 'white-space', 'width'] + + # survey of common keywords found in feeds + acceptable_css_keywords = ['auto', 'aqua', 'black', 'block', 'blue', + 'bold', 'both', 'bottom', 'brown', 'center', 'collapse', 'dashed', + 'dotted', 'fuchsia', 'gray', 'green', '!important', 'italic', 'left', + 'lime', 'maroon', 'medium', 'none', 'navy', 'normal', 'nowrap', 'olive', + 'pointer', 'purple', 'red', 'right', 'solid', 'silver', 'teal', 'top', + 'transparent', 'underline', 'white', 'yellow'] + + valid_css_values = re.compile('^(#[0-9a-f]+|rgb$\d+%?,\d*%?,?\d*%?$?|' + + '\d{0,2}\.?\d{0,2}(cm|em|ex|in|mm|pc|pt|px|%|,|\))?)$') + + mathml_elements = ['annotation', 'annotation-xml', 'maction', 'math', + 'merror', 'mfenced', 'mfrac', 'mi', 'mmultiscripts', 'mn', 'mo', 'mover', 'mpadded', + 'mphantom', 'mprescripts', 'mroot', 'mrow', 'mspace', 'msqrt', 'mstyle', + 'msub', 'msubsup', 'msup', 'mtable', 'mtd', 'mtext', 'mtr', 'munder', + 'munderover', 'none', 'semantics'] + + mathml_attributes = ['actiontype', 'align', 'columnalign', 'columnalign', + 'columnalign', 'close', 'columnlines', 'columnspacing', 'columnspan', 'depth', + 'display', 'displaystyle', 'encoding', 'equalcolumns', 'equalrows', + 'fence', 'fontstyle', 'fontweight', 'frame', 'height', 'linethickness', + 'lspace', 'mathbackground', 'mathcolor', 'mathvariant', 'mathvariant', + 'maxsize', 'minsize', 'open', 'other', 'rowalign', 'rowalign', 'rowalign', + 'rowlines', 'rowspacing', 'rowspan', 'rspace', 'scriptlevel', 'selection', + 'separator', 'separators', 'stretchy', 'width', 'width', 'xlink:href', + 'xlink:show', 'xlink:type', 'xmlns', 'xmlns:xlink'] + + # svgtiny - foreignObject + linearGradient + radialGradient + stop + svg_elements = ['a', 'animate', 'animateColor', 'animateMotion', + 'animateTransform', 'circle', 'defs', 'desc', 'ellipse', 'foreignObject', + 'font-face', 'font-face-name', 'font-face-src', 'g', 'glyph', 'hkern', + 'linearGradient', 'line', 'marker', 'metadata', 'missing-glyph', 'mpath', + 'path', 'polygon', 'polyline', 'radialGradient', 'rect', 'set', 'stop', + 'svg', 'switch', 'text', 'title', 'tspan', 'use'] + + # svgtiny + class + opacity + offset + xmlns + xmlns:xlink + svg_attributes = ['accent-height', 'accumulate', 'additive', 'alphabetic', + 'arabic-form', 'ascent', 'attributeName', 'attributeType', + 'baseProfile', 'bbox', 'begin', 'by', 'calcMode', 'cap-height', + 'class', 'color', 'color-rendering', 'content', 'cx', 'cy', 'd', 'dx', + 'dy', 'descent', 'display', 'dur', 'end', 'fill', 'fill-opacity', + 'fill-rule', 'font-family', 'font-size', 'font-stretch', 'font-style', + 'font-variant', 'font-weight', 'from', 'fx', 'fy', 'g1', 'g2', + 'glyph-name', 'gradientUnits', 'hanging', 'height', 'horiz-adv-x', + 'horiz-origin-x', 'id', 'ideographic', 'k', 'keyPoints', 'keySplines', + 'keyTimes', 'lang', 'mathematical', 'marker-end', 'marker-mid', + 'marker-start', 'markerHeight', 'markerUnits', 'markerWidth', 'max', + 'min', 'name', 'offset', 'opacity', 'orient', 'origin', + 'overline-position', 'overline-thickness', 'panose-1', 'path', + 'pathLength', 'points', 'preserveAspectRatio', 'r', 'refX', 'refY', + 'repeatCount', 'repeatDur', 'requiredExtensions', 'requiredFeatures', + 'restart', 'rotate', 'rx', 'ry', 'slope', 'stemh', 'stemv', + 'stop-color', 'stop-opacity', 'strikethrough-position', + 'strikethrough-thickness', 'stroke', 'stroke-dasharray', + 'stroke-dashoffset', 'stroke-linecap', 'stroke-linejoin', + 'stroke-miterlimit', 'stroke-opacity', 'stroke-width', 'systemLanguage', + 'target', 'text-anchor', 'to', 'transform', 'type', 'u1', 'u2', + 'underline-position', 'underline-thickness', 'unicode', 'unicode-range', + 'units-per-em', 'values', 'version', 'viewBox', 'visibility', 'width', + 'widths', 'x', 'x-height', 'x1', 'x2', 'xlink:actuate', 'xlink:arcrole', + 'xlink:href', 'xlink:role', 'xlink:show', 'xlink:title', 'xlink:type', + 'xml:base', 'xml:lang', 'xml:space', 'xmlns', 'xmlns:xlink', 'y', 'y1', + 'y2', 'zoomAndPan'] + + svg_attr_map = None + svg_elem_map = None + + acceptable_svg_properties = [ 'fill', 'fill-opacity', 'fill-rule', + 'stroke', 'stroke-width', 'stroke-linecap', 'stroke-linejoin', + 'stroke-opacity'] + + def reset(self): + _BaseHTMLProcessor.reset(self) + self.unacceptablestack = 0 + self.mathmlOK = 0 + self.svgOK = 0 + + def unknown_starttag(self, tag, attrs): + acceptable_attributes = self.acceptable_attributes + keymap = {} + if not tag in self.acceptable_elements or self.svgOK: + if tag in self.unacceptable_elements_with_end_tag: + self.unacceptablestack += 1 + + # not otherwise acceptable, perhaps it is MathML or SVG? + if tag=='math' and ('xmlns','http://www.w3.org/1998/Math/MathML') in attrs: + self.mathmlOK += 1 + if tag=='svg' and ('xmlns','http://www.w3.org/2000/svg') in attrs: + self.svgOK += 1 + + # chose acceptable attributes based on tag class, else bail + if self.mathmlOK and tag in self.mathml_elements: + acceptable_attributes = self.mathml_attributes + elif self.svgOK and tag in self.svg_elements: + # for most vocabularies, lowercasing is a good idea. Many + # svg elements, however, are camel case + if not self.svg_attr_map: + lower=[attr.lower() for attr in self.svg_attributes] + mix=[a for a in self.svg_attributes if a not in lower] + self.svg_attributes = lower + self.svg_attr_map = dict([(a.lower(),a) for a in mix]) + + lower=[attr.lower() for attr in self.svg_elements] + mix=[a for a in self.svg_elements if a not in lower] + self.svg_elements = lower + self.svg_elem_map = dict([(a.lower(),a) for a in mix]) + acceptable_attributes = self.svg_attributes + tag = self.svg_elem_map.get(tag,tag) + keymap = self.svg_attr_map + elif not tag in self.acceptable_elements: + return + + # declare xlink namespace, if needed + if self.mathmlOK or self.svgOK: + if filter(lambda (n,v): n.startswith('xlink:'),attrs): + if not ('xmlns:xlink','http://www.w3.org/1999/xlink') in attrs: + attrs.append(('xmlns:xlink','http://www.w3.org/1999/xlink')) + + clean_attrs = [] + for key, value in self.normalize_attrs(attrs): + if key in acceptable_attributes: + key=keymap.get(key,key) + clean_attrs.append((key,value)) + elif key=='style': + pass + ## clean_value = self.sanitize_style(value) + ## if clean_value: clean_attrs.append((key,clean_value)) + _BaseHTMLProcessor.unknown_starttag(self, tag, clean_attrs) + + def unknown_endtag(self, tag): + if not tag in self.acceptable_elements: + if tag in self.unacceptable_elements_with_end_tag: + self.unacceptablestack -= 1 + if self.mathmlOK and tag in self.mathml_elements: + if tag == 'math' and self.mathmlOK: self.mathmlOK -= 1 + elif self.svgOK and tag in self.svg_elements: + tag = self.svg_elem_map.get(tag,tag) + if tag == 'svg' and self.svgOK: self.svgOK -= 1 + else: + return + _BaseHTMLProcessor.unknown_endtag(self, tag) + + def handle_pi(self, text): + pass + + def handle_decl(self, text): + pass + + def handle_data(self, text): + if not self.unacceptablestack: + _BaseHTMLProcessor.handle_data(self, text) + + def sanitize_style(self, style): + # disallow urls + style=re.compile('url\s*$\s*[^\s)]+?\s*$\s*').sub(' ',style) + + # gauntlet + if not re.match("""^([:,;#%.\sa-zA-Z0-9!]|\w-\w|'[\s\w]+'|"[\s\w]+"|$[\d,\s]+$)*$""", style): return '' + if not re.match("^(\s*[-\w]+\s*:\s*[^:;]*(;|$))*$", style): return '' + + clean = [] + for prop,value in re.findall("([-\w]+)\s*:\s*([^:;]*)",style): + if not value: continue + if prop.lower() in self.acceptable_css_properties: + clean.append(prop + ': ' + value + ';') + elif prop.split('-')[0].lower() in ['background','border','margin','padding']: + for keyword in value.split(): + if not keyword in self.acceptable_css_keywords and \ + not self.valid_css_values.match(keyword): + break + else: + clean.append(prop + ': ' + value + ';') + elif self.svgOK and prop.lower() in self.acceptable_svg_properties: + clean.append(prop + ': ' + value + ';') + + return ' '.join(clean) + + +def sanitize_html(htmlSource, encoding, type): + p = _HTMLSanitizer(encoding, type) + p.feed(htmlSource) + data = p.output() + data = data.strip().replace('\r\n', '\n') + return data \ No newline at end of file diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py Mon Aug 24 15:27:27 2009 -0400 +++ b/lib/galaxy/web/__init__.py Mon Aug 24 15:53:17 2009 -0400 @@ -3,4 +3,5 @@ """ from framework import expose, json, require_login, require_admin, url_for, error, form, FormBuilder +from framework.base import httpexceptions diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Mon Aug 24 15:27:27 2009 -0400 +++ b/lib/galaxy/web/buildapp.py Mon Aug 24 15:53:17 2009 -0400 @@ -74,6 +74,7 @@ webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='root', action='index' ) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) + webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/web/controllers/page.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/controllers/page.py Mon Aug 24 15:53:17 2009 -0400 @@ -0,0 +1,142 @@ +from galaxy.web.base.controller import * +from galaxy.web.framework.helpers import * +from galaxy.util.sanitize_html import sanitize_html + +import re + +VALID_SLUG_RE = re.compile( "^[a-z0-9\-]+$" ) + +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=trans.user.username, slug=item.slug ) + else: + return None + # Grid definition + use_panels = True + title = "Your pages" + model_class = model.Page + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Title", key="title", attach_popup=True ), + URLColumn( "Public URL" ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + ] + global_actions = [ + grids.GridAction( "Add new page", dict( action='create' ) ) + ] + operations = [ + grids.GridOperation( "View", allow_multiple=False, url_args=dict( action='display') ), + grids.GridOperation( "Edit", allow_multiple=False, url_args=dict( action='edit') ) + ] + +class PageController( BaseController ): + + list = PageListGrid() + + @web.expose + @web.require_admin + def index( self, trans, *args, **kwargs ): + grid = self.list( trans, *args, **kwargs ) + return trans.fill_template( "page/index.mako", grid=grid ) + + @web.expose + @web.require_admin + @web.require_login( "create pages" ) + def create( self, trans, page_title="", page_slug="" ): + """ + Create a new page + """ + user = trans.get_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 model.Page.filter_by( user=user, slug=page_slug ).first(): + page_slug_err = "Page id must be unique" + else: + # Create the new stored workflow + page = model.Page() + page.title = page_title + page.slug = page_slug + page.user = user + # And the first (empty) workflow revision + page_revision = model.PageRevision() + page_revision.title = page_title + page_revision.page = page + page.latest_revision = page_revision + page_revision.content = "" + # Persist + session = trans.sa_session + session.save_or_update( page ) + session.flush() + # Display the management page + trans.set_message( "Page '%s' created" % page.title ) + return self.list( trans ) + return trans.show_form( + web.FormBuilder( web.url_for(), "Create new page", 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_admin + @web.require_login( "edit pages" ) + def edit( self, trans, id ): + """ + Render the main page editor interface. + """ + id = trans.security.decode_id( id ) + page = trans.sa_session.query( model.Page ).get( id ) + assert page.user == trans.user + return trans.fill_template( "page/editor.mako", page=page ) + + @web.expose + @web.require_admin + def save( self, trans, id, content ): + id = trans.security.decode_id( id ) + page = trans.sa_session.query( model.Page ).get( id ) + assert page.user == trans.user + # Sanitize content + content = sanitize_html( content, 'utf-8', 'text/html' ) + # Add a new revision to the page with the provided content + page_revision = model.PageRevision() + page_revision.title = page.title + page_revision.page = page + page.latest_revision = page_revision + page_revision.content = content + trans.sa_session.flush() + + @web.expose + @web.require_admin + def display( self, trans, id ): + id = trans.security.decode_id( id ) + page = trans.sa_session.query( model.Page ).get( id ) + return trans.fill_template( "page/display.mako", page=page ) + + @web.expose + def display_by_username_and_slug( self, trans, username, slug ): + session = trans.sa_session + 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() + if page is None: + raise web.httpexceptions.HTTPNotFound() + return trans.fill_template( "page/display.mako", page=page ) + + \ No newline at end of file diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Mon Aug 24 15:27:27 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Mon Aug 24 15:53:17 2009 -0400 @@ -4,7 +4,7 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy import util -import logging, os, string +import logging, os, string, re from random import choice log = logging.getLogger( __name__ ) @@ -19,6 +19,8 @@ """ require_login_nocreation_template = require_login_template % "" require_login_creation_template = require_login_template % " If you don't already have an account, <a href='%s'>you may create one</a>." + +VALID_USERNAME_RE = re.compile( "^[a-z0-9\-]+$" ) class User( BaseController ): edit_address_id = None @@ -78,6 +80,37 @@ .add_text( "email", "Email", value=email, error=email_err ) .add_text( "conf_email", "Confirm Email", value='', error=conf_email_err ) .add_password( "password", "Password", value='', error=pass_err ) ) + + @web.expose + def change_username(self, trans, username='', **kwd): + username_err = '' + user = trans.get_user() + if not user: + trans.response.send_redirect( web.url_for( action='login' ) ) + if trans.request.method == "POST": + if len( username ) < 4: + username_err = "Username must be at least 4 characters in length" + elif len( username ) > 255: + username_err = "USername must be at most 255 characters in length" + elif not( VALID_USERNAME_RE.match( username ) ): + username_err = "Username must contain only letters, numbers, '-', and '_'" + elif trans.app.model.User.filter_by( username=username ).first(): + username_err = "This username is not available" + else: + user.username = username + user.flush() + trans.log_event( "User change username" ) + return trans.show_ok_message( "Username been set to: " + user.username ) + else: + username = user.username or '' + return trans.show_form( + web.FormBuilder( web.url_for(), "Change username", submit_text="Submit" ) + .add_text( "username", "Username", value=username, error=username_err, + help="""Your username is an optional identifier that + will be used to generate adresses for information + you share publicly. Usernames must be at least + four characters in length and contain only lowercase + letters, numbers, and the '-' character.""" ) ) @web.expose def login( self, trans, email='', password='' ): diff -r 4ff4be2f436f -r 9c325f3656b5 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Aug 24 15:27:27 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Aug 24 15:53:17 2009 -0400 @@ -15,6 +15,7 @@ exposed = True model_class = None template = "grid.mako" + global_actions = [] columns = [] operations = [] standard_filters = [] @@ -22,7 +23,12 @@ default_sort_key = None pass_through_operations = {} def __init__( self ): - pass + # Determine if any multiple row operations are defined + self.has_multiple_item_operations = False + for operation in self.operations: + if operation.allow_multiple: + self.has_multiple_item_operations = True + break def __call__( self, trans, **kwargs ): status = kwargs.get( 'status', None ) message = kwargs.get( 'message', None ) @@ -65,7 +71,13 @@ current_item = self.get_current_item( trans ) # Render def url( *args, **kwargs ): - new_kwargs = dict( extra_url_args ) + # Only include sort/filter arguments if not linking to another + # page. This is a bit of a hack. + if 'action' in kwargs: + new_kwargs = dict() + else: + new_kwargs = dict( extra_url_args ) + # Extend new_kwargs with first argument if found if len(args) > 0: new_kwargs.update( args[0] ) new_kwargs.update( kwargs ) @@ -158,16 +170,31 @@ return query class GridOperation( object ): - def __init__( self, label, key=None, condition=None, allow_multiple=True ): + def __init__( self, label, key=None, condition=None, allow_multiple=True, target=None, url_args=None ): self.label = label self.key = key self.allow_multiple = allow_multiple self.condition = condition + self.target = target + self.url_args = url_args + def get_url_args( self, item ): + if self.url_args: + temp = dict( self.url_args ) + temp['id'] = item.id + return temp + else: + return dict( operation=operation.label, id=item.id ) + def allowed( self, item ): if self.condition: return self.condition( item ) else: return True + +class GridAction( object ): + def __init__( self, label=None, url_args=None ): + self.label = label + self.url_args = url_args class GridColumnFilter( object ): def __init__( self, label, args=None ): diff -r 4ff4be2f436f -r 9c325f3656b5 static/scripts/jquery.wymeditor.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/jquery.wymeditor.js Mon Aug 24 15:53:17 2009 -0400 @@ -0,0 +1,4707 @@ +/** + * @version 0.5-rc1 + * + * WYMeditor : what you see is What You Mean web-based editor + * Copyright (c) 2005 - 2009 Jean-Francois Hovinne, http://www.wymeditor.org/ + * Dual licensed under the MIT (MIT-license.txt) + * and GPL (GPL-license.txt) licenses. + * + * For further information visit: + * http://www.wymeditor.org/ + * + * File: jquery.wymeditor.js + * + * Main JS file with core classes and functions. + * See the documentation for more info. + * + * About: authors + * + * Jean-Francois Hovinne (jf.hovinne a-t wymeditor dotorg) + * Volker Mische (vmx a-t gmx dotde) + * Scott Lewis (lewiscot a-t gmail dotcom) + * Bermi Ferrer (wymeditor a-t bermi dotorg) + * Daniel Reszka (d.reszka a-t wymeditor dotorg) + * Jonatan Lundin (jonatan.lundin _at_ gmail.com) + */ + +/* + Namespace: WYMeditor + Global WYMeditor namespace. +*/ +if(!WYMeditor) var WYMeditor = {}; + +//Wrap the Firebug console in WYMeditor.console +(function() { + if ( !window.console || !console.firebug ) { + var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml", + "group", "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd"]; + + WYMeditor.console = {}; + for (var i = 0; i < names.length; ++i) + WYMeditor.console[names[i]] = function() {} + + } else WYMeditor.console = window.console; +})(); + +jQuery.extend(WYMeditor, { + +/* + Constants: Global WYMeditor constants. + + VERSION - Defines WYMeditor version. + INSTANCES - An array of loaded WYMeditor.editor instances. + STRINGS - An array of loaded WYMeditor language pairs/values. + SKINS - An array of loaded WYMeditor skins. + NAME - The "name" attribute. + INDEX - A string replaced by the instance index. + WYM_INDEX - A string used to get/set the instance index. + BASE_PATH - A string replaced by WYMeditor's base path. + SKIN_PATH - A string replaced by WYMeditor's skin path. + WYM_PATH - A string replaced by WYMeditor's main JS file path. + SKINS_DEFAULT_PATH - The skins default base path. + SKINS_DEFAULT_CSS - The skins default CSS file. + LANG_DEFAULT_PATH - The language files default path. + IFRAME_BASE_PATH - A string replaced by the designmode iframe's base path. + IFRAME_DEFAULT - The iframe's default base path. + JQUERY_PATH - A string replaced by the computed jQuery path. + DIRECTION - A string replaced by the text direction (rtl or ltr). + LOGO - A string replaced by WYMeditor logo. + TOOLS - A string replaced by the toolbar's HTML. + TOOLS_ITEMS - A string replaced by the toolbar items. + TOOL_NAME - A string replaced by a toolbar item's name. + TOOL_TITLE - A string replaced by a toolbar item's title. + TOOL_CLASS - A string replaced by a toolbar item's class. + CLASSES - A string replaced by the classes panel's HTML. + CLASSES_ITEMS - A string replaced by the classes items. + CLASS_NAME - A string replaced by a class item's name. + CLASS_TITLE - A string replaced by a class item's title. + CONTAINERS - A string replaced by the containers panel's HTML. + CONTAINERS_ITEMS - A string replaced by the containers items. + CONTAINER_NAME - A string replaced by a container item's name. + CONTAINER_TITLE - A string replaced by a container item's title. + CONTAINER_CLASS - A string replaced by a container item's class. + HTML - A string replaced by the HTML view panel's HTML. + IFRAME - A string replaced by the designmode iframe. + STATUS - A string replaced by the status panel's HTML. + DIALOG_TITLE - A string replaced by a dialog's title. + DIALOG_BODY - A string replaced by a dialog's HTML body. + BODY - The BODY element. + STRING - The "string" type. + BODY,DIV,P, + H1,H2,H3,H4,H5,H6, + PRE,BLOCKQUOTE, + A,BR,IMG, + TABLE,TD,TH, + UL,OL,LI - HTML elements string representation. + CLASS,HREF,SRC, + TITLE,ALT - HTML attributes string representation. + DIALOG_LINK - A link dialog type. + DIALOG_IMAGE - An image dialog type. + DIALOG_TABLE - A table dialog type. + DIALOG_PASTE - A 'Paste from Word' dialog type. + BOLD - Command: (un)set selection to <strong>. + ITALIC - Command: (un)set selection to <em>. + CREATE_LINK - Command: open the link dialog or (un)set link. + INSERT_IMAGE - Command: open the image dialog or insert an image. + INSERT_TABLE - Command: open the table dialog. + PASTE - Command: open the paste dialog. + INDENT - Command: nest a list item. + OUTDENT - Command: unnest a list item. + TOGGLE_HTML - Command: display/hide the HTML view. + FORMAT_BLOCK - Command: set a block element to another type. + PREVIEW - Command: open the preview dialog. + UNLINK - Command: unset a link. + INSERT_UNORDEREDLIST- Command: insert an unordered list. + INSERT_ORDEREDLIST - Command: insert an ordered list. + MAIN_CONTAINERS - An array of the main HTML containers used in WYMeditor. + BLOCKS - An array of the HTML block elements. + KEY - Standard key codes. + NODE - Node types. + +*/ + + VERSION : "0.5-rc1", + INSTANCES : [], + STRINGS : [], + SKINS : [], + NAME : "name", + INDEX : "{Wym_Index}", + WYM_INDEX : "wym_index", + BASE_PATH : "{Wym_Base_Path}", + CSS_PATH : "{Wym_Css_Path}", + WYM_PATH : "{Wym_Wym_Path}", + SKINS_DEFAULT_PATH : "skins/", + SKINS_DEFAULT_CSS : "skin.css", + SKINS_DEFAULT_JS : "skin.js", + LANG_DEFAULT_PATH : "lang/", + IFRAME_BASE_PATH : "{Wym_Iframe_Base_Path}", + IFRAME_DEFAULT : "iframe/default/", + JQUERY_PATH : "{Wym_Jquery_Path}", + DIRECTION : "{Wym_Direction}", + LOGO : "{Wym_Logo}", + TOOLS : "{Wym_Tools}", + TOOLS_ITEMS : "{Wym_Tools_Items}", + TOOL_NAME : "{Wym_Tool_Name}", + TOOL_TITLE : "{Wym_Tool_Title}", + TOOL_CLASS : "{Wym_Tool_Class}", + CLASSES : "{Wym_Classes}", + CLASSES_ITEMS : "{Wym_Classes_Items}", + CLASS_NAME : "{Wym_Class_Name}", + CLASS_TITLE : "{Wym_Class_Title}", + CONTAINERS : "{Wym_Containers}", + CONTAINERS_ITEMS : "{Wym_Containers_Items}", + CONTAINER_NAME : "{Wym_Container_Name}", + CONTAINER_TITLE : "{Wym_Containers_Title}", + CONTAINER_CLASS : "{Wym_Container_Class}", + HTML : "{Wym_Html}", + IFRAME : "{Wym_Iframe}", + STATUS : "{Wym_Status}", + DIALOG_TITLE : "{Wym_Dialog_Title}", + DIALOG_BODY : "{Wym_Dialog_Body}", + STRING : "string", + BODY : "body", + DIV : "div", + P : "p", + H1 : "h1", + H2 : "h2", + H3 : "h3", + H4 : "h4", + H5 : "h5", + H6 : "h6", + PRE : "pre", + BLOCKQUOTE : "blockquote", + A : "a", + BR : "br", + IMG : "img", + TABLE : "table", + TD : "td", + TH : "th", + UL : "ul", + OL : "ol", + LI : "li", + CLASS : "class", + HREF : "href", + SRC : "src", + TITLE : "title", + ALT : "alt", + DIALOG_LINK : "Link", + DIALOG_IMAGE : "Image", + DIALOG_TABLE : "Table", + DIALOG_PASTE : "Paste_From_Word", + BOLD : "Bold", + ITALIC : "Italic", + CREATE_LINK : "CreateLink", + INSERT_IMAGE : "InsertImage", + INSERT_TABLE : "InsertTable", + INSERT_HTML : "InsertHTML", + PASTE : "Paste", + INDENT : "Indent", + OUTDENT : "Outdent", + TOGGLE_HTML : "ToggleHtml", + FORMAT_BLOCK : "FormatBlock", + PREVIEW : "Preview", + UNLINK : "Unlink", + INSERT_UNORDEREDLIST: "InsertUnorderedList", + INSERT_ORDEREDLIST : "InsertOrderedList", + + MAIN_CONTAINERS : new Array("p","h1","h2","h3","h4","h5","h6","pre","blockquote"), + + BLOCKS : new Array("address", "blockquote", "div", "dl", + "fieldset", "form", "h1", "h2", "h3", "h4", "h5", "h6", "hr", + "noscript", "ol", "p", "pre", "table", "ul", "dd", "dt", + "li", "tbody", "td", "tfoot", "th", "thead", "tr"), + + KEY : { + BACKSPACE: 8, + ENTER: 13, + END: 35, + HOME: 36, + LEFT: 37, + UP: 38, + RIGHT: 39, + DOWN: 40, + CURSOR: new Array(37, 38, 39, 40), + DELETE: 46 + }, + + NODE : { + ELEMENT: 1, + ATTRIBUTE: 2, + TEXT: 3 + }, + + /* + Class: WYMeditor.editor + WYMeditor editor main class, instanciated for each editor occurrence. + */ + + editor : function(elem, options) { + + /* + Constructor: WYMeditor.editor + + Initializes main values (index, elements, paths, ...) + and call WYMeditor.editor.init which initializes the editor. + + Parameters: + + elem - The HTML element to be replaced by the editor. + options - The hash of options. + + Returns: + + Nothing. + + See Also: + + <WYMeditor.editor.init> + */ + + //store the instance in the INSTANCES array and store the index + this._index = WYMeditor.INSTANCES.push(this) - 1; + //store the element replaced by the editor + this._element = elem; + //store the options + this._options = options; + //store the element's inner value + this._html = jQuery(elem).val(); + + //store the HTML option, if any + if(this._options.html) this._html = this._options.html; + //get or compute the base path (where the main JS file is located) + this._options.basePath = this._options.basePath + || this.computeBasePath(); + //get or set the skin path (where the skin files are located) + this._options.skinPath = this._options.skinPath + || this._options.basePath + WYMeditor.SKINS_DEFAULT_PATH + + this._options.skin + '/'; + //get or compute the main JS file location + this._options.wymPath = this._options.wymPath + || this.computeWymPath(); + //get or set the language files path + this._options.langPath = this._options.langPath + || this._options.basePath + WYMeditor.LANG_DEFAULT_PATH; + //get or set the designmode iframe's base path + this._options.iframeBasePath = this._options.iframeBasePath + || this._options.basePath + WYMeditor.IFRAME_DEFAULT; + //get or compute the jQuery JS file location + this._options.jQueryPath = this._options.jQueryPath + || this.computeJqueryPath(); + + //initialize the editor instance + this.init(); + + } + +}); + + +/********** JQUERY **********/ + +/** + * Replace an HTML element by WYMeditor + * + * @example jQuery(".wymeditor").wymeditor( + * { + * + * } + * ); + * @desc Example description here + * + * @name WYMeditor + * @description WYMeditor is a web-based WYSIWYM XHTML editor + * @param Hash hash A hash of parameters + * @option Integer iExample Description here + * @option String sExample Description here + * + * @type jQuery + * @cat Plugins/WYMeditor + * @author Jean-Francois Hovinne + */ +jQuery.fn.wymeditor = function(options) { + + options = jQuery.extend({ + + html: "", + + basePath: false, + + skinPath: false, + + wymPath: false, + + iframeBasePath: false, + + jQueryPath: false, + + styles: false, + + stylesheet: false, + + skin: "default", + initSkin: true, + loadSkin: true, + + lang: "en", + + direction: "ltr", + + boxHtml: "<div class='wym_box'>" + + "<div class='wym_area_top'>" + + WYMeditor.TOOLS + + "</div>" + + "<div class='wym_area_left'></div>" + + "<div class='wym_area_right'>" + + WYMeditor.CONTAINERS + + WYMeditor.CLASSES + + "</div>" + + "<div class='wym_area_main'>" + + WYMeditor.HTML + + WYMeditor.IFRAME + + WYMeditor.STATUS + + "</div>" + + "<div class='wym_area_bottom'>" + + WYMeditor.LOGO + + "</div>" + + "</div>", + + logoHtml: "<a class='wym_wymeditor_link' " + + "href='http://www.wymeditor.org/'>WYMeditor</a>", + + iframeHtml:"<div class='wym_iframe wym_section'>" + + "<iframe " + + "src='" + + WYMeditor.IFRAME_BASE_PATH + + "wymiframe.html' " + + "onload='this.contentWindow.parent.WYMeditor.INSTANCES[" + + WYMeditor.INDEX + "].initIframe(this)'" + + "></iframe>" + + "</div>", + + editorStyles: [], + + toolsHtml: "<div class='wym_tools wym_section'>" + + "<h2>{Tools}</h2>" + + "<ul>" + + WYMeditor.TOOLS_ITEMS + + "</ul>" + + "</div>", + + toolsItemHtml: "<li class='" + + WYMeditor.TOOL_CLASS + + "'><a href='#' name='" + + WYMeditor.TOOL_NAME + + "' title='" + + WYMeditor.TOOL_TITLE + + "'>" + + WYMeditor.TOOL_TITLE + + "</a></li>", + + toolsItems: [ + {'name': 'Bold', 'title': 'Strong', 'css': 'wym_tools_strong'}, + {'name': 'Italic', 'title': 'Emphasis', 'css': 'wym_tools_emphasis'}, + {'name': 'Superscript', 'title': 'Superscript', + 'css': 'wym_tools_superscript'}, + {'name': 'Subscript', 'title': 'Subscript', + 'css': 'wym_tools_subscript'}, + {'name': 'InsertOrderedList', 'title': 'Ordered_List', + 'css': 'wym_tools_ordered_list'}, + {'name': 'InsertUnorderedList', 'title': 'Unordered_List', + 'css': 'wym_tools_unordered_list'}, + {'name': 'Indent', 'title': 'Indent', 'css': 'wym_tools_indent'}, + {'name': 'Outdent', 'title': 'Outdent', 'css': 'wym_tools_outdent'}, + {'name': 'Undo', 'title': 'Undo', 'css': 'wym_tools_undo'}, + {'name': 'Redo', 'title': 'Redo', 'css': 'wym_tools_redo'}, + {'name': 'CreateLink', 'title': 'Link', 'css': 'wym_tools_link'}, + {'name': 'Unlink', 'title': 'Unlink', 'css': 'wym_tools_unlink'}, + {'name': 'InsertImage', 'title': 'Image', 'css': 'wym_tools_image'}, + {'name': 'InsertTable', 'title': 'Table', 'css': 'wym_tools_table'}, + {'name': 'Paste', 'title': 'Paste_From_Word', + 'css': 'wym_tools_paste'}, + {'name': 'ToggleHtml', 'title': 'HTML', 'css': 'wym_tools_html'}, + {'name': 'Preview', 'title': 'Preview', 'css': 'wym_tools_preview'} + ], + + containersHtml: "<div class='wym_containers wym_section'>" + + "<h2>{Containers}</h2>" + + "<ul>" + + WYMeditor.CONTAINERS_ITEMS + + "</ul>" + + "</div>", + + containersItemHtml:"<li class='" + + WYMeditor.CONTAINER_CLASS + + "'>" + + "<a href='#' name='" + + WYMeditor.CONTAINER_NAME + + "'>" + + WYMeditor.CONTAINER_TITLE + + "</a></li>", + + containersItems: [ + {'name': 'P', 'title': 'Paragraph', 'css': 'wym_containers_p'}, + {'name': 'H1', 'title': 'Heading_1', 'css': 'wym_containers_h1'}, + {'name': 'H2', 'title': 'Heading_2', 'css': 'wym_containers_h2'}, + {'name': 'H3', 'title': 'Heading_3', 'css': 'wym_containers_h3'}, + {'name': 'H4', 'title': 'Heading_4', 'css': 'wym_containers_h4'}, + {'name': 'H5', 'title': 'Heading_5', 'css': 'wym_containers_h5'}, + {'name': 'H6', 'title': 'Heading_6', 'css': 'wym_containers_h6'}, + {'name': 'PRE', 'title': 'Preformatted', 'css': 'wym_containers_pre'}, + {'name': 'BLOCKQUOTE', 'title': 'Blockquote', + 'css': 'wym_containers_blockquote'}, + {'name': 'TH', 'title': 'Table_Header', 'css': 'wym_containers_th'} + ], + + classesHtml: "<div class='wym_classes wym_section'>" + + "<h2>{Classes}</h2><ul>" + + WYMeditor.CLASSES_ITEMS + + "</ul></div>", + + classesItemHtml: "<li><a href='#' name='" + + WYMeditor.CLASS_NAME + + "'>" + + WYMeditor.CLASS_TITLE + + "</a></li>", + + classesItems: [], + + statusHtml: "<div class='wym_status wym_section'>" + + "<h2>{Status}</h2>" + + "</div>", + + htmlHtml: "<div class='wym_html wym_section'>" + + "<h2>{Source_Code}</h2>" + + "<textarea class='wym_html_val'></textarea>" + + "</div>", + + boxSelector: ".wym_box", + toolsSelector: ".wym_tools", + toolsListSelector: " ul", + containersSelector:".wym_containers", + classesSelector: ".wym_classes", + htmlSelector: ".wym_html", + iframeSelector: ".wym_iframe iframe", + iframeBodySelector:".wym_iframe", + statusSelector: ".wym_status", + toolSelector: ".wym_tools a", + containerSelector: ".wym_containers a", + classSelector: ".wym_classes a", + htmlValSelector: ".wym_html_val", + + hrefSelector: ".wym_href", + srcSelector: ".wym_src", + titleSelector: ".wym_title", + altSelector: ".wym_alt", + textSelector: ".wym_text", + + rowsSelector: ".wym_rows", + colsSelector: ".wym_cols", + captionSelector: ".wym_caption", + summarySelector: ".wym_summary", + + submitSelector: ".wym_submit", + cancelSelector: ".wym_cancel", + previewSelector: "", + + dialogTypeSelector: ".wym_dialog_type", + dialogLinkSelector: ".wym_dialog_link", + dialogImageSelector: ".wym_dialog_image", + dialogTableSelector: ".wym_dialog_table", + dialogPasteSelector: ".wym_dialog_paste", + dialogPreviewSelector: ".wym_dialog_preview", + + updateSelector: ".wymupdate", + updateEvent: "click", + + dialogFeatures: "menubar=no,titlebar=no,toolbar=no,resizable=no" + + ",width=560,height=300,top=0,left=0", + dialogFeaturesPreview: "menubar=no,titlebar=no,toolbar=no,resizable=no" + + ",scrollbars=yes,width=560,height=300,top=0,left=0", + + dialogHtml: "<!DOCTYPE html PUBLIC '-//W3C//DTD XHTML 1.0 Strict//EN'" + + " 'http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd'>" + + "<html dir='" + + WYMeditor.DIRECTION + + "'><head>" + + "<link rel='stylesheet' type='text/css' media='screen'" + + " href='" + + WYMeditor.CSS_PATH + + "' />" + + "<title>" + + WYMeditor.DIALOG_TITLE + + "</title>" + + "<script type='text/javascript'" + + " src='" + + WYMeditor.JQUERY_PATH + + "'></script>" + + "<script type='text/javascript'" + + " src='" + + WYMeditor.WYM_PATH + + "'></script>" + + "</head>" + + WYMeditor.DIALOG_BODY + + "</html>", + + dialogLinkHtml: "<body class='wym_dialog wym_dialog_link'" + + " onload='WYMeditor.INIT_DIALOG(" + WYMeditor.INDEX + ")'" + + ">" + + "<form>" + + "<fieldset>" + + "<input type='hidden' class='wym_dialog_type' value='" + + WYMeditor.DIALOG_LINK + + "' />" + + "<legend>{Link}</legend>" + + "<div class='row'>" + + "<label>{URL}</label>" + + "<input type='text' class='wym_href' value='' size='40' />" + + "</div>" + + "<div class='row'>" + + "<label>{Title}</label>" + + "<input type='text' class='wym_title' value='' size='40' />" + + "</div>" + + "<div class='row row-indent'>" + + "<input class='wym_submit' type='button'" + + " value='{Submit}' />" + + "<input class='wym_cancel' type='button'" + + "value='{Cancel}' />" + + "</div>" + + "</fieldset>" + + "</form>" + + "</body>", + + dialogImageHtml: "<body class='wym_dialog wym_dialog_image'" + + " onload='WYMeditor.INIT_DIALOG(" + WYMeditor.INDEX + ")'" + + ">" + + "<form>" + + "<fieldset>" + + "<input type='hidden' class='wym_dialog_type' value='" + + WYMeditor.DIALOG_IMAGE + + "' />" + + "<legend>{Image}</legend>" + + "<div class='row'>" + + "<label>{URL}</label>" + + "<input type='text' class='wym_src' value='' size='40' />" + + "</div>" + + "<div class='row'>" + + "<label>{Alternative_Text}</label>" + + "<input type='text' class='wym_alt' value='' size='40' />" + + "</div>" + + "<div class='row'>" + + "<label>{Title}</label>" + + "<input type='text' class='wym_title' value='' size='40' />" + + "</div>" + + "<div class='row row-indent'>" + + "<input class='wym_submit' type='button'" + + " value='{Submit}' />" + + "<input class='wym_cancel' type='button'" + + "value='{Cancel}' />" + + "</div>" + + "</fieldset>" + + "</form>" + + "</body>", + + dialogTableHtml: "<body class='wym_dialog wym_dialog_table'" + + " onload='WYMeditor.INIT_DIALOG(" + WYMeditor.INDEX + ")'" + + ">" + + "<form>" + + "<fieldset>" + + "<input type='hidden' class='wym_dialog_type' value='" + + WYMeditor.DIALOG_TABLE + + "' />" + + "<legend>{Table}</legend>" + + "<div class='row'>" + + "<label>{Caption}</label>" + + "<input type='text' class='wym_caption' value='' size='40' />" + + "</div>" + + "<div class='row'>" + + "<label>{Summary}</label>" + + "<input type='text' class='wym_summary' value='' size='40' />" + + "</div>" + + "<div class='row'>" + + "<label>{Number_Of_Rows}</label>" + + "<input type='text' class='wym_rows' value='3' size='3' />" + + "</div>" + + "<div class='row'>" + + "<label>{Number_Of_Cols}</label>" + + "<input type='text' class='wym_cols' value='2' size='3' />" + + "</div>" + + "<div class='row row-indent'>" + + "<input class='wym_submit' type='button'" + + " value='{Submit}' />" + + "<input class='wym_cancel' type='button'" + + "value='{Cancel}' />" + + "</div>" + + "</fieldset>" + + "</form>" + + "</body>", + + dialogPasteHtml: "<body class='wym_dialog wym_dialog_paste'" + + " onload='WYMeditor.INIT_DIALOG(" + WYMeditor.INDEX + ")'" + + ">" + + "<form>" + + "<input type='hidden' class='wym_dialog_type' value='" + + WYMeditor.DIALOG_PASTE + + "' />" + + "<fieldset>" + + "<legend>{Paste_From_Word}</legend>" + + "<div class='row'>" + + "<textarea class='wym_text' rows='10' cols='50'></textarea>" + + "</div>" + + "<div class='row'>" + + "<input class='wym_submit' type='button'" + + " value='{Submit}' />" + + "<input class='wym_cancel' type='button'" + + "value='{Cancel}' />" + + "</div>" + + "</fieldset>" + + "</form>" + + "</body>", + + dialogPreviewHtml: "<body class='wym_dialog wym_dialog_preview'" + + " onload='WYMeditor.INIT_DIALOG(" + WYMeditor.INDEX + ")'" + + "></body>", + + dialogStyles: [], + + stringDelimiterLeft: "{", + stringDelimiterRight:"}", + + preInit: null, + preBind: null, + postInit: null, + + preInitDialog: null, + postInitDialog: null + + }, options); + + return this.each(function() { + + new WYMeditor.editor(jQuery(this),options); + }); +}; + +/* @name extend + * @description Returns the WYMeditor instance based on its index + */ +jQuery.extend({ + wymeditors: function(i) { + return (WYMeditor.INSTANCES[i]); + } +}); + + +/********** WYMeditor **********/ + +/* @name Wymeditor + * @description WYMeditor class + */ + +/* @name init + * @description Initializes a WYMeditor instance + */ +WYMeditor.editor.prototype.init = function() { + + //load subclass - browser specific + //unsupported browsers: do nothing + if (jQuery.browser.msie) { + var WymClass = new WYMeditor.WymClassExplorer(this); + } + else if (jQuery.browser.mozilla) { + var WymClass = new WYMeditor.WymClassMozilla(this); + } + else if (jQuery.browser.opera) { + var WymClass = new WYMeditor.WymClassOpera(this); + } + else if (jQuery.browser.safari) { + var WymClass = new WYMeditor.WymClassSafari(this); + } + + if(WymClass) { + + if(jQuery.isFunction(this._options.preInit)) this._options.preInit(this); + + var SaxListener = new WYMeditor.XhtmlSaxListener(); + jQuery.extend(SaxListener, WymClass); + this.parser = new WYMeditor.XhtmlParser(SaxListener); + + if(this._options.styles || this._options.stylesheet){ + this.configureEditorUsingRawCss(); + } + + this.helper = new WYMeditor.XmlHelper(); + + //extend the Wymeditor object + //don't use jQuery.extend since 1.1.4 + //jQuery.extend(this, WymClass); + for (var prop in WymClass) { this[prop] = WymClass[prop]; } + + //load wymbox + this._box = jQuery(this._element).hide().after(this._options.boxHtml).next().addClass('wym_box_' + this._index); + + //store the instance index in wymbox and element replaced by editor instance + //but keep it compatible with jQuery < 1.2.3, see #122 + if( jQuery.isFunction( jQuery.fn.data ) ) { + jQuery.data(this._box.get(0), WYMeditor.WYM_INDEX, this._index); + jQuery.data(this._element.get(0), WYMeditor.WYM_INDEX, this._index); + } + + var h = WYMeditor.Helper; + + //construct the iframe + var iframeHtml = this._options.iframeHtml; + iframeHtml = h.replaceAll(iframeHtml, WYMeditor.INDEX, this._index); + iframeHtml = h.replaceAll(iframeHtml, WYMeditor.IFRAME_BASE_PATH, this._options.iframeBasePath); + + //construct wymbox + var boxHtml = jQuery(this._box).html(); + + boxHtml = h.replaceAll(boxHtml, WYMeditor.LOGO, this._options.logoHtml); + boxHtml = h.replaceAll(boxHtml, WYMeditor.TOOLS, this._options.toolsHtml); + boxHtml = h.replaceAll(boxHtml, WYMeditor.CONTAINERS,this._options.containersHtml); + boxHtml = h.replaceAll(boxHtml, WYMeditor.CLASSES, this._options.classesHtml); + boxHtml = h.replaceAll(boxHtml, WYMeditor.HTML, this._options.htmlHtml); + boxHtml = h.replaceAll(boxHtml, WYMeditor.IFRAME, iframeHtml); + boxHtml = h.replaceAll(boxHtml, WYMeditor.STATUS, this._options.statusHtml); + + //construct tools list + var aTools = eval(this._options.toolsItems); + var sTools = ""; + + for(var i = 0; i < aTools.length; i++) { + var oTool = aTools[i]; + if(oTool.name && oTool.title) + var sTool = this._options.toolsItemHtml; + var sTool = h.replaceAll(sTool, WYMeditor.TOOL_NAME, oTool.name); + sTool = h.replaceAll(sTool, WYMeditor.TOOL_TITLE, this._options.stringDelimiterLeft + + oTool.title + + this._options.stringDelimiterRight); + sTool = h.replaceAll(sTool, WYMeditor.TOOL_CLASS, oTool.css); + sTools += sTool; + } + + boxHtml = h.replaceAll(boxHtml, WYMeditor.TOOLS_ITEMS, sTools); + + //construct classes list + var aClasses = eval(this._options.classesItems); + var sClasses = ""; + + for(var i = 0; i < aClasses.length; i++) { + var oClass = aClasses[i]; + if(oClass.name && oClass.title) + var sClass = this._options.classesItemHtml; + sClass = h.replaceAll(sClass, WYMeditor.CLASS_NAME, oClass.name); + sClass = h.replaceAll(sClass, WYMeditor.CLASS_TITLE, oClass.title); + sClasses += sClass; + } + + boxHtml = h.replaceAll(boxHtml, WYMeditor.CLASSES_ITEMS, sClasses); + + //construct containers list + var aContainers = eval(this._options.containersItems); + var sContainers = ""; + + for(var i = 0; i < aContainers.length; i++) { + var oContainer = aContainers[i]; + if(oContainer.name && oContainer.title) + var sContainer = this._options.containersItemHtml; + sContainer = h.replaceAll(sContainer, WYMeditor.CONTAINER_NAME, oContainer.name); + sContainer = h.replaceAll(sContainer, WYMeditor.CONTAINER_TITLE, + this._options.stringDelimiterLeft + + oContainer.title + + this._options.stringDelimiterRight); + sContainer = h.replaceAll(sContainer, WYMeditor.CONTAINER_CLASS, oContainer.css); + sContainers += sContainer; + } + + boxHtml = h.replaceAll(boxHtml, WYMeditor.CONTAINERS_ITEMS, sContainers); + + //l10n + boxHtml = this.replaceStrings(boxHtml); + + //load html in wymbox + jQuery(this._box).html(boxHtml); + + //hide the html value + jQuery(this._box).find(this._options.htmlSelector).hide(); + + //enable the skin + this.loadSkin(); + + } +}; + +WYMeditor.editor.prototype.bindEvents = function() { + + //copy the instance + var wym = this; + + //handle click event on tools buttons + jQuery(this._box).find(this._options.toolSelector).click(function() { + wym._iframe.contentWindow.focus(); //See #154 + wym.exec(jQuery(this).attr(WYMeditor.NAME)); + return(false); + }); + + //handle click event on containers buttons + jQuery(this._box).find(this._options.containerSelector).click(function() { + wym.container(jQuery(this).attr(WYMeditor.NAME)); + return(false); + }); + + //handle keyup event on html value: set the editor value + //handle focus/blur events to check if the element has focus, see #147 + jQuery(this._box).find(this._options.htmlValSelector) + .keyup(function() { jQuery(wym._doc.body).html(jQuery(this).val());}) + .focus(function() { jQuery(this).toggleClass('hasfocus'); }) + .blur(function() { jQuery(this).toggleClass('hasfocus'); }); + + //handle click event on classes buttons + jQuery(this._box).find(this._options.classSelector).click(function() { + + var aClasses = eval(wym._options.classesItems); + var sName = jQuery(this).attr(WYMeditor.NAME); + + var oClass = WYMeditor.Helper.findByName(aClasses, sName); + + if(oClass) { + var jqexpr = oClass.expr; + wym.toggleClass(sName, jqexpr); + } + wym._iframe.contentWindow.focus(); //See #154 + return(false); + }); + + //handle event on update element + jQuery(this._options.updateSelector) + .bind(this._options.updateEvent, function() { + wym.update(); + }); +}; + +WYMeditor.editor.prototype.ready = function() { + return(this._doc != null); +}; + + +/********** METHODS **********/ + +/* @name box + * @description Returns the WYMeditor container + */ +WYMeditor.editor.prototype.box = function() { + return(this._box); +}; + +/* @name html + * @description Get/Set the html value + */ +WYMeditor.editor.prototype.html = function(html) { + + if(typeof html === 'string') jQuery(this._doc.body).html(html); + else return(jQuery(this._doc.body).html()); +}; + +/* @name xhtml + * @description Cleans up the HTML + */ +WYMeditor.editor.prototype.xhtml = function() { + return this.parser.parse(this.html()); +}; + +/* @name exec + * @description Executes a button command + */ +WYMeditor.editor.prototype.exec = function(cmd) { + + //base function for execCommand + //open a dialog or exec + switch(cmd) { + case WYMeditor.CREATE_LINK: + var container = this.container(); + if(container || this._selected_image) this.dialog(WYMeditor.DIALOG_LINK); + break; + + case WYMeditor.INSERT_IMAGE: + this.dialog(WYMeditor.DIALOG_IMAGE); + break; + + case WYMeditor.INSERT_TABLE: + this.dialog(WYMeditor.DIALOG_TABLE); + break; + + case WYMeditor.PASTE: + this.dialog(WYMeditor.DIALOG_PASTE); + break; + + case WYMeditor.TOGGLE_HTML: + this.update(); + this.toggleHtml(); + + //partially fixes #121 when the user manually inserts an image + if(!jQuery(this._box).find(this._options.htmlSelector).is(':visible')) + this.listen(); + break; + + case WYMeditor.PREVIEW: + this.dialog(WYMeditor.PREVIEW, this._options.dialogFeaturesPreview); + break; + + default: + this._exec(cmd); + break; + } +}; + +/* @name container + * @description Get/Set the selected container + */ +WYMeditor.editor.prototype.container = function(sType) { + + if(sType) { + + var container = null; + + if(sType.toLowerCase() == WYMeditor.TH) { + + container = this.container(); + + //find the TD or TH container + switch(container.tagName.toLowerCase()) { + + case WYMeditor.TD: case WYMeditor.TH: + break; + default: + var aTypes = new Array(WYMeditor.TD,WYMeditor.TH); + container = this.findUp(this.container(), aTypes); + break; + } + + //if it exists, switch + if(container!=null) { + + sType = (container.tagName.toLowerCase() == WYMeditor.TD)? WYMeditor.TH: WYMeditor.TD; + this.switchTo(container,sType); + this.update(); + } + } else { + + //set the container type + var aTypes=new Array(WYMeditor.P,WYMeditor.H1,WYMeditor.H2,WYMeditor.H3,WYMeditor.H4,WYMeditor.H5, + WYMeditor.H6,WYMeditor.PRE,WYMeditor.BLOCKQUOTE); + container = this.findUp(this.container(), aTypes); + + if(container) { + + var newNode = null; + + //blockquotes must contain a block level element + if(sType.toLowerCase() == WYMeditor.BLOCKQUOTE) { + + var blockquote = this.findUp(this.container(), WYMeditor.BLOCKQUOTE); + + if(blockquote == null) { + + newNode = this._doc.createElement(sType); + container.parentNode.insertBefore(newNode,container); + newNode.appendChild(container); + this.setFocusToNode(newNode.firstChild); + + } else { + + var nodes = blockquote.childNodes; + var lgt = nodes.length; + var firstNode = null; + + if(lgt > 0) firstNode = nodes.item(0); + for(var x=0; x<lgt; x++) { + blockquote.parentNode.insertBefore(nodes.item(0),blockquote); + } + blockquote.parentNode.removeChild(blockquote); + if(firstNode) this.setFocusToNode(firstNode); + } + } + + else this.switchTo(container,sType); + + this.update(); + } + } + } + else return(this.selected()); +}; + +/* @name toggleClass + * @description Toggles class on selected element, or one of its parents + */ +WYMeditor.editor.prototype.toggleClass = function(sClass, jqexpr) { + + var container = (this._selected_image + ? this._selected_image + : jQuery(this.selected())); + container = jQuery(container).parentsOrSelf(jqexpr); + jQuery(container).toggleClass(sClass); + + if(!jQuery(container).attr(WYMeditor.CLASS)) jQuery(container).removeAttr(this._class); + +}; + +/* @name findUp + * @description Returns the first parent or self container, based on its type + */ +WYMeditor.editor.prototype.findUp = function(node, filter) { + + //filter is a string or an array of strings + + if(node) { + + var tagname = node.tagName.toLowerCase(); + + if(typeof(filter) == WYMeditor.STRING) { + + while(tagname != filter && tagname != WYMeditor.BODY) { + + node = node.parentNode; + tagname = node.tagName.toLowerCase(); + } + + } else { + + var bFound = false; + + while(!bFound && tagname != WYMeditor.BODY) { + for(var i = 0; i < filter.length; i++) { + if(tagname == filter[i]) { + bFound = true; + break; + } + } + if(!bFound) { + node = node.parentNode; + tagname = node.tagName.toLowerCase(); + } + } + } + + if(tagname != WYMeditor.BODY) return(node); + else return(null); + + } else return(null); +}; + +/* @name switchTo + * @description Switch the node's type + */ +WYMeditor.editor.prototype.switchTo = function(node,sType) { + + var newNode = this._doc.createElement(sType); + var html = jQuery(node).html(); + node.parentNode.replaceChild(newNode,node); + jQuery(newNode).html(html); + this.setFocusToNode(newNode); +}; + +WYMeditor.editor.prototype.replaceStrings = function(sVal) { + //check if the language file has already been loaded + //if not, get it via a synchronous ajax call + if(!WYMeditor.STRINGS[this._options.lang]) { + try { + eval(jQuery.ajax({url:this._options.langPath + + this._options.lang + '.js', async:false}).responseText); + } catch(e) { + WYMeditor.console.error("WYMeditor: error while parsing language file."); + return sVal; + } + } + + //replace all the strings in sVal and return it + for (var key in WYMeditor.STRINGS[this._options.lang]) { + sVal = WYMeditor.Helper.replaceAll(sVal, this._options.stringDelimiterLeft + key + + this._options.stringDelimiterRight, + WYMeditor.STRINGS[this._options.lang][key]); + }; + return(sVal); +}; + +WYMeditor.editor.prototype.encloseString = function(sVal) { + + return(this._options.stringDelimiterLeft + + sVal + + this._options.stringDelimiterRight); +}; + +/* @name status + * @description Prints a status message + */ +WYMeditor.editor.prototype.status = function(sMessage) { + + //print status message + jQuery(this._box).find(this._options.statusSelector).html(sMessage); +}; + +/* @name update + * @description Updates the element and textarea values + */ +WYMeditor.editor.prototype.update = function() { + + var html = this.xhtml(); + jQuery(this._element).val(html); + jQuery(this._box).find(this._options.htmlValSelector).not('.hasfocus').val(html); //#147 +}; + +/* @name dialog + * @description Opens a dialog box + */ +WYMeditor.editor.prototype.dialog = function( dialogType, dialogFeatures, bodyHtml ) { + + var features = dialogFeatures || this._wym._options.dialogFeatures; + var wDialog = window.open('', 'dialog', features); + + if(wDialog) { + + var sBodyHtml = ""; + + switch( dialogType ) { + + case(WYMeditor.DIALOG_LINK): + sBodyHtml = this._options.dialogLinkHtml; + break; + case(WYMeditor.DIALOG_IMAGE): + sBodyHtml = this._options.dialogImageHtml; + break; + case(WYMeditor.DIALOG_TABLE): + sBodyHtml = this._options.dialogTableHtml; + break; + case(WYMeditor.DIALOG_PASTE): + sBodyHtml = this._options.dialogPasteHtml; + break; + case(WYMeditor.PREVIEW): + sBodyHtml = this._options.dialogPreviewHtml; + break; + + default: + sBodyHtml = bodyHtml; + } + + var h = WYMeditor.Helper; + + //construct the dialog + var dialogHtml = this._options.dialogHtml; + dialogHtml = h.replaceAll(dialogHtml, WYMeditor.BASE_PATH, this._options.basePath); + dialogHtml = h.replaceAll(dialogHtml, WYMeditor.DIRECTION, this._options.direction); + dialogHtml = h.replaceAll(dialogHtml, WYMeditor.CSS_PATH, this._options.skinPath + WYMeditor.SKINS_DEFAULT_CSS); + dialogHtml = h.replaceAll(dialogHtml, WYMeditor.WYM_PATH, this._options.wymPath); + dialogHtml = h.replaceAll(dialogHtml, WYMeditor.JQUERY_PATH, this._options.jQueryPath); + dialogHtml = h.replaceAll(dialogHtml, WYMeditor.DIALOG_TITLE, this.encloseString( dialogType )); + dialogHtml = h.replaceAll(dialogHtml, WYMeditor.DIALOG_BODY, sBodyHtml); + dialogHtml = h.replaceAll(dialogHtml, WYMeditor.INDEX, this._index); + + dialogHtml = this.replaceStrings(dialogHtml); + + var doc = wDialog.document; + doc.write(dialogHtml); + doc.close(); + } +}; + +/* @name toggleHtml + * @description Shows/Hides the HTML + */ +WYMeditor.editor.prototype.toggleHtml = function() { + jQuery(this._box).find(this._options.htmlSelector).toggle(); +}; + +WYMeditor.editor.prototype.uniqueStamp = function() { + var now = new Date(); + return("wym-" + now.getTime()); +}; + +WYMeditor.editor.prototype.paste = function(sData) { + + var sTmp; + var container = this.selected(); + + //split the data, using double newlines as the separator + var aP = sData.split(this._newLine + this._newLine); + var rExp = new RegExp(this._newLine, "g"); + + //add a P for each item + if(container && container.tagName.toLowerCase() != WYMeditor.BODY) { + for(x = aP.length - 1; x >= 0; x--) { + sTmp = aP[x]; + //simple newlines are replaced by a break + sTmp = sTmp.replace(rExp, "<br />"); + jQuery(container).after("<p>" + sTmp + "</p>"); + } + } else { + for(x = 0; x < aP.length; x++) { + sTmp = aP[x]; + //simple newlines are replaced by a break + sTmp = sTmp.replace(rExp, "<br />"); + jQuery(this._doc.body).append("<p>" + sTmp + "</p>"); + } + + } +}; + +WYMeditor.editor.prototype.insert = function(html) { + // Do we have a selection? + if (this._iframe.contentWindow.getSelection().focusNode != null) { + // Overwrite selection with provided html + this._exec( WYMeditor.INSERT_HTML, html); + } else { + // Fall back to the internal paste function if there's no selection + this.paste(html) + } +}; + +WYMeditor.editor.prototype.wrap = function(left, right) { + // Do we have a selection? + if (this._iframe.contentWindow.getSelection().focusNode != null) { + // Wrap selection with provided html + this._exec( WYMeditor.INSERT_HTML, left + this._iframe.contentWindow.getSelection().toString() + right); + } +}; + +WYMeditor.editor.prototype.unwrap = function() { + // Do we have a selection? + if (this._iframe.contentWindow.getSelection().focusNode != null) { + // Unwrap selection + this._exec( WYMeditor.INSERT_HTML, this._iframe.contentWindow.getSelection().toString() ); + } +}; + +WYMeditor.editor.prototype.addCssRules = function(doc, aCss) { + var styles = doc.styleSheets[0]; + if(styles) { + for(var i = 0; i < aCss.length; i++) { + var oCss = aCss[i]; + if(oCss.name && oCss.css) this.addCssRule(styles, oCss); + } + } +}; + +/********** CONFIGURATION **********/ + +WYMeditor.editor.prototype.computeBasePath = function() { + return jQuery(jQuery.grep(jQuery('script'), function(s){ + return (s.src && s.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/ )) + })).attr('src').replace(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/, ''); +}; + +WYMeditor.editor.prototype.computeWymPath = function() { + return jQuery(jQuery.grep(jQuery('script'), function(s){ + return (s.src && s.src.match(/jquery\.wymeditor(\.pack|\.min|\.packed)?\.js(\?.*)?$/ )) + })).attr('src'); +}; + +WYMeditor.editor.prototype.computeJqueryPath = function() { + return jQuery(jQuery.grep(jQuery('script'), function(s){ + return (s.src && s.src.match(/jquery(-(.*)){0,1}(\.pack|\.min|\.packed)?\.js(\?.*)?$/ )) + })).attr('src'); +}; + +WYMeditor.editor.prototype.computeCssPath = function() { + return jQuery(jQuery.grep(jQuery('link'), function(s){ + return (s.href && s.href.match(/wymeditor\/skins\/(.*)screen\.css(\?.*)?$/ )) + })).attr('href'); +}; + +WYMeditor.editor.prototype.configureEditorUsingRawCss = function() { + + var CssParser = new WYMeditor.WymCssParser(); + if(this._options.stylesheet){ + CssParser.parse(jQuery.ajax({url: this._options.stylesheet,async:false}).responseText); + }else{ + CssParser.parse(this._options.styles, false); + } + + if(this._options.classesItems.length == 0) { + this._options.classesItems = CssParser.css_settings.classesItems; + } + if(this._options.editorStyles.length == 0) { + this._options.editorStyles = CssParser.css_settings.editorStyles; + } + if(this._options.dialogStyles.length == 0) { + this._options.dialogStyles = CssParser.css_settings.dialogStyles; + } +}; + +/********** EVENTS **********/ + +WYMeditor.editor.prototype.listen = function() { + + //don't use jQuery.find() on the iframe body + //because of MSIE + jQuery + expando issue (#JQ1143) + //jQuery(this._doc.body).find("*").bind("mouseup", this.mouseup); + + jQuery(this._doc.body).bind("mousedown", this.mousedown); + var images = this._doc.body.getElementsByTagName("img"); + for(var i=0; i < images.length; i++) { + jQuery(images[i]).bind("mousedown", this.mousedown); + } +}; + +WYMeditor.editor.prototype.mousedown = function(evt) { + + var wym = WYMeditor.INSTANCES[this.ownerDocument.title]; + wym._selected_image = (this.tagName.toLowerCase() == WYMeditor.IMG) ? this : null; + evt.stopPropagation(); +}; + +/********** SKINS **********/ + +/* + * Function: WYMeditor.loadCss + * Loads a stylesheet in the document. + * + * Parameters: + * href - The CSS path. + */ +WYMeditor.loadCss = function(href) { + + var link = document.createElement('link'); + link.rel = 'stylesheet'; + link.href = href; + + var head = jQuery('head').get(0); + head.appendChild(link); +}; + +/* + * Function: WYMeditor.editor.loadSkin + * Loads the skin CSS and initialization script (if needed). + */ +WYMeditor.editor.prototype.loadSkin = function() { + + //does the user want to automatically load the CSS (default: yes)? + //we also test if it hasn't been already loaded by another instance + //see below for a better (second) test + if(this._options.loadSkin && !WYMeditor.SKINS[this._options.skin]) { + + //check if it hasn't been already loaded + //so we don't load it more than once + //(we check the existing <link> elements) + + var found = false; + var rExp = new RegExp(this._options.skin + + '\/' + WYMeditor.SKINS_DEFAULT_CSS + '$'); + + jQuery('link').each( function() { + if(this.href.match(rExp)) found = true; + }); + + //load it, using the skin path + if(!found) WYMeditor.loadCss( this._options.skinPath + + WYMeditor.SKINS_DEFAULT_CSS ); + } + + //put the classname (ex. wym_skin_default) on wym_box + jQuery(this._box).addClass( "wym_skin_" + this._options.skin ); + + //does the user want to use some JS to initialize the skin (default: yes)? + //also check if it hasn't already been loaded by another instance + if(this._options.initSkin && !WYMeditor.SKINS[this._options.skin]) { + + eval(jQuery.ajax({url:this._options.skinPath + + WYMeditor.SKINS_DEFAULT_JS, async:false}).responseText); + } + + //init the skin, if needed + if(WYMeditor.SKINS[this._options.skin] + && WYMeditor.SKINS[this._options.skin].init) + WYMeditor.SKINS[this._options.skin].init(this); + +}; + + +/********** DIALOGS **********/ + +WYMeditor.INIT_DIALOG = function(index) { + + var wym = window.opener.WYMeditor.INSTANCES[index]; + var doc = window.document; + var selected = wym.selected(); + var dialogType = jQuery(wym._options.dialogTypeSelector).val(); + var sStamp = wym.uniqueStamp(); + + switch(dialogType) { + + case WYMeditor.DIALOG_LINK: + //ensure that we select the link to populate the fields + if(selected && selected.tagName && selected.tagName.toLowerCase != WYMeditor.A) + selected = jQuery(selected).parentsOrSelf(WYMeditor.A); + + //fix MSIE selection if link image has been clicked + if(!selected && wym._selected_image) + selected = jQuery(wym._selected_image).parentsOrSelf(WYMeditor.A); + break; + + } + + //pre-init functions + if(jQuery.isFunction(wym._options.preInitDialog)) + wym._options.preInitDialog(wym,window); + + //add css rules from options + var styles = doc.styleSheets[0]; + var aCss = eval(wym._options.dialogStyles); + + wym.addCssRules(doc, aCss); + + //auto populate fields if selected container (e.g. A) + if(selected) { + jQuery(wym._options.hrefSelector).val(jQuery(selected).attr(WYMeditor.HREF)); + jQuery(wym._options.srcSelector).val(jQuery(selected).attr(WYMeditor.SRC)); + jQuery(wym._options.titleSelector).val(jQuery(selected).attr(WYMeditor.TITLE)); + jQuery(wym._options.altSelector).val(jQuery(selected).attr(WYMeditor.ALT)); + } + + //auto populate image fields if selected image + if(wym._selected_image) { + jQuery(wym._options.dialogImageSelector + " " + wym._options.srcSelector) + .val(jQuery(wym._selected_image).attr(WYMeditor.SRC)); + jQuery(wym._options.dialogImageSelector + " " + wym._options.titleSelector) + .val(jQuery(wym._selected_image).attr(WYMeditor.TITLE)); + jQuery(wym._options.dialogImageSelector + " " + wym._options.altSelector) + .val(jQuery(wym._selected_image).attr(WYMeditor.ALT)); + } + + jQuery(wym._options.dialogLinkSelector + " " + + wym._options.submitSelector).click(function() { + + var sUrl = jQuery(wym._options.hrefSelector).val(); + if(sUrl.length > 0) { + + wym._exec(WYMeditor.CREATE_LINK, sStamp); + + jQuery("a[href=" + sStamp + "]", wym._doc.body) + .attr(WYMeditor.HREF, sUrl) + .attr(WYMeditor.TITLE, jQuery(wym._options.titleSelector).val()); + + } + window.close(); + }); + + jQuery(wym._options.dialogImageSelector + " " + + wym._options.submitSelector).click(function() { + + var sUrl = jQuery(wym._options.srcSelector).val(); + if(sUrl.length > 0) { + + wym._exec(WYMeditor.INSERT_IMAGE, sStamp); + + jQuery("img[src$=" + sStamp + "]", wym._doc.body) + .attr(WYMeditor.SRC, sUrl) + .attr(WYMeditor.TITLE, jQuery(wym._options.titleSelector).val()) + .attr(WYMeditor.ALT, jQuery(wym._options.altSelector).val()); + } + window.close(); + }); + + jQuery(wym._options.dialogTableSelector + " " + + wym._options.submitSelector).click(function() { + + var iRows = jQuery(wym._options.rowsSelector).val(); + var iCols = jQuery(wym._options.colsSelector).val(); + + if(iRows > 0 && iCols > 0) { + + var table = wym._doc.createElement(WYMeditor.TABLE); + var newRow = null; + var newCol = null; + + var sCaption = jQuery(wym._options.captionSelector).val(); + + //we create the caption + var newCaption = table.createCaption(); + newCaption.innerHTML = sCaption; + + //we create the rows and cells + for(x=0; x<iRows; x++) { + newRow = table.insertRow(x); + for(y=0; y<iCols; y++) {newRow.insertCell(y);} + } + + //set the summary attr + jQuery(table).attr('summary', + jQuery(wym._options.summarySelector).val()); + + //append the table after the selected container + var node = jQuery(wym.findUp(wym.container(), + WYMeditor.MAIN_CONTAINERS)).get(0); + if(!node || !node.parentNode) jQuery(wym._doc.body).append(table); + else jQuery(node).after(table); + } + window.close(); + }); + + jQuery(wym._options.dialogPasteSelector + " " + + wym._options.submitSelector).click(function() { + + var sText = jQuery(wym._options.textSelector).val(); + wym.paste(sText); + window.close(); + }); + + jQuery(wym._options.dialogPreviewSelector + " " + + wym._options.previewSelector) + .html(wym.xhtml()); + + //cancel button + jQuery(wym._options.cancelSelector).mousedown(function() { + window.close(); + }); + + //pre-init functions + if(jQuery.isFunction(wym._options.postInitDialog)) + wym._options.postInitDialog(wym,window); + +}; + +/********** XHTML LEXER/PARSER **********/ + +/* +* @name xml +* @description Use these methods to generate XML and XHTML compliant tags and +* escape tag attributes correctly +* @author Bermi Ferrer - http://bermi.org +* @author David Heinemeier Hansson http://loudthinking.com +*/ +WYMeditor.XmlHelper = function() +{ + this._entitiesDiv = document.createElement('div'); + return this; +}; + + +/* +* @name tag +* @description +* Returns an empty HTML tag of type *name* which by default is XHTML +* compliant. Setting *open* to true will create an open tag compatible +* with HTML 4.0 and below. Add HTML attributes by passing an attributes +* array to *options*. For attributes with no value like (disabled and +* readonly), give it a value of true in the *options* array. +* +* Examples: +* +* this.tag('br') +* # => <br /> +* this.tag ('br', false, true) +* # => <br> +* this.tag ('input', jQuery({type:'text',disabled:true }) ) +* # => <input type="text" disabled="disabled" /> +*/ +WYMeditor.XmlHelper.prototype.tag = function(name, options, open) +{ + options = options || false; + open = open || false; + return '<'+name+(options ? this.tagOptions(options) : '')+(open ? '>' : ' />'); +}; + +/* +* @name contentTag +* @description +* Returns a XML block tag of type *name* surrounding the *content*. Add +* XML attributes by passing an attributes array to *options*. For attributes +* with no value like (disabled and readonly), give it a value of true in +* the *options* array. You can use symbols or strings for the attribute names. +* +* this.contentTag ('p', 'Hello world!' ) +* # => <p>Hello world!</p> +* this.contentTag('div', this.contentTag('p', "Hello world!"), jQuery({class : "strong"})) +* # => <div class="strong"><p>Hello world!</p></div> +* this.contentTag("select", options, jQuery({multiple : true})) +* # => <select multiple="multiple">...options...</select> +*/ +WYMeditor.XmlHelper.prototype.contentTag = function(name, content, options) +{ + options = options || false; + return '<'+name+(options ? this.tagOptions(options) : '')+'>'+content+'</'+name+'>'; +}; + +/* +* @name cdataSection +* @description +* Returns a CDATA section for the given +content+. CDATA sections +* are used to escape blocks of text containing characters which would +* otherwise be recognized as markup. CDATA sections begin with the string +* <tt><![CDATA[</tt> and } with (and may not contain) the string +* <tt>]]></tt>. +*/ +WYMeditor.XmlHelper.prototype.cdataSection = function(content) +{ + return '<![CDATA['+content+']]>'; +}; + + +/* +* @name escapeOnce +* @description +* Returns the escaped +xml+ without affecting existing escaped entities. +* +* this.escapeOnce( "1 > 2 & 3") +* # => "1 > 2 & 3" +*/ +WYMeditor.XmlHelper.prototype.escapeOnce = function(xml) +{ + return this._fixDoubleEscape(this.escapeEntities(xml)); +}; + +/* +* @name _fixDoubleEscape +* @description +* Fix double-escaped entities, such as &amp;, &#123;, etc. +*/ +WYMeditor.XmlHelper.prototype._fixDoubleEscape = function(escaped) +{ + return escaped.replace(/&([a-z]+|(#\d+));/ig, "&$1;"); +}; + +/* +* @name tagOptions +* @description +* Takes an array like the one generated by Tag.parseAttributes +* [["src", "http://www.editam.com/?a=b&c=d&f=g"], ["title", "Editam, <Simplified> CMS"]] +* or an object like {src:"http://www.editam.com/?a=b&c=d&f=g", title:"Editam, <Simplified> CMS"} +* and returns a string properly escaped like +* ' src = "http://www.editam.com/?a=b&c=d&f=g" title = "Editam, <Simplified> CMS"' +* which is valid for strict XHTML +*/ +WYMeditor.XmlHelper.prototype.tagOptions = function(options) +{ + var xml = this; + xml._formated_options = ''; + + for (var key in options) { + var formated_options = ''; + var value = options[key]; + if(typeof value != 'function' && value.length > 0) { + + if(parseInt(key) == key && typeof value == 'object'){ + key = value.shift(); + value = value.pop(); + } + if(key != '' && value != ''){ + xml._formated_options += ' '+key+'="'+xml.escapeOnce(value)+'"'; + } + } + } + return xml._formated_options; +}; + +/* +* @name escapeEntities +* @description +* Escapes XML/HTML entities <, >, & and ". If seccond parameter is set to false it +* will not escape ". If set to true it will also escape ' +*/ +WYMeditor.XmlHelper.prototype.escapeEntities = function(string, escape_quotes) +{ + this._entitiesDiv.innerHTML = string; + this._entitiesDiv.textContent = string; + var result = this._entitiesDiv.innerHTML; + if(typeof escape_quotes == 'undefined'){ + if(escape_quotes != false) result = result.replace('"', '"'); + if(escape_quotes == true) result = result.replace('"', '''); + } + return result; +}; + +/* +* Parses a string conatining tag attributes and values an returns an array formated like +* [["src", "http://www.editam.com"], ["title", "Editam, Simplified CMS"]] +*/ +WYMeditor.XmlHelper.prototype.parseAttributes = function(tag_attributes) +{ + // Use a compounded regex to match single quoted, double quoted and unquoted attribute pairs + var result = []; + var matches = tag_attributes.split(/((=\s*")(")("))|((=\s*\')(\')(\'))|((=\s*[^>\s]*))/g); + if(matches.toString() != tag_attributes){ + for (var k in matches) { + var v = matches[k]; + if(typeof v != 'function' && v.length != 0){ + var re = new RegExp('(\\w+)\\s*'+v); + if(match = tag_attributes.match(re) ){ + var value = v.replace(/^[\s=]+/, ""); + var delimiter = value.charAt(0); + delimiter = delimiter == '"' ? '"' : (delimiter=="'"?"'":''); + if(delimiter != ''){ + value = delimiter == '"' ? value.replace(/^"|"+$/g, '') : value.replace(/^'|'+$/g, ''); + } + tag_attributes = tag_attributes.replace(match[0],''); + result.push([match[1] , value]); + } + } + } + } + return result; +}; + +/** +* XhtmlValidator for validating tag attributes +* +* @author Bermi Ferrer - http://bermi.org +*/ +WYMeditor.XhtmlValidator = { + "_attributes": + { + "core": + { + "except":[ + "base", + "head", + "html", + "meta", + "param", + "script", + "style", + "title" + ], + "attributes":[ + "class", + "id", + "style", + "title", + "accesskey", + "tabindex" + ] + }, + "language": + { + "except":[ + "base", + "br", + "hr", + "iframe", + "param", + "script" + ], + "attributes": + { + "dir":[ + "ltr", + "rtl" + ], + "0":"lang", + "1":"xml:lang" + } + }, + "keyboard": + { + "attributes": + { + "accesskey":/^(\w){1}$/, + "tabindex":/^(\d)+$/ + } + } + }, + "_events": + { + "window": + { + "only":[ + "body" + ], + "attributes":[ + "onload", + "onunload" + ] + }, + "form": + { + "only":[ + "form", + "input", + "textarea", + "select", + "a", + "label", + "button" + ], + "attributes":[ + "onchange", + "onsubmit", + "onreset", + "onselect", + "onblur", + "onfocus" + ] + }, + "keyboard": + { + "except":[ + "base", + "bdo", + "br", + "frame", + "frameset", + "head", + "html", + "iframe", + "meta", + "param", + "script", + "style", + "title" + ], + "attributes":[ + "onkeydown", + "onkeypress", + "onkeyup" + ] + }, + "mouse": + { + "except":[ + "base", + "bdo", + "br", + "head", + "html", + "meta", + "param", + "script", + "style", + "title" + ], + "attributes":[ + "onclick", + "ondblclick", + "onmousedown", + "onmousemove", + "onmouseover", + "onmouseout", + "onmouseup" + ] + } + }, + "_tags": + { + "a": + { + "attributes": + { + "0":"charset", + "1":"coords", + "2":"href", + "3":"hreflang", + "4":"name", + "rel":/^(alternate|designates|stylesheet|start|next|prev|contents|index|glossary|copyright|chapter|section|subsection|appendix|help|bookmark| |shortcut|icon)+$/, + "rev":/^(alternate|designates|stylesheet|start|next|prev|contents|index|glossary|copyright|chapter|section|subsection|appendix|help|bookmark| |shortcut|icon)+$/, + "shape":/^(rect|rectangle|circ|circle|poly|polygon)$/, + "5":"type" + } + }, + "0":"abbr", + "1":"acronym", + "2":"address", + "area": + { + "attributes": + { + "0":"alt", + "1":"coords", + "2":"href", + "nohref":/^(true|false)$/, + "shape":/^(rect|rectangle|circ|circle|poly|polygon)$/ + }, + "required":[ + "alt" + ] + }, + "3":"b", + "base": + { + "attributes":[ + "href" + ], + "required":[ + "href" + ] + }, + "bdo": + { + "attributes": + { + "dir":/^(ltr|rtl)$/ + }, + "required":[ + "dir" + ] + }, + "4":"big", + "blockquote": + { + "attributes":[ + "cite" + ] + }, + "5":"body", + "6":"br", + "button": + { + "attributes": + { + "disabled":/^(disabled)$/, + "type":/^(button|reset|submit)$/, + "0":"value" + }, + "inside":"form" + }, + "7":"caption", + "8":"cite", + "9":"code", + "col": + { + "attributes": + { + "align":/^(right|left|center|justify)$/, + "0":"char", + "1":"charoff", + "span":/^(\d)+$/, + "valign":/^(top|middle|bottom|baseline)$/, + "2":"width" + }, + "inside":"colgroup" + }, + "colgroup": + { + "attributes": + { + "align":/^(right|left|center|justify)$/, + "0":"char", + "1":"charoff", + "span":/^(\d)+$/, + "valign":/^(top|middle|bottom|baseline)$/, + "2":"width" + } + }, + "10":"dd", + "del": + { + "attributes": + { + "0":"cite", + "datetime":/^([0-9]){8}/ + } + }, + "11":"div", + "12":"dfn", + "13":"dl", + "14":"dt", + "15":"em", + "fieldset": + { + "inside":"form" + }, + "form": + { + "attributes": + { + "0":"action", + "1":"accept", + "2":"accept-charset", + "3":"enctype", + "method":/^(get|post)$/ + }, + "required":[ + "action" + ] + }, + "head": + { + "attributes":[ + "profile" + ] + }, + "16":"h1", + "17":"h2", + "18":"h3", + "19":"h4", + "20":"h5", + "21":"h6", + "22":"hr", + "html": + { + "attributes":[ + "xmlns" + ] + }, + "23":"i", + "img": + { + "attributes":[ + "alt", + "src", + "height", + "ismap", + "longdesc", + "usemap", + "width" + ], + "required":[ + "alt", + "src" + ] + }, + "input": + { + "attributes": + { + "0":"accept", + "1":"alt", + "checked":/^(checked)$/, + "disabled":/^(disabled)$/, + "maxlength":/^(\d)+$/, + "2":"name", + "readonly":/^(readonly)$/, + "size":/^(\d)+$/, + "3":"src", + "type":/^(button|checkbox|file|hidden|image|password|radio|reset|submit|text)$/, + "4":"value" + }, + "inside":"form" + }, + "ins": + { + "attributes": + { + "0":"cite", + "datetime":/^([0-9]){8}/ + } + }, + "24":"kbd", + "label": + { + "attributes":[ + "for" + ], + "inside":"form" + }, + "25":"legend", + "26":"li", + "link": + { + "attributes": + { + "0":"charset", + "1":"href", + "2":"hreflang", + "media":/^(all|braille|print|projection|screen|speech|,|;| )+$/i, + //next comment line required by Opera! + /*"rel":/^(alternate|appendix|bookmark|chapter|contents|copyright|glossary|help|home|index|next|prev|section|start|stylesheet|subsection| |shortcut|icon)+$/i,*/ + "rel":/^(alternate|appendix|bookmark|chapter|contents|copyright|glossary|help|home|index|next|prev|section|start|stylesheet|subsection| |shortcut|icon)+$/i, + "rev":/^(alternate|appendix|bookmark|chapter|contents|copyright|glossary|help|home|index|next|prev|section|start|stylesheet|subsection| |shortcut|icon)+$/i, + "3":"type" + }, + "inside":"head" + }, + "map": + { + "attributes":[ + "id", + "name"

1 0

[hg] galaxy 2612: Repack jstore without comments
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/278df6aa7139 changeset: 2612:278df6aa7139 user: James Taylor <james(a)jamestaylor.org> date: Fri Aug 21 14:28:46 2009 -0400 description: Repack jstore without comments 2 file(s) affected in this change: static/scripts/jquery.jstore-all.js static/scripts/packed/jquery.jstore-all.js diffs (118 lines): diff -r 52a145b22b69 -r 278df6aa7139 static/scripts/jquery.jstore-all.js --- a/static/scripts/jquery.jstore-all.js Sun Aug 23 12:31:20 2009 -0400 +++ b/static/scripts/jquery.jstore-all.js Fri Aug 21 14:28:46 2009 -0400 @@ -1,4 +1,4 @@ -/*! +/* * jStore - Persistent Client-Side Storage * * Copyright (c) 2009 Eric Garside (http://eric.garside.name) @@ -71,7 +71,7 @@ return Class; }; })(); -/*! +/* * jStore Delegate Framework * Copyright (c) 2009 Eric Garside (http://eric.garside.name) */ @@ -357,7 +357,7 @@ }); })(jQuery); -/*! +/* * jStore DOM Storage Engine * Copyright (c) 2009 Eric Garside (http://eric.garside.name) */ @@ -426,7 +426,7 @@ $.jStore.EngineOrder[ 1 ] = 'local'; })(jQuery); -/*! +/* * jStore Flash Storage Engine * Copyright (c) 2009 Eric Garside (http://eric.garside.name) * jStore.swf Copyright (c) 2008 Daniel Bulli (http://www.nuff-respec.com) @@ -551,7 +551,7 @@ function flash_ready(){ $.jStore.delegate.trigger('flash-ready'); } -/*! +/* * jStore Google Gears Storage Engine * Copyright (c) 2009 Eric Garside (http://eric.garside.name) */ @@ -621,7 +621,7 @@ $.jStore.EngineOrder[ 3 ] = 'gears'; })(jQuery); -/*! +/* * jStore HTML5 Specification Storage Engine * Copyright (c) 2009 Eric Garside (http://eric.garside.name) */ @@ -693,7 +693,7 @@ $.jStore.EngineOrder[ 0 ] = 'html5'; })(jQuery); -/*!* +/* * jStore IE Storage Engine * Copyright (c) 2009 Eric Garside (http://eric.garside.name) */ @@ -745,4 +745,4 @@ // Store the ordering preference $.jStore.EngineOrder[ 4 ] = 'ie'; -})(jQuery); \ No newline at end of file +})(jQuery); diff -r 52a145b22b69 -r 278df6aa7139 static/scripts/packed/jquery.jstore-all.js --- a/static/scripts/packed/jquery.jstore-all.js Sun Aug 23 12:31:20 2009 -0400 +++ b/static/scripts/packed/jquery.jstore-all.js Fri Aug 21 14:28:46 2009 -0400 @@ -1,41 +1,1 @@ -/* - * jStore - Persistent Client-Side Storage - * - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - * - * Dual licensed under: - * MIT: http://www.opensource.org/licenses/mit-license.php - * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html - */ -(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=typeof g[d]=="function"&&typeof f[d]=="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}})(d,g[d]):g[d]}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}})(); -/* - * jStore Delegate Framework - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function(a){this.jStoreDelegate=Class.extend({init:function(b){this.parent=b;this.callbacks={}},bind:function(b,c){if(!a.isFunction(c)){return this}if(!this.callbacks[b]){this.callbacks[b]=[]}this.callbacks[b].push(c);return this},trigger:function(){var d=this.parent,c=[].slice.call(arguments),e=c.shift(),b=this.callbacks[e];if(!b){return false}a.each(b,function(){this.apply(d,c)});return this}})})(jQuery);(function(a){a.jStore={};a.extend(a.jStore,{EngineOrder:[],Availability:{},Engines:{},Instances:{},CurrentEngine:null,defaults:{project:null,engine:null,autoload:true,flash:"jStore.Flash.html"},isReady:false,isFlashReady:false,delegate:new jStoreDelegate(a.jStore).bind("jStore-ready",function(b){a.jStore.isReady=true;if(a.jStore.defaults.autoload){b.connect()}}).bind("flash-ready",function(){a.jStore.isFlashReady=true})});a.jStore.ready=function(b){if(a.jStore.isReady){b.apply(a.jStore,[a.jStore.CurrentEngine])}else{a.jStore.delegate.bind("jStore-ready",b)}};a.jStore.fail =function(b){a.jStore.delegate.bind("jStore-failure",b)};a.jStore.flashReady=function(b){if(a.jStore.isFlashReady){b.apply(a.jStore,[a.jStore.CurrentEngine])}else{a.jStore.delegate.bind("flash-ready",b)}};a.jStore.use=function(d,g,c){g=g||a.jStore.defaults.project||location.hostname.replace(/\./g,"-")||"unknown";var f=a.jStore.Engines[d.toLowerCase()]||null,b=(c?c+".":"")+g+"."+d;if(!f){throw"JSTORE_ENGINE_UNDEFINED"}f=new f(g,b);if(a.jStore.Instances[b]){throw"JSTORE_JRI_CONFLICT"}if(f.isAvailable()){a.jStore.Instances[b]=f;if(!a.jStore.CurrentEngine){a.jStore.CurrentEngine=f}a.jStore.delegate.trigger("jStore-ready",f)}else{if(!f.autoload){throw"JSTORE_ENGINE_UNAVILABLE"}else{f.included(function(){if(this.isAvailable()){a.jStore.Instances[b]=this;if(!a.jStore.CurrentEngine){a.jStore.CurrentEngine=this}a.jStore.delegate.trigger("jStore-ready",this)}else{a.jStore.delegate.trigger("jStore-failure",this)}}).include()}}};a.jStore.setCurrentEngine=function(b){if(!a.jStore.Instanc es.length){return a.jStore.FindEngine()}if(!b&&a.jStore.Instances.length>=1){a.jStore.delegate.trigger("jStore-ready",a.jStore.Instances[0]);return a.jStore.CurrentEngine=a.jStore.Instances[0]}if(b&&a.jStore.Instances[b]){a.jStore.delegate.trigger("jStore-ready",a.jStore.Instances[b]);return a.jStore.CurrentEngine=a.jStore.Instances[b]}throw"JSTORE_JRI_NO_MATCH"};a.jStore.FindEngine=function(){a.each(a.jStore.EngineOrder,function(b){if(a.jStore.Availability[this]()){a.jStore.use(this,a.jStore.defaults.project,"default");return false}})};a.jStore.store=function(b,c){if(!a.jStore.CurrentEngine){return false}if(!c){return a.jStore.CurrentEngine.get(b)}return a.jStore.CurrentEngine.set(b,c)};a.jStore.remove=function(b){if(!a.jStore.CurrentEngine){return false}return a.jStore.CurrentEngine.rem(b)};a.fn.store=function(c,d){if(!a.jStore.CurrentEngine){return this}var b=a.jStore.store(c,d);return !d?b:this};a.fn.removeStore=function(b){a.jStore.remove(b);return this};a.jStore.load=f unction(){if(a.jStore.defaults.engine){return a.jStore.use(a.jStore.defaults.engine,a.jStore.defaults.project,"default")}try{a.jStore.FindEngine()}catch(b){}}})(jQuery);(function(a){this.StorageEngine=Class.extend({init:function(c,b){this.project=c;this.jri=b;this.data={};this.limit=-1;this.includes=[];this.delegate=new jStoreDelegate(this).bind("engine-ready",function(){this.isReady=true}).bind("engine-included",function(){this.hasIncluded=true});this.autoload=false;this.isReady=false;this.hasIncluded=false},include:function(){var b=this,d=this.includes.length,c=0;a.each(this.includes,function(){a.ajax({type:"get",url:this,dataType:"script",cache:true,success:function(){c++;if(c==d){b.delegate.trigger("engine-included")}}})})},isAvailable:function(){return false},ready:function(b){if(this.isReady){b.apply(this)}else{this.delegate.bind("engine-ready",b)}return this},included:function(b){if(this.hasIncluded){b.apply(this)}else{this.delegate.bind("engine-included",b)}return th is},get:function(b){return this.data[b]||null},set:function(b,c){this.data[b]=c;return c},rem:function(b){var c=this.data[b];this.data[b]=null;return c}})})(jQuery); -/* - * jStore DOM Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function(c){var b=c.jStore.Availability.session=function(){return !!window.sessionStorage},a=c.jStore.Availability.local=function(){return !!(window.localStorage||window.globalStorage)};this.jStoreDom=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="DOM";this.limit=5*1024*1024},connect:function(){this.delegate.trigger("engine-ready")},get:function(e){var d=this.db.getItem(e);return d&&d.value?d.value:d},set:function(d,e){this.db.setItem(d,e);return e},rem:function(e){var d=this.get(e);this.db.removeItem(e);return d}});this.jStoreLocal=jStoreDom.extend({connect:function(){this.db=!window.globalStorage?window.localStorage:window.globalStorage[location.hostname];this._super()},isAvailable:a});this.jStoreSession=jStoreDom.extend({connect:function(){this.db=sessionStorage;this._super()},isAvailable:b});c.jStore.Engines.local=jStoreLocal;c.jStore.Engines.session=jStoreSession;c.jStore.EngineOrder[1]="local"})(jQuery); -/* - * jStore Flash Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - * jStore.swf Copyright (c) 2008 Daniel Bulli (http://www.nuff-respec.com) - */ -(function(b){var a=b.jStore.Availability.flash=function(){return !!(b.jStore.hasFlash("8.0.0"))};this.jStoreFlash=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="Flash";var c=this;b.jStore.flashReady(function(){c.flashReady()})},connect:function(){var c="jstore-flash-embed-"+this.project;b(document.body).append('<iframe 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d=0;d<3;d++){e[d]=parseInt(e[d]||0);f[d]=parseInt(f[d]||0);if(e[d]<f[d]){return false}if(e[d]>f[d]){return true}}return true};b.jStore.flashVersion=function(){try{try{var c=new ActiveXObject("ShockwaveFlash.ShockwaveFlash.6");try{c.AllowScriptAccess="always"}catch(d){return"6,0,0"}}catch(d){}return new ActiveXObject("ShockwaveFlash.ShockwaveFlash").GetVariable("$version").replace(/\D+/g,",").match(/^,?(.+),?$/)[1]}catch(d){try{if(navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin){return(navigator.plugins["Shockwave Flash 2.0"]||navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g,",").match(/^,?(.+),?$/)[1]}}catch(d){}}r eturn"0,0,0"}})(jQuery);function flash_ready(){$.jStore.delegate.trigger("flash-ready")} -/* - * jStore Google Gears Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function(b){var a=b.jStore.Availability.gears=function(){return !!(window.google&&window.google.gears)};this.jStoreGears=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="Google Gears";this.includes.push("http://code.google.com/apis/gears/gears_init.js");this.autoload=true},connect:function(){var c=this.db=google.gears.factory.create("beta.database");c.open("jstore-"+this.project);c.execute("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)");this.updateCache()},updateCache:function(){var c=this.db.execute("SELECT k,v FROM jstore");while(c.isValidRow()){this.data[c.field(0)]=c.field(1);c.next()}c.close();this.delegate.trigger("engine-ready")},isAvailable:a,set:function(d,e){var c=this.db;c.execute("BEGIN");c.execute("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[d,e]);c.execute("COMMIT");return this._super(d,e)},rem:function(d){var c=this.db;c.execute("BEGIN");c.execute("DELETE FROM jstore WHERE k = ?",[d]);c.ex ecute("COMMIT");return this._super(d)}});b.jStore.Engines.gears=jStoreGears;b.jStore.EngineOrder[3]="gears"})(jQuery); -/* - * jStore HTML5 Specification Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function(b){var a=b.jStore.Availability.html5=function(){return !!window.openDatabase};this.jStoreHtml5=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="HTML5";this.limit=1024*200},connect:function(){var c=this.db=openDatabase("jstore-"+this.project,"1.0",this.project,this.limit);if(!c){throw"JSTORE_ENGINE_HTML5_NODB"}c.transaction(function(d){d.executeSql("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)")});this.updateCache()},updateCache:function(){var c=this;this.db.transaction(function(d){d.executeSql("SELECT k,v FROM jstore",[],function(f,e){var h=e.rows,g=0,j;for(;g<h.length;++g){j=h.item(g);c.data[j.k]=j.v}c.delegate.trigger("engine-ready")})})},isAvailable:a,set:function(c,d){this.db.transaction(function(e){e.executeSql("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[c,d])});return this._super(c,d)},rem:function(c){this.db.transaction(function(d){d.executeSql("DELETE FROM jstore WHERE k = ?",[c])});ret urn this._super(c)}});b.jStore.Engines.html5=jStoreHtml5;b.jStore.EngineOrder[0]="html5"})(jQuery); -/** - * jStore IE Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function(b){var a=b.jStore.Availability.ie=function(){return !!window.ActiveXObject};this.jStoreIE=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="IE";this.limit=64*1024},connect:function(){this.db=b('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-'+this.project+'"></div>').appendTo(document.body).get(0);this.delegate.trigger("engine-ready")},isAvailable:a,get:function(c){this.db.load(this.project);return this.db.getAttribute(c)},set:function(c,d){this.db.setAttribute(c,d);this.db.save(this.project);return d},rem:function(c){var d=this.get(c);this.db.removeAttribute(c);this.db.save(this.project);return d}});b.jStore.Engines.ie=jStoreIE;b.jStore.EngineOrder[4]="ie"})(jQuery); \ No newline at end of file +(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=typeof g[d]=="function"&&typeof f[d]=="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}})(d,g[d]):g[d]}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}})();(function(a){this.jStoreDelegate=Class.extend({init:function(b){this.parent=b;this.callbacks={}},bind:function(b,c){if(!a.isFunction(c)){return this}if(!this.callbacks[b]){this.callbacks[b]=[]}this.callbacks[b].push(c);return this},trigger:function(){var d=this.parent,c=[].slice.call(arguments),e=c.shift(),b=this.callbacks[e];if(!b){return false}a.each(b,function(){this.apply(d,c)});return this}})})(jQuery);(function(a){a.jStore={};a.extend(a.jStore,{Engin eOrder:[],Availability:{},Engines:{},Instances:{},CurrentEngine:null,defaults:{project:null,engine:null,autoload:true,flash:"jStore.Flash.html"},isReady:false,isFlashReady:false,delegate:new jStoreDelegate(a.jStore).bind("jStore-ready",function(b){a.jStore.isReady=true;if(a.jStore.defaults.autoload){b.connect()}}).bind("flash-ready",function(){a.jStore.isFlashReady=true})});a.jStore.ready=function(b){if(a.jStore.isReady){b.apply(a.jStore,[a.jStore.CurrentEngine])}else{a.jStore.delegate.bind("jStore-ready",b)}};a.jStore.fail=function(b){a.jStore.delegate.bind("jStore-failure",b)};a.jStore.flashReady=function(b){if(a.jStore.isFlashReady){b.apply(a.jStore,[a.jStore.CurrentEngine])}else{a.jStore.delegate.bind("flash-ready",b)}};a.jStore.use=function(d,g,c){g=g||a.jStore.defaults.project||location.hostname.replace(/\./g,"-")||"unknown";var f=a.jStore.Engines[d.toLowerCase()]||null,b=(c?c+".":"")+g+"."+d;if(!f){throw"JSTORE_ENGINE_UNDEFINED"}f=new f(g,b);if(a.jStore.Instances[b]){ throw"JSTORE_JRI_CONFLICT"}if(f.isAvailable()){a.jStore.Instances[b]=f;if(!a.jStore.CurrentEngine){a.jStore.CurrentEngine=f}a.jStore.delegate.trigger("jStore-ready",f)}else{if(!f.autoload){throw"JSTORE_ENGINE_UNAVILABLE"}else{f.included(function(){if(this.isAvailable()){a.jStore.Instances[b]=this;if(!a.jStore.CurrentEngine){a.jStore.CurrentEngine=this}a.jStore.delegate.trigger("jStore-ready",this)}else{a.jStore.delegate.trigger("jStore-failure",this)}}).include()}}};a.jStore.setCurrentEngine=function(b){if(!a.jStore.Instances.length){return a.jStore.FindEngine()}if(!b&&a.jStore.Instances.length>=1){a.jStore.delegate.trigger("jStore-ready",a.jStore.Instances[0]);return a.jStore.CurrentEngine=a.jStore.Instances[0]}if(b&&a.jStore.Instances[b]){a.jStore.delegate.trigger("jStore-ready",a.jStore.Instances[b]);return a.jStore.CurrentEngine=a.jStore.Instances[b]}throw"JSTORE_JRI_NO_MATCH"};a.jStore.FindEngine=function(){a.each(a.jStore.EngineOrder,function(b){if(a.jStore.Availabilit y[this]()){a.jStore.use(this,a.jStore.defaults.project,"default");return false}})};a.jStore.store=function(b,c){if(!a.jStore.CurrentEngine){return false}if(!c){return a.jStore.CurrentEngine.get(b)}return a.jStore.CurrentEngine.set(b,c)};a.jStore.remove=function(b){if(!a.jStore.CurrentEngine){return false}return a.jStore.CurrentEngine.rem(b)};a.fn.store=function(c,d){if(!a.jStore.CurrentEngine){return this}var b=a.jStore.store(c,d);return !d?b:this};a.fn.removeStore=function(b){a.jStore.remove(b);return this};a.jStore.load=function(){if(a.jStore.defaults.engine){return a.jStore.use(a.jStore.defaults.engine,a.jStore.defaults.project,"default")}try{a.jStore.FindEngine()}catch(b){}}})(jQuery);(function(a){this.StorageEngine=Class.extend({init:function(c,b){this.project=c;this.jri=b;this.data={};this.limit=-1;this.includes=[];this.delegate=new jStoreDelegate(this).bind("engine-ready",function(){this.isReady=true}).bind("engine-included",function(){this.hasIncluded=true});this.aut oload=false;this.isReady=false;this.hasIncluded=false},include:function(){var b=this,d=this.includes.length,c=0;a.each(this.includes,function(){a.ajax({type:"get",url:this,dataType:"script",cache:true,success:function(){c++;if(c==d){b.delegate.trigger("engine-included")}}})})},isAvailable:function(){return false},ready:function(b){if(this.isReady){b.apply(this)}else{this.delegate.bind("engine-ready",b)}return this},included:function(b){if(this.hasIncluded){b.apply(this)}else{this.delegate.bind("engine-included",b)}return this},get:function(b){return this.data[b]||null},set:function(b,c){this.data[b]=c;return c},rem:function(b){var c=this.data[b];this.data[b]=null;return c}})})(jQuery);(function(c){var b=c.jStore.Availability.session=function(){return !!window.sessionStorage},a=c.jStore.Availability.local=function(){return !!(window.localStorage||window.globalStorage)};this.jStoreDom=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="DOM";this.limit=5*1024*1 024},connect:function(){this.delegate.trigger("engine-ready")},get:function(e){var d=this.db.getItem(e);return d&&d.value?d.value:d},set:function(d,e){this.db.setItem(d,e);return e},rem:function(e){var d=this.get(e);this.db.removeItem(e);return d}});this.jStoreLocal=jStoreDom.extend({connect:function(){this.db=!window.globalStorage?window.localStorage:window.globalStorage[location.hostname];this._super()},isAvailable:a});this.jStoreSession=jStoreDom.extend({connect:function(){this.db=sessionStorage;this._super()},isAvailable:b});c.jStore.Engines.local=jStoreLocal;c.jStore.Engines.session=jStoreSession;c.jStore.EngineOrder[1]="local"})(jQuery);(function(b){var a=b.jStore.Availability.flash=function(){return !!(b.jStore.hasFlash("8.0.0"))};this.jStoreFlash=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="Flash";var c=this;b.jStore.flashReady(function(){c.flashReady()})},connect:function(){var c="jstore-flash-embed-"+this.project;b(document.body).append('<if rame style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" id="jStoreFlashFrame" src="'+b.jStore.defaults.flash+'"></iframe>')},flashReady:function(f){var c=b("#jStoreFlashFrame")[0];if(c.Document&&b.isFunction(c.Document.jStoreFlash.f_get_cookie)){this.db=c.Document.jStoreFlash}else{if(c.contentWindow&&c.contentWindow.document){var d=c.contentWindow.document;if(b.isFunction(b("object",b(d))[0].f_get_cookie)){this.db=b("object",b(d))[0]}else{if(b.isFunction(b("embed",b(d))[0].f_get_cookie)){this.db=b("embed",b(d))[0]}}}}if(this.db){this.delegate.trigger("engine-ready")}},isAvailable:a,get:function(d){var c=this.db.f_get_cookie(d);return c=="null"?null:c},set:function(c,d){this.db.f_set_cookie(c,d);return d},rem:function(c){var d=this.get(c);this.db.f_delete_cookie(c);return d}});b.jStore.Engines.flash=jStoreFlash;b.jStore.EngineOrder[2]="flash";b.jStore.hasFlash=function(c){var e=b.jStore.flashVersion().match(/\d+/g),f=c.match(/\d+/g);for(var d=0;d< 3;d++){e[d]=parseInt(e[d]||0);f[d]=parseInt(f[d]||0);if(e[d]<f[d]){return false}if(e[d]>f[d]){return true}}return true};b.jStore.flashVersion=function(){try{try{var c=new ActiveXObject("ShockwaveFlash.ShockwaveFlash.6");try{c.AllowScriptAccess="always"}catch(d){return"6,0,0"}}catch(d){}return new ActiveXObject("ShockwaveFlash.ShockwaveFlash").GetVariable("$version").replace(/\D+/g,",").match(/^,?(.+),?$/)[1]}catch(d){try{if(navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin){return(navigator.plugins["Shockwave Flash 2.0"]||navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g,",").match(/^,?(.+),?$/)[1]}}catch(d){}}return"0,0,0"}})(jQuery);function flash_ready(){$.jStore.delegate.trigger("flash-ready")}(function(b){var a=b.jStore.Availability.gears=function(){return !!(window.google&&window.google.gears)};this.jStoreGears=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="Google Gears";this.includes.push("http://code.google.com/ap is/gears/gears_init.js");this.autoload=true},connect:function(){var c=this.db=google.gears.factory.create("beta.database");c.open("jstore-"+this.project);c.execute("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)");this.updateCache()},updateCache:function(){var c=this.db.execute("SELECT k,v FROM jstore");while(c.isValidRow()){this.data[c.field(0)]=c.field(1);c.next()}c.close();this.delegate.trigger("engine-ready")},isAvailable:a,set:function(d,e){var c=this.db;c.execute("BEGIN");c.execute("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[d,e]);c.execute("COMMIT");return this._super(d,e)},rem:function(d){var c=this.db;c.execute("BEGIN");c.execute("DELETE FROM jstore WHERE k = ?",[d]);c.execute("COMMIT");return this._super(d)}});b.jStore.Engines.gears=jStoreGears;b.jStore.EngineOrder[3]="gears"})(jQuery);(function(b){var a=b.jStore.Availability.html5=function(){return !!window.openDatabase};this.jStoreHtml5=StorageEngine.extend({init: function(d,c){this._super(d,c);this.type="HTML5";this.limit=1024*200},connect:function(){var c=this.db=openDatabase("jstore-"+this.project,"1.0",this.project,this.limit);if(!c){throw"JSTORE_ENGINE_HTML5_NODB"}c.transaction(function(d){d.executeSql("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)")});this.updateCache()},updateCache:function(){var c=this;this.db.transaction(function(d){d.executeSql("SELECT k,v FROM jstore",[],function(f,e){var h=e.rows,g=0,j;for(;g<h.length;++g){j=h.item(g);c.data[j.k]=j.v}c.delegate.trigger("engine-ready")})})},isAvailable:a,set:function(c,d){this.db.transaction(function(e){e.executeSql("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[c,d])});return this._super(c,d)},rem:function(c){this.db.transaction(function(d){d.executeSql("DELETE FROM jstore WHERE k = ?",[c])});return this._super(c)}});b.jStore.Engines.html5=jStoreHtml5;b.jStore.EngineOrder[0]="html5"})(jQuery);(function(b){var a=b.jStore.Avail ability.ie=function(){return !!window.ActiveXObject};this.jStoreIE=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="IE";this.limit=64*1024},connect:function(){this.db=b('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-'+this.project+'"></div>').appendTo(document.body).get(0);this.delegate.trigger("engine-ready")},isAvailable:a,get:function(c){this.db.load(this.project);return this.db.getAttribute(c)},set:function(c,d){this.db.setAttribute(c,d);this.db.save(this.project);return d},rem:function(c){var d=this.get(c);this.db.removeAttribute(c);this.db.save(this.project);return d}});b.jStore.Engines.ie=jStoreIE;b.jStore.EngineOrder[4]="ie"})(jQuery); \ No newline at end of file

1 0

[hg] galaxy 2613: Remove logging from galaxy.base
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5f60d79f483f changeset: 2613:5f60d79f483f user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 14:01:08 2009 -0400 description: Remove logging from galaxy.base 2 file(s) affected in this change: static/scripts/galaxy.base.js static/scripts/packed/galaxy.base.js diffs (26 lines): diff -r 278df6aa7139 -r 5f60d79f483f static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Aug 21 14:28:46 2009 -0400 +++ b/static/scripts/galaxy.base.js Sun Aug 23 14:01:08 2009 -0400 @@ -77,14 +77,12 @@ }; function attach_popupmenu( button_element, wrapper ) { - console.log( button_element, wrapper ); var clean = function() { wrapper.unbind().hide(); $("#popup-helper").unbind( "click.popupmenu" ).hide(); // $(document).unbind( "click.popupmenu" ); }; var click = function( e ) { - console.log( e ); var o = $(button_element).offset(); $("#popup-helper").bind( "click.popupmenu", clean ).show(); // $(document).bind( "click.popupmenu", clean ); diff -r 278df6aa7139 -r 5f60d79f483f static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Aug 21 14:28:46 2009 -0400 +++ b/static/scripts/packed/galaxy.base.js Sun Aug 23 14:01:08 2009 -0400 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ens ure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></div>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){console.log(b,d);var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){console.log(g);var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}; \ No newline at end of file +$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ens ure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></div>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}; \ No newline at end of file

1 0

[hg] galaxy 2614: Use small messages by default
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b8205e8e077f changeset: 2614:b8205e8e077f user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 15:16:43 2009 -0400 description: Use small messages by default 5 file(s) affected in this change: static/june_2007_style/base.css.tmpl static/june_2007_style/blue/base.css static/welcome.html templates/message.mako templates/tool_executed.mako diffs (406 lines): diff -r 5f60d79f483f -r b8205e8e077f static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Sun Aug 23 14:01:08 2009 -0400 +++ b/static/june_2007_style/base.css.tmpl Sun Aug 23 15:16:43 2009 -0400 @@ -187,8 +187,7 @@ ## Messages -.errormessage, .warningmessage, .donemessage, .infomessage, .welcomeBlue, .welcomeRed , .screencastBox, .yellowbox, .redbox, .bluebox, .greenbox -{ +.errormessagelarge, .warningmessagelarge, .donemessagelarge, .infomessagelarge { padding: 10px; padding-left: 52px; min-height: 32px; @@ -199,127 +198,35 @@ background-position: 10px 10px; } -.warningmessage -{ +.warningmessagelarge { background-image: url(warn_message_icon.png); border-color: $warn_message_border; background-color: $warn_message_bg; } -.donemessage -{ +.donemessagelarge { background-image: url(done_message_icon.png); border-color: $done_message_border; background-color: $done_message_bg; } -.infomessage -{ +.infomessagelarge { background-image: url(info_message_icon.png); border-color: $info_message_border; background-color: $info_message_bg; } -.welcomeBlue -{ - padding-left: 10px; - border-color: $info_message_border; - background-color: $info_message_bg; - background-image: none; -} - -.welcomeRed -{ - padding-left: 10px; - border-color: $error_message_border; - background-color: $error_message_bg; - background-image: none; -} - -.screencastBox -{ +.screencastBox { padding-left: 10px; border-color: #AAAA66; background-color: #FFFFCC; background-image: none; } -.redbox -{ - border: none; - padding: 10px; - border-color: #000000; - background-color: #FF6666; - background-image: none; - border-right-width: 1px; - border-right-style: dotted; - border-bottom-width: 1px; - border-bottom-style: dotted; - margin-top: 5px; - min-height: 32px; - -} - -.yellowbox -{ - border: none; - padding: 10px; - border-color: #000000; - background-color: #FFCC00; - background-image: none; - border-right-width: 1px; - border-right-style: dotted; - border-bottom-width: 1px; - border-bottom-style: dotted; - margin-top: 5px; - min-height: 32px; -} - -.bluebox -{ - border: none; - padding: 10px; - border-color: #000000; - background-color: #6666FF; - background-image: none; - border-right-width: 1px; - border-right-style: dotted; - border-bottom-width: 1px; - border-bottom-style: dotted; - margin-top: 5px; - color: #FFFFFF; - min-height: 32px; -} - -.greenbox -{ - border: none; - padding: 10px; - border-color: #000000; - background-color: #00CC00; - background-image: none; - border-right-width: 1px; - border-right-style: dotted; - border-bottom-width: 1px; - border-bottom-style: dotted; - margin-top: 5px; - min-height: 32px; -} - -.redbox li, .yellowbox li, .bluebox li, .greenbox li { - list-style: disc; - text-transform: none; - list-style-position: inside; - list-style-image: none; - margin: 3px; -} - - -.errormessagesmall, .warningmessagesmall, .donemessagesmall, .infomessagesmall -{ +.errormessage, .warningmessage, .donemessage, .infomessage, .errormessagesmall, .warningmessagesmall, .donemessagesmall, .infomessagesmall { padding: 5px; padding-left: 25px; - min-height: 25px; + min-height: 15px; border: 1px solid $error_message_border; background-color: $error_message_bg; background-image: url(error_small.png); @@ -327,83 +234,70 @@ background-position: 5px 5px; } -.warningmessagesmall -{ +.warningmessage, .warningmessagesmall { background-image: url(warn_small.png); border-color: $warn_message_border; background-color: $warn_message_bg; } -.donemessagesmall -{ +.donemessage, .donemessagesmall { background-image: url(ok_small.png); border-color: $done_message_border; background-color: $done_message_bg; } -.infomessagesmall -{ +.infomessage, .infomessagesmall { background-image: url(info_small.png); border-color: $info_message_border; background-color: $info_message_bg; } -.errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr -{ +.errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr { padding-left: 20px; min-height: 15px; background: url(error_small.png) no-repeat; } -.warningmark -{ +.warningmark { background-image: url(warn_small.png); } -.donemark -{ +.donemark { background-image: url(ok_small.png); } -.infomark, .ok_bgr -{ +.infomark, .ok_bgr { background-image: url(info_small.png); } -table.colored -{ - border-top: solid $table_border 1px; - border-bottom: solid $table_border 1px; +table.colored { + border-top: solid $table_border 1px; + border-bottom: solid $table_border 1px; } -table.colored td, table.colored th -{ +table.colored td, table.colored th { text-align: left; padding: 5px; } -table.colored tr.header -{ - background: $table_header_bg; - background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-bottom: solid $table_border 1px; - font-weight: bold; +table.colored tr.header { + background: $table_header_bg; + background-image: url(form_title_bg.png); + background-repeat: repeat-x; + background-position: top; + border-bottom: solid $table_border 1px; + font-weight: bold; } -table.colored tr -{ - background: $table_row_bg; +table.colored tr { + background: $table_row_bg; } -table.colored tr.odd_row -{ - background: $odd_row_bg; +table.colored tr.odd_row { + background: $odd_row_bg; } -div.debug -{ +div.debug { margin: 10px; padding: 5px; background: #FFFF99; @@ -411,8 +305,7 @@ color: black; } -div.odd_row -{ +div.odd_row { background: $odd_row_bg; } @@ -422,51 +315,44 @@ ## Tool panel stuff -td.panel-body -{ +td.panel-body { background: white; color: $base_text; background: $menu_bg_over url(menu_bg.png) top repeat-x; } -div.toolSectionPad -{ +div.toolSectionPad { margin: 0; padding: 0; height: 5px; font-size: 0px; } -div.toolSectionDetailsInner -{ - margin-left: 5px; - margin-right: 5px; +div.toolSectionDetailsInner { + margin-left: 5px; + margin-right: 5px; } -div.toolSectionTitle -{ - padding-bottom: 0px; - font-weight: bold; +div.toolSectionTitle { + padding-bottom: 0px; + font-weight: bold; } -div.toolTitle -{ - padding-top: 5px; - padding-bottom: 5px; - margin-left: 16px; - margin-right: 10px; - display: list-item; - list-style: square outside; +div.toolTitle { + padding-top: 5px; + padding-bottom: 5px; + margin-left: 16px; + margin-right: 10px; + display: list-item; + list-style: square outside; } -span.toolParameterExpandableCollapsable -{ - font-weight: bold; - cursor: pointer; +span.toolParameterExpandableCollapsable { + font-weight: bold; + cursor: pointer; } -ul.toolParameterExpandableCollapsable -{ - list-style: none; +ul.toolParameterExpandableCollapsable { + list-style: none; } ul.manage-table-actions { diff -r 5f60d79f483f -r b8205e8e077f static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Sun Aug 23 14:01:08 2009 -0400 +++ b/static/june_2007_style/blue/base.css Sun Aug 23 15:16:43 2009 -0400 @@ -35,22 +35,15 @@ div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;} select,input,textarea{font:inherit;font-size:115%;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{-webkit-box-sizing:border-box;max-width:300px;} -.errormessage,.warningmessage,.donemessage,.infomessage,.welcomeBlue,.welcomeRed,.screencastBox,.yellowbox,.redbox,.bluebox,.greenbox{padding:10px;padding-left:52px;min-height:32px;border:1px solid #AA6666;background-color:#FFCCCC;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} -.warningmessage{background-image:url(warn_message_icon.png);border-color:#AAAA66;background-color:#FFFFCC;} -.donemessage{background-image:url(done_message_icon.png);border-color:#66AA66;background-color:#CCFFCC;} -.infomessage{background-image:url(info_message_icon.png);border-color:#6666AA;background-color:#CCCCFF;} -.welcomeBlue{padding-left:10px;border-color:#6666AA;background-color:#CCCCFF;background-image:none;} -.welcomeRed{padding-left:10px;border-color:#AA6666;background-color:#FFCCCC;background-image:none;} +.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:10px;padding-left:52px;min-height:32px;border:1px solid #AA6666;background-color:#FFCCCC;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} +.warningmessagelarge{background-image:url(warn_message_icon.png);border-color:#AAAA66;background-color:#FFFFCC;} +.donemessagelarge{background-image:url(done_message_icon.png);border-color:#66AA66;background-color:#CCFFCC;} +.infomessagelarge{background-image:url(info_message_icon.png);border-color:#6666AA;background-color:#CCCCFF;} .screencastBox{padding-left:10px;border-color:#AAAA66;background-color:#FFFFCC;background-image:none;} -.redbox{border:none;padding:10px;border-color:#000000;background-color:#FF6666;background-image:none;border-right-width:1px;border-right-style:dotted;border-bottom-width:1px;border-bottom-style:dotted;margin-top:5px;min-height:32px;} -.yellowbox{border:none;padding:10px;border-color:#000000;background-color:#FFCC00;background-image:none;border-right-width:1px;border-right-style:dotted;border-bottom-width:1px;border-bottom-style:dotted;margin-top:5px;min-height:32px;} -.bluebox{border:none;padding:10px;border-color:#000000;background-color:#6666FF;background-image:none;border-right-width:1px;border-right-style:dotted;border-bottom-width:1px;border-bottom-style:dotted;margin-top:5px;color:#FFFFFF;min-height:32px;} -.greenbox{border:none;padding:10px;border-color:#000000;background-color:#00CC00;background-image:none;border-right-width:1px;border-right-style:dotted;border-bottom-width:1px;border-bottom-style:dotted;margin-top:5px;min-height:32px;} -.redbox li,.yellowbox li,.bluebox li,.greenbox li{list-style:disc;text-transform:none;list-style-position:inside;list-style-image:none;margin:3px;} -.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:5px;padding-left:25px;min-height:25px;border:1px solid #AA6666;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} -.warningmessagesmall{background-image:url(warn_small.png);border-color:#AAAA66;background-color:#FFFFCC;} -.donemessagesmall{background-image:url(ok_small.png);border-color:#66AA66;background-color:#CCFFCC;} -.infomessagesmall{background-image:url(info_small.png);border-color:#6666AA;background-color:#CCCCFF;} +.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:5px;padding-left:25px;min-height:15px;border:1px solid #AA6666;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} +.warningmessage,.warningmessagesmall{background-image:url(warn_small.png);border-color:#AAAA66;background-color:#FFFFCC;} +.donemessage,.donemessagesmall{background-image:url(ok_small.png);border-color:#66AA66;background-color:#CCFFCC;} +.infomessage,.infomessagesmall{background-image:url(info_small.png);border-color:#6666AA;background-color:#CCCCFF;} .errormark,.warningmark,.donemark,.infomark,.ok_bgr,.err_bgr{padding-left:20px;min-height:15px;background:url(error_small.png) no-repeat;} .warningmark{background-image:url(warn_small.png);} .donemark{background-image:url(ok_small.png);} diff -r 5f60d79f483f -r b8205e8e077f static/welcome.html --- a/static/welcome.html Sun Aug 23 14:01:08 2009 -0400 +++ b/static/welcome.html Sun Aug 23 15:16:43 2009 -0400 @@ -37,7 +37,7 @@ <body> <div class="document"> -<div class="infomessage"> +<div class="infomessagelarge"> <strong>We are hiring!</strong> <hr> Thanks to your support and an unprecedented level of usage, we are looking for an experienced software developer to join our team. For more information about this position, please, click <a target="_blank" href="https://www.bx.psu.edu/cgi-bin/trac.cgi/galaxy/wiki/PythonDeveloper">here</a>. diff -r 5f60d79f483f -r b8205e8e077f templates/message.mako --- a/templates/message.mako Sun Aug 23 14:01:08 2009 -0400 +++ b/templates/message.mako Sun Aug 23 15:16:43 2009 -0400 @@ -45,7 +45,7 @@ </script> </%def> -<div class="${message_type}message">${_(message)}</div> +<div class="${message_type}messagelarge">${_(message)}</div> ## Render a message <%def name="render_msg( msg, messagetype='done' )"> diff -r 5f60d79f483f -r b8205e8e077f templates/tool_executed.mako --- a/templates/tool_executed.mako Sun Aug 23 14:01:08 2009 -0400 +++ b/templates/tool_executed.mako Sun Aug 23 15:16:43 2009 -0400 @@ -37,7 +37,7 @@ <body onLoad="main()"> -<div class="donemessage"> +<div class="donemessagelarge"> <p>The following job has been succesfully added to the queue:</p>

1 0

[hg] galaxy 2615: IE fixes for menu buttons
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/168a6ef6a99a changeset: 2615:168a6ef6a99a user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 17:13:04 2009 -0400 description: IE fixes for menu buttons 3 file(s) affected in this change: static/scripts/galaxy.base.js templates/history/grid.mako templates/workflow/list.mako diffs (36 lines): diff -r b8205e8e077f -r 168a6ef6a99a static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Sun Aug 23 15:16:43 2009 -0400 +++ b/static/scripts/galaxy.base.js Sun Aug 23 17:13:04 2009 -0400 @@ -59,7 +59,7 @@ // container_element = container_element.parent(); // } // ontainer_element).css( "position", "relative" ); - var menu_element = $( "<ul id='" + button_element.attr('id') + "-menu'></div>" ); + var menu_element = $( "<ul id='" + button_element.attr('id') + "-menu'></ul>" ); $.each( options, function( k, v ) { if ( v ) { $( "<li/>" ).html( k ).click( v ).appendTo( menu_element ); diff -r b8205e8e077f -r 168a6ef6a99a templates/history/grid.mako --- a/templates/history/grid.mako Sun Aug 23 15:16:43 2009 -0400 +++ b/templates/history/grid.mako Sun Aug 23 17:13:04 2009 -0400 @@ -158,7 +158,7 @@ extra = "" %> %if href: - <td><div class="menubutton split"><a class="label" href="${href}">${v}${extra}</a></td> + <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td> %else: <td >${v}${extra}</td> %endif diff -r b8205e8e077f -r 168a6ef6a99a templates/workflow/list.mako --- a/templates/workflow/list.mako Sun Aug 23 15:16:43 2009 -0400 +++ b/templates/workflow/list.mako Sun Aug 23 17:13:04 2009 -0400 @@ -37,7 +37,7 @@ %for i, workflow in enumerate( workflows ): <tr> <td> - <div class="menubutton"> + <div class="menubutton" style="float: left;"> <a id="wf-${i}-popup" class="arrow" style="display: none;"><span>▼</span></a> ${workflow.name} </div>

1 0

[hg] galaxy 2607: Fix clone history tests
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/77b761ff6cd3 changeset: 2607:77b761ff6cd3 user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 09:22:19 2009 -0400 description: Fix clone history tests 1 file(s) affected in this change: templates/history/clone.mako diffs (12 lines): diff -r e6dda627e6b0 -r 77b761ff6cd3 templates/history/clone.mako --- a/templates/history/clone.mako Sat Aug 22 23:20:09 2009 -0400 +++ b/templates/history/clone.mako Sun Aug 23 09:22:19 2009 -0400 @@ -8,7 +8,7 @@ <form action="${h.url_for( controller='history', action='clone' )}" method="post" > <div class="form-row"> %if id_argument is not None: - <input type="hidden" name="id" value="${trans.security.encode_id( id_argument )}"> + <input type="hidden" name="id" value="${id_argument}"> %endif You can clone the history such that the clone will include all items in the original history, or you can eliminate the original history's deleted items from the clone.

1 0

[hg] galaxy 2606: Merge
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e6dda627e6b0 changeset: 2606:e6dda627e6b0 user: James Taylor <james(a)jamestaylor.org> date: Sat Aug 22 23:20:09 2009 -0400 description: Merge 2 file(s) affected in this change: templates/base_panels.mako templates/history/grid.mako diffs (2711 lines): diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/model/migrate/versions/0009_request_table.py --- a/lib/galaxy/model/migrate/versions/0009_request_table.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0009_request_table.py Sat Aug 22 23:20:09 2009 -0400 @@ -9,6 +9,7 @@ from migrate.changeset import * import sys, logging from galaxy.model.custom_types import * +from sqlalchemy.exceptions import * log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Sat Aug 22 23:20:09 2009 -0400 @@ -1534,10 +1534,19 @@ child_dataset.flush() child_dataset.set_size() child_dataset.name = "Secondary Dataset (%s)" % ( designation ) - child_dataset.state = child_dataset.states.OK child_dataset.init_meta() child_dataset.set_meta() child_dataset.set_peek() + # Associate new dataset with job + job = None + for assoc in outdata.creating_job_associations: + job = assoc.job + break + if job: + assoc = self.app.model.JobToOutputDatasetAssociation( '__new_child_file_%s|%s__' % ( name, designation ), child_dataset ) + assoc.job = job + assoc.flush() + child_dataset.state = outdata.state child_dataset.flush() # Add child to return dict children[name][designation] = child_dataset @@ -1550,7 +1559,7 @@ def collect_primary_datasets( self, output): primary_datasets = {} - #Loop through output file names, looking for generated primary datasets in form of 'primary_associatedWithDatasetID_designation_visibility_extension' + #Loop through output file names, looking for generated primary datasets in form of 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)' for name, outdata in output.items(): for filename in glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ): if not name in primary_datasets: @@ -1563,19 +1572,32 @@ if visible == "visible": visible = True else: visible = False ext = fields.pop(0).lower() + dbkey = outdata.dbkey + if fields: + dbkey = fields[ 0 ] # Create new primary dataset - primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=outdata.dbkey, create_dataset=True ) + primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=dbkey, create_dataset=True ) self.app.security_agent.copy_dataset_permissions( outdata.dataset, primary_data.dataset ) primary_data.flush() # Move data from temp location to dataset location shutil.move( filename, primary_data.file_name ) primary_data.set_size() - primary_data.name = dataset.name - primary_data.info = dataset.info - primary_data.state = primary_data.states.OK - primary_data.init_meta( copy_from=dataset ) + primary_data.name = outdata.name + primary_data.info = outdata.info + primary_data.init_meta( copy_from=outdata ) + primary_data.dbkey = dbkey primary_data.set_meta() primary_data.set_peek() + # Associate new dataset with job + job = None + for assoc in outdata.creating_job_associations: + job = assoc.job + break + if job: + assoc = self.app.model.JobToOutputDatasetAssociation( '__new_primary_file_%s|%s__' % ( name, designation ), primary_data ) + assoc.job = job + assoc.flush() + primary_data.state = outdata.state primary_data.flush() outdata.history.add_dataset( primary_data ) # Add dataset to return dict diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Sat Aug 22 23:20:09 2009 -0400 @@ -20,12 +20,10 @@ for upload_dataset in incoming['files']: f = upload_dataset['file_data'] if isinstance( f, FieldStorage ): - # very small files can be StringIOs - if 'name' in dir( f.file ) and f.file.name != '<fdopen>': - local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' ) - f.file.close() - else: - local_filename = datatypes.sniff.stream_to_file( f.file, prefix="strio_upload_file_" )[0] + assert not isinstance( f.file, StringIO.StringIO ) + assert f.file.name != '<fdopen>' + local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' ) + f.file.close() upload_dataset['file_data'] = dict( filename = f.filename, local_filename = local_filename ) if upload_dataset['url_paste'].strip() != '': diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Sat Aug 22 23:20:09 2009 -0400 @@ -242,6 +242,55 @@ rval.append( add_value ) return rval +class RemoveValueFilter( Filter ): + """ + Removes a value from an options list. + + Type: remove_value + + Required Attributes: + value: value to remove from select list + or + ref: param to refer to + or + meta_ref: dataset to refer to + key: metadata key to compare to + """ + def __init__( self, d_option, elem ): + Filter.__init__( self, d_option, elem ) + self.value = elem.get( "value", None ) + self.ref_name = elem.get( "ref", None ) + self.meta_ref = elem.get( "meta_ref", None ) + self.metadata_key = elem.get( "key", None ) + assert self.value is not None or ( ( self.ref_name is not None or self.meta_ref is not None )and self.metadata_key is not None ), ValueError( "Required 'value' or 'ref' and 'key' attributes missing from filter" ) + self.multiple = string_as_bool( elem.get( "multiple", "False" ) ) + self.separator = elem.get( "separator", "," ) + def filter_options( self, options, trans, other_values ): + if trans is not None and trans.workflow_building_mode: return options + assert self.value is not None or ( self.ref_name is not None and self.ref_name in other_values ) or (self.meta_ref is not None and self.meta_ref in other_values ) or ( trans is not None and trans.workflow_building_mode), Exception( "Required dependency '%s' or '%s' not found in incoming values" % ( self.ref_name, self.meta_ref ) ) + def compare_value( option_value, filter_value ): + if isinstance( filter_value, list ): + if self.multiple: + option_value = option_value.split( self.separator ) + for value in filter_value: + if value not in filter_value: + return False + return True + return option_value in filter_value + if self.multiple: + return filter_value in option_value.split( self.separator ) + return option_value == filter_value + value = self.value + if value is None: + if self.ref_name is not None: + value = other_values.get( self.ref_name ) + else: + data_ref = other_values.get( self.meta_ref ) + if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ): + return options #cannot modify options + value = data_ref.metadata.get( self.metadata_key, None ) + return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ] + class SortByColumnFilter( Filter ): """ Sorts an options list by a column @@ -274,6 +323,7 @@ unique_value = UniqueValueFilter, multiple_splitter = MultipleSplitterFilter, add_value = AdditionalValueFilter, + remove_value = RemoveValueFilter, sort_by = SortByColumnFilter ) class DynamicOptions( object ): diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Sat Aug 22 23:20:09 2009 -0400 @@ -764,11 +764,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -965,11 +961,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -1220,11 +1212,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -2027,7 +2015,7 @@ num_states = int( util.restore_text( params.get( 'num_states', 0 ) )) proceed = True for i in range( num_states ): - if not util.restore_text( params.get( 'new_element_name_%i' % i, None ) ): + if not util.restore_text( params.get( 'state_name_%i' % i, None ) ): proceed = False break if not proceed: @@ -2045,8 +2033,8 @@ ss.delete() ss.flush() for i in range( num_states ): - name = util.restore_text( params.get( 'new_element_name_%i' % i, None )) - desc = util.restore_text( params.get( 'new_element_description_%i' % i, None )) + name = util.restore_text( params.get( 'state_name_%i' % i, None )) + desc = util.restore_text( params.get( 'state_desc_%i' % i, None )) ss = trans.app.model.SampleState(name, desc, rt) ss.flush() msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states) diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Sat Aug 22 23:20:09 2009 -0400 @@ -175,7 +175,7 @@ 'visible': True, 'required': False, 'type': BaseField.form_field_types()[0], - 'selectlist': '' } + 'selectlist': [] } self.current_form['fields'].append(empty_field) def __get_field(self, index, **kwd): params = util.Params( kwd ) @@ -183,10 +183,10 @@ # To reproduce, create a new form, click the "add field" button, click the # browser back arrow, then click the "add field" button again. # You should never attempt to "restore_text()" on a None object... - name = util.restore_text( params.get( 'field_name_%i' % index, None ) ) - helptext = util.restore_text( params.get( 'field_helptext_%i' % index, None ) ) + name = util.restore_text( params.get( 'field_name_%i' % index, '' ) ) + helptext = util.restore_text( params.get( 'field_helptext_%i' % index, '' ) ) required = params.get( 'field_required_%i' % index, False ) - field_type = util.restore_text( params.get( 'field_type_%i' % index, None ) ) + field_type = util.restore_text( params.get( 'field_type_%i' % index, '' ) ) if field_type == 'SelectField': selectlist = self.__get_selectbox_options(index, **kwd) return {'label': name, @@ -419,22 +419,39 @@ else: fdc_list = trans.app.model.FormDefinitionCurrent.query().all() return [ fdc.latest_form for fdc in fdc_list ] -def get_form_widgets( trans, form, contents={} ): + + +def get_form_widgets( trans, form, contents=[], user=None, **kwd ): ''' Return the list of widgets that comprise a form definition, including field contents if any. ''' + params = util.Params( kwd ) + if not user: + user = trans.user widgets = [] for index, field in enumerate( form.fields ): field_name = 'field_%i' % index - if field_name in contents: - value = contents[ field_name ] - elif field[ 'type' ] == 'CheckboxField': - # Since we do not have contents, set checkbox value to False - value = False + # determine the value of the field + if field_name in kwd: + # the user had already filled out this field and the same form is re-rendered + # due to some reason like required fields have been left out. + if field[ 'type' ] == 'CheckboxField': + value = CheckboxField.is_checked( util.restore_text( params.get( field_name, False ) ) ) + else: + value = util.restore_text( params.get( field_name, '' ) ) + elif contents: + # this field has a saved value + value = str(contents[ index ]) else: - # Set other field types to empty string - value = '' + # if none of the above, then leave the field empty + if field[ 'type' ] == 'CheckboxField': + # Since we do not have contents, set checkbox value to False + value = False + else: + # Set other field types to empty string + value = '' + # create the field widget field_widget = eval( field[ 'type' ] )( field_name ) if field[ 'type' ] == 'TextField': field_widget.set_size( 40 ) @@ -442,6 +459,10 @@ elif field[ 'type' ] == 'TextArea': field_widget.set_size( 3, 40 ) field_widget.value = value + elif field['type'] == 'AddressField': + field_widget.user = user + field_widget.value = value + field_widget.params = params elif field[ 'type' ] == 'SelectField': for option in field[ 'selectlist' ]: if option == value: diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Sat Aug 22 23:20:09 2009 -0400 @@ -137,11 +137,7 @@ # See if we have any field contents info = library.info_association[0].info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -475,11 +471,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -996,11 +988,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -1173,3 +1161,13 @@ edit_info=True, msg=util.sanitize_text( msg ), messagetype='done' ) ) + + +def get_authorized_libs(trans, user): + all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() + authorized_libraries = [] + for library in all_libraries: + if trans.app.security_agent.allow_action(user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) \ + or trans.app.security_agent.allow_action(user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library): + authorized_libraries.append(library) + return authorized_libraries \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Sat Aug 22 23:20:09 2009 -0400 @@ -8,6 +8,8 @@ from galaxy.web.form_builder import * from datetime import datetime, timedelta from cgi import escape, FieldStorage +from galaxy.web.controllers.forms import get_form_widgets +from galaxy.web.controllers.library import get_authorized_libs log = logging.getLogger( __name__ ) @@ -62,18 +64,12 @@ request_grid = RequestsListGrid() @web.expose + @web.require_login( "create/submit sequencing requests" ) def index( self, trans ): return trans.fill_template( "requests/index.mako" ) - - def get_authorized_libs(self, trans): - all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() - authorized_libraries = [] - for library in all_libraries: - if trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) \ - or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library): - authorized_libraries.append(library) - return authorized_libraries + @web.expose + @web.require_login( "create/submit sequencing requests" ) def list( self, trans, **kwargs ): ''' List all request made by the current user @@ -137,7 +133,6 @@ Shows the request details ''' request = trans.app.model.Request.get(id) - libraries = self.get_authorized_libs(trans) # list of widgets to be rendered on the request form request_details = [] # main details @@ -146,6 +141,9 @@ helptext='')) request_details.append(dict(label='Type', value=request.type.name, + helptext='')) + request_details.append(dict(label='State', + value=request.state, helptext='')) request_details.append(dict(label='Date created', value=request.create_time, @@ -201,6 +199,7 @@ copy_list.add_option(s[0], i) return copy_list @web.expose + @web.require_login( "create/submit sequencing requests" ) def show_request(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -326,6 +325,7 @@ @web.expose + @web.require_login( "create/submit sequencing requests" ) def delete_sample(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -348,6 +348,7 @@ edit_mode=self.edit_mode) @web.expose + @web.require_login( "create/submit sequencing requests" ) def toggle_request_details(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -384,6 +385,7 @@ select_reqtype.add_option(rt.name, rt.id) return select_reqtype @web.expose + @web.require_login( "create/submit sequencing requests" ) def new(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -413,8 +415,8 @@ if params.get('create_request_button', False) == 'Save': return trans.response.send_redirect( web.url_for( controller='requests', action='list', - msg=msg , - messagetype='done') ) + message=msg , + status='done') ) elif params.get('create_request_samples_button', False) == 'Add samples': new_kwd = {} new_kwd['id'] = trans.security.encode_id(request.id) @@ -457,12 +459,10 @@ helptext='(Optional)')) # libraries selectbox - libraries = self.get_authorized_libs(trans) + libraries = get_authorized_libs(trans, trans.user) libui = self.__library_ui(libraries, **kwd) widgets = widgets + libui - widgets = self.__create_form(trans, request_type.request_form_id, widgets, - form_values, **kwd) - title = 'Add a new request of type: %s' % request_type.name + widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], **kwd) return trans.fill_template( '/requests/new_request.mako', select_request_type=select_request_type, request_type=request_type, @@ -502,58 +502,13 @@ return [widget, new_lib] else: return [widget] - - def __create_form(self, trans, form_id, widgets=[], form_values=None, **kwd): - # TODO: RC - replace this method by importing as follows: - # from galaxy.web.controllers.forms import get_form_widgets - params = util.Params( kwd ) - form = trans.app.model.FormDefinition.get(form_id) - # form fields - for index, field in enumerate(form.fields): - # value of the field - if field['type'] == 'CheckboxField': - value = util.restore_text( params.get( 'field_%i' % index, False ) ) - else: - value = util.restore_text( params.get( 'field_%i' % index, '' ) ) - if not value: - if form_values: - value = str(form_values.content[index]) - # create the field - fw = eval(field['type'])('field_%i' % index) - if field['type'] == 'TextField': - fw.set_size(40) - fw.value = value - elif field['type'] == 'TextArea': - fw.set_size(3, 40) - fw.value = value - elif field['type'] == 'AddressField': - fw.user = trans.user - fw.value = value - fw.params = params - elif field['type'] == 'SelectField': - for option in field['selectlist']: - if option == value: - fw.add_option(option, option, selected=True) - else: - fw.add_option(option, option) - elif field['type'] == 'CheckboxField': - fw.checked = value - # require/optional - if field['required'] == 'required': - req = 'Required' - else: - req = 'Optional' - widgets.append(dict(label=field['label'], - widget=fw, - helptext=field['helptext']+' ('+req+')')) - return widgets def __validate(self, trans, request): ''' Validates the request entered by the user ''' empty_fields = [] - if not request.library: - empty_fields.append('Data library') +# if not request.library: +# empty_fields.append('Data library') # check rest of the fields of the form for index, field in enumerate(request.type.request_form.fields): if field['required'] == 'required' and request.values.content[index] in ['', None]: @@ -622,6 +577,7 @@ request.flush() return request @web.expose + @web.require_login( "create/submit sequencing requests" ) def edit(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -698,11 +654,10 @@ helptext='(Optional)')) # libraries selectbox - libraries = self.get_authorized_libs(trans) + libraries = get_authorized_libs(trans, trans.user) libui = self.__library_ui(libraries, request, **kwd) widgets = widgets + libui - widgets = self.__create_form(trans, request.type.request_form_id, widgets, - request.values, **kwd) + widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, **kwd) return trans.fill_template( '/requests/edit_request.mako', select_request_type=select_request_type, request_type=request.type, @@ -735,6 +690,8 @@ kwd['id'] = trans.security.encode_id(request.id) return trans.response.send_redirect( web.url_for( controller='requests', action='list', + status='done', + message='The request <b>%s</b> has been deleted.' % request.name, **kwd) ) def __undelete_request(self, trans, id): try: @@ -754,6 +711,8 @@ kwd['id'] = trans.security.encode_id(request.id) return trans.response.send_redirect( web.url_for( controller='requests', action='list', + status='done', + message='The request <b>%s</b> has been undeleted.' % request.name, **kwd) ) def __submit(self, trans, id): try: @@ -784,10 +743,14 @@ request.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name return trans.response.send_redirect( web.url_for( controller='requests', action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, **kwd) ) @web.expose + @web.require_login( "create/submit sequencing requests" ) def submit_request(self, trans, **kwd): params = util.Params( kwd ) try: @@ -817,13 +780,16 @@ # change request's submitted field request.state = request.states.SUBMITTED request.flush() - ## TODO kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name return trans.response.send_redirect( web.url_for( controller='requests', action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, **kwd) ) @web.expose + @web.require_login( "create/submit sequencing requests" ) def show_events(self, trans, **kwd): params = util.Params( kwd ) try: diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Sat Aug 22 23:20:09 2009 -0400 @@ -7,19 +7,20 @@ import logging, tempfile, zipfile, tarfile, os, sys from galaxy.web.form_builder import * from datetime import datetime, timedelta +from galaxy.web.controllers.forms import get_form_widgets +from galaxy.web.controllers.library import get_authorized_libs log = logging.getLogger( __name__ ) - -# States for passing messages -SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" class RequestsListGrid( grids.Grid ): title = "Sequencing Requests" model_class = model.Request default_sort_key = "-create_time" + show_filter = model.Request.states.SUBMITTED columns = [ grids.GridColumn( "Name", key="name", - link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) )), + link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), + attach_popup=True ), grids.GridColumn( "Description", key="desc"), grids.GridColumn( "Sample(s)", method='number_of_samples', link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ), @@ -30,15 +31,18 @@ ] operations = [ -# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), -# grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted ) ), -# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), -# grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), + grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples ) ), + grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Delete", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() ) ), + grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), ] standard_filters = [ + grids.GridColumnFilter( model.Request.states.UNSUBMITTED, + args=dict( state=model.Request.states.UNSUBMITTED, deleted=False ) ), grids.GridColumnFilter( model.Request.states.SUBMITTED, args=dict( state=model.Request.states.SUBMITTED, deleted=False ) ), grids.GridColumnFilter( model.Request.states.COMPLETE, args=dict( state=model.Request.states.COMPLETE, deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted=False ) ) ] def get_user(self, trans, request): @@ -48,9 +52,9 @@ def get_request_type(self, trans, request): request_type = trans.app.model.RequestType.get(request.request_type_id) return request_type.name - def apply_default_filter( self, trans, query ): - return query.filter(or_(self.model_class.state==self.model_class.states.SUBMITTED, - self.model_class.state==self.model_class.states.COMPLETE)) +# def apply_default_filter( self, trans, query ): +# return query.filter(or_(self.model_class.state==self.model_class.states.SUBMITTED, +# self.model_class.state==self.model_class.states.COMPLETE)) def number_of_samples(self, trans, request): return str(len(request.samples)) @@ -67,32 +71,277 @@ ''' List all request made by the current user ''' - status = message = None + message = util.restore_text( kwargs.get( 'message', '' ) ) + status = kwargs.get( 'status', 'done' ) self.request_grid.default_filter = dict(state=trans.app.model.Request.states.SUBMITTED, deleted=False) if 'operation' in kwargs: operation = kwargs['operation'].lower() if operation == "show_request": id = trans.security.decode_id(kwargs['id']) - return self.__show_request(trans, id) - + return self.__show_request(trans, id, status, message) + elif operation == "submit": + id = trans.security.decode_id(kwargs['id']) + return self.__submit(trans, id) + elif operation == "edit": + id = trans.security.decode_id(kwargs['id']) + return self.__edit_request(trans, id) + elif operation == "delete": + id = trans.security.decode_id(kwargs['id']) + return self.__delete_request(trans, id) + elif operation == "undelete": + id = trans.security.decode_id(kwargs['id']) + return self.__undelete_request(trans, id) if 'show_filter' in kwargs.keys(): if kwargs['show_filter'] == 'All': - self.request_grid.default_filter = dict(deleted=False) + self.request_grid.default_filter = {} + elif kwargs['show_filter'] == 'Deleted': + self.request_grid.default_filter = dict(deleted=True) else: - self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) + self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) + self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED) # Render the list view return self.request_grid( trans, template='/admin/requests/grid.mako', **kwargs ) - def __show_request(self, trans, id): + @web.expose + @web.require_admin + def edit(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request = trans.app.model.Request.get(int(params.get('request_id', None))) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message="Invalid request ID", + **kwd) ) + if params.get('show', False) == 'True': + return self.__edit_request(trans, request.id, **kwd) + elif params.get('save_changes_request_button', False) == 'Save changes' \ + or params.get('edit_samples_button', False) == 'Edit samples': + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + if not util.restore_text(params.get('name', '')): + msg = 'Please enter the <b>Name</b> of the request' + kwd['messagetype'] = 'error' + kwd['msg'] = msg + kwd['show'] = 'True' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + **kwd) ) + request = self.__save_request(trans, request, **kwd) + msg = 'The changes made to the request named %s has been saved' % request.name + if params.get('save_changes_request_button', False) == 'Save changes': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + message=msg , + status='done') ) + elif params.get('edit_samples_button', False) == 'Edit samples': + new_kwd = {} + new_kwd['request_id'] = request.id + new_kwd['edit_samples_button'] = 'Edit samples' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='show_request', + msg=msg , + messagetype='done', + **new_kwd) ) + elif params.get('refresh', False) == 'true': + return self.__edit_request(trans, request.id, **kwd) + def __edit_request(self, trans, id, **kwd): try: request = trans.app.model.Request.get(id) except: - return trans.response.send_redirect( web.url_for( controller='requests', + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg) ) + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + select_request_type = self.__select_request_type(trans, request.type.id) + # list of widgets to be rendered on the request form + widgets = [] + if util.restore_text( params.get( 'name', '' ) ): + name = util.restore_text( params.get( 'name', '' ) ) + else: + name = request.name + widgets.append(dict(label='Name', + widget=TextField('name', 40, name), + helptext='(Required)')) + if util.restore_text( params.get( 'desc', '' ) ): + desc = util.restore_text( params.get( 'desc', '' ) ) + else: + desc = request.desc + widgets.append(dict(label='Description', + widget=TextField('desc', 40, desc), + helptext='(Optional)')) + # libraries selectbox + libui = self.__library_ui(trans, request.user, request, **kwd) + widgets = widgets + libui + widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, request.user, **kwd) + return trans.fill_template( '/admin/requests/edit_request.mako', + select_request_type=select_request_type, + request_type=request.type, + request=request, + widgets=widgets, + msg=msg, + messagetype=messagetype) + return self.__show_request_form(trans) + def __delete_request(self, trans, id): + try: + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + # change request's submitted field + if not request.unsubmitted(): + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message='This request cannot be deleted as it is already been submitted', + **kwd) ) + request.deleted = True + request.flush() + kwd = {} + kwd['id'] = trans.security.encode_id(request.id) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.UNSUBMITTED, + status='done', + message='The request <b>%s</b> has been deleted.' % request.name, + **kwd) ) + def __undelete_request(self, trans, id): + try: + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + # change request's submitted field + request.deleted = False + request.flush() + kwd = {} + kwd['id'] = trans.security.encode_id(request.id) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.UNSUBMITTED, + status='done', + message='The request <b>%s</b> has been undeleted.' % request.name, + **kwd) ) + def __submit(self, trans, id): + try: + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + msg = self.__validate(trans, request) + if msg: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + messagetype = 'error', + msg=msg, + request_id=request.id, + show='True') ) + # get the new state + new_state = request.type.states[0] + for s in request.samples: + event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') + event.flush() + # change request's submitted field + request.state = request.states.SUBMITTED + request.flush() + kwd = {} + kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, + **kwd) ) + @web.expose + @web.require_admin + def submit_request(self, trans, **kwd): + params = util.Params( kwd ) + try: + id = int(params.get('id', False)) + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + msg = self.__validate(trans, request) + if msg: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + messagetype='error', + msg=msg, + request_id=request.id, + show='True') ) + # get the new state + new_state = request.type.states[0] + for s in request.samples: + event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') + event.flush() + # change request's submitted field + request.state = request.states.SUBMITTED + request.flush() + kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, + **kwd) ) + def __copy_sample(self): + copy_list = SelectField('copy_sample') + copy_list.add_option('None', -1, selected=True) + for i, s in enumerate(self.current_samples): + copy_list.add_option(s[0], i) + return copy_list + def __update_samples(self, request, **kwd): + params = util.Params( kwd ) + num_samples = len(self.current_samples) + self.current_samples = [] + for s in request.samples: + self.current_samples.append([s.name, s.values.content]) + for index in range(num_samples-len(request.samples)): + sample_index = index + len(request.samples) + sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + self.current_samples.append([sample_name, sample_values]) + def __show_request(self, trans, id, messagetype, msg): + try: + request = trans.app.model.Request.get(id) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', message="Invalid request ID", **kwd) ) self.current_samples = [] + self.edit_mode = False for s in request.samples: self.current_samples.append([s.name, s.values.content]) self.details_state = 'Show request details' @@ -100,8 +349,163 @@ request=request, request_details=self.request_details(trans, id), current_samples = self.current_samples, - details_state=self.details_state) + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode, + msg=msg, messagetype=messagetype) @web.expose + @web.require_admin + def show_request(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request = trans.app.model.Request.get(int(params.get('request_id', None))) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message="Invalid request ID", + **kwd) ) + if params.get('import_samples_button', False) == 'Import samples': + try: + file_obj = params.get('file_data', '') + import csv + reader = csv.reader(file_obj.file) + for row in reader: + self.current_samples.append([row[0], row[1:]]) + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=self.current_samples, + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + operation='show_request', + id=trans.security.encode_id(request.id), + message='Error in importing samples from the given file.', + **kwd)) + elif params.get('add_sample_button', False) == 'Add New': + # save the all (saved+unsaved) sample info in 'current_samples' + self.__update_samples(request, **kwd) + # add an empty or filled sample + # if the user has selected a sample no. to copy then copy the contents + # of the src sample to the new sample else an empty sample + src_sample_index = int(params.get( 'copy_sample', -1 )) + if src_sample_index == -1: + # empty sample + self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]]) + else: + self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1), + [val for val in self.current_samples[src_sample_index][1]]]) + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=self.current_samples, + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode) + elif params.get('save_samples_button', False) == 'Save': + # update current_samples + self.__update_samples(request, **kwd) + # check for duplicate sample names + msg = '' + for index in range(len(self.current_samples)-len(request.samples)): + sample_index = index + len(request.samples) + sample_name = self.current_samples[sample_index][0] + if not sample_name.strip(): + msg = 'Please enter the name of sample number %i' % sample_index + break + count = 0 + for i in range(len(self.current_samples)): + if sample_name == self.current_samples[i][0]: + count = count + 1 + if count > 1: + msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) + break + if msg: + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples = self.current_samples, + sample_copy=self.__copy_sample(), details_state=self.details_state, + messagetype='error', msg=msg) + # save all the new/unsaved samples entered by the user + if not self.edit_mode: + for index in range(len(self.current_samples)-len(request.samples)): + sample_index = index + len(request.samples) + sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + form_values = trans.app.model.FormValues(request.type.sample_form, sample_values) + form_values.flush() + s = trans.app.model.Sample(sample_name, '', request, form_values) + s.flush() + else: + for index in range(len(self.current_samples)): + sample_index = index + sample_name = self.current_samples[sample_index][0] + new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + sample = request.has_sample(sample_name) + if sample: + form_values = trans.app.model.FormValues.get(sample.values.id) + form_values.content = sample_values + form_values.flush() + sample.name = new_sample_name + sample.flush() + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + id=trans.security.encode_id(request.id)) ) + elif params.get('edit_samples_button', False) == 'Edit samples': + self.edit_mode = True + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=self.current_samples, + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode) + elif params.get('cancel_changes_button', False) == 'Cancel': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + id=trans.security.encode_id(request.id)) ) + + + @web.expose + @web.require_admin + def delete_sample(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + request = trans.app.model.Request.get(int(params.get('request_id', 0))) + sample_index = int(params.get('sample_id', 0)) + sample_name = self.current_samples[sample_index][0] + s = request.has_sample(sample_name) + if s: + s.delete() + s.flush() + request.flush() + del self.current_samples[sample_index] + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples = self.current_samples, + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode) + + @web.expose + @web.require_admin def toggle_request_details(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -128,24 +532,28 @@ # list of widgets to be rendered on the request form request_details = [] # main details + request_details.append(dict(label='User', + value=str(request.user.email), + helptext='')) request_details.append(dict(label='Description', value=request.desc, helptext='')) request_details.append(dict(label='Type', value=request.type.name, helptext='')) + request_details.append(dict(label='State', + value=request.state, + helptext='')) request_details.append(dict(label='Date created', value=request.create_time, helptext='')) - request_details.append(dict(label='Date updated', - value=request.create_time, - helptext='')) - request_details.append(dict(label='User', - value=str(request.user.email), - helptext='')) # library associated + if request.library: + value=request.library.name + else: + value = None request_details.append(dict(label='Data library', - value=trans.app.model.Library.get(request.library_id).name, + value=value, helptext='Data library where the resultant dataset will be stored')) # form fields for index, field in enumerate(request.type.request_form.fields): @@ -167,15 +575,262 @@ value=request.values.content[index], helptext=field['helptext']+' ('+req+')')) return request_details + + def __select_request_type(self, trans, rtid): + rt_ids = ['none'] + for rt in trans.app.model.RequestType.query().all(): + if not rt.deleted: + rt_ids.append(str(rt.id)) + select_reqtype = SelectField('select_request_type', + refresh_on_change=True, + refresh_on_change_values=rt_ids[1:]) + if rtid == 'none': + select_reqtype.add_option('Select one', 'none', selected=True) + else: + select_reqtype.add_option('Select one', 'none') + for rt in trans.app.model.RequestType.query().all(): + if not rt.deleted: + if rtid == rt.id: + select_reqtype.add_option(rt.name, rt.id, selected=True) + else: + select_reqtype.add_option(rt.name, rt.id) + return select_reqtype + @web.expose + @web.require_admin + def new(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get('select_request_type', False) == 'True': + return trans.fill_template( '/admin/requests/new_request.mako', + select_request_type=self.__select_request_type(trans, 'none'), + widgets=[], + msg=msg, + messagetype=messagetype) + elif params.get('create', False) == 'True': + if params.get('create_request_button', False) == 'Save' \ + or params.get('create_request_samples_button', False) == 'Add samples': + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + if not util.restore_text(params.get('name', '')) \ + or util.restore_text(params.get('select_user', '')) == unicode('none'): + msg = 'Please enter the <b>Name</b> of the request and the <b>user</b> on behalf of whom this request will be submitted before saving this request' + kwd['create'] = 'True' + kwd['messagetype'] = 'error' + kwd['msg'] = msg + kwd['create_request_button'] = None + kwd['create_request_samples_button'] = None + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='new', + **kwd) ) + request = self.__save_request(trans, None, **kwd) + msg = 'The new request named %s has been created' % request.name + if params.get('create_request_button', False) == 'Save': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.UNSUBMITTED, + message=msg , + status='done') ) + elif params.get('create_request_samples_button', False) == 'Add samples': + new_kwd = {} + new_kwd['id'] = trans.security.encode_id(request.id) + new_kwd['operation'] = 'show_request' + new_kwd['add_sample'] = True + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + message=msg , + status='done', + **new_kwd) ) + else: + return self.__show_request_form(trans, **kwd) + elif params.get('refresh', False) == 'true': + return self.__show_request_form(trans, **kwd) + def __show_request_form(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + except: + return trans.fill_template( '/admin/requests/new_request.mako', + select_request_type=self.__select_request_type(trans, 'none'), + widgets=[], + msg=msg, + messagetype=messagetype) + form_values = None + select_request_type = self.__select_request_type(trans, request_type.id) + # user + user_id = params.get( 'select_user', 'none' ) + try: + user = trans.app.model.User.get(int(user_id)) + except: + user = None + # list of widgets to be rendered on the request form + widgets = [] + widgets.append(dict(label='Select user', + widget=self.__select_user(trans, user_id), + helptext='The request would be submitted on behalf of this user (Required)')) + widgets.append(dict(label='Name', + widget=TextField('name', 40, + util.restore_text( params.get( 'name', '' ) )), + helptext='(Required)')) + widgets.append(dict(label='Description', + widget=TextField('desc', 40, + util.restore_text( params.get( 'desc', '' ) )), + helptext='(Optional)')) + # libraries selectbox + libui = self.__library_ui(trans, user, **kwd) + widgets = widgets + libui + widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], user=user, **kwd) + return trans.fill_template( '/admin/requests/new_request.mako', + select_request_type=select_request_type, + request_type=request_type, + widgets=widgets, + msg=msg, + messagetype=messagetype) + def __select_user(self, trans, userid): + user_ids = ['none'] + for user in trans.app.model.User.query().all(): + if not user.deleted: + user_ids.append(str(user.id)) + select_user = SelectField('select_user', + refresh_on_change=True, + refresh_on_change_values=user_ids[1:]) + if userid == 'none': + select_user.add_option('Select one', 'none', selected=True) + else: + select_user.add_option('Select one', 'none') + for user in trans.app.model.User.query().all(): + if not user.deleted: + if userid == str(user.id): + select_user.add_option(user.email, user.id, selected=True) + else: + select_user.add_option(user.email, user.id) + return select_user + + def __library_ui(self, trans, user, request=None, **kwd): + params = util.Params( kwd ) + lib_id = params.get( 'library_id', 'none' ) + if not user: + libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() + else: + libraries = get_authorized_libs(trans, user) + lib_list = SelectField('library_id', refresh_on_change=True, + refresh_on_change_values=['new']) + if request and lib_id == 'none': + if request.library: + lib_id = str(request.library.id) + if lib_id == 'none': + lib_list.add_option('Select one', 'none', selected=True) + else: + lib_list.add_option('Select one', 'none') + for lib in libraries: + if str(lib.id) == lib_id: + lib_list.add_option(lib.name, lib.id, selected=True) + else: + lib_list.add_option(lib.name, lib.id) + if lib_id == 'new': + lib_list.add_option('Create a new data library', 'new', selected=True) + else: + lib_list.add_option('Create a new data library', 'new') + widget = dict(label='Data library', + widget=lib_list, + helptext='Data library where the resultant dataset will be stored.') + if lib_id == 'new': + new_lib = dict(label='Create a new Library', + widget=TextField('new_library_name', 40, + util.restore_text( params.get( 'new_library_name', '' ) )), + helptext='Enter a library name here to request a new library') + return [widget, new_lib] + else: + return [widget] + def __validate(self, trans, request): + ''' + Validates the request entered by the user + ''' + empty_fields = [] +# if not request.library: +# empty_fields.append('Library') + # check rest of the fields of the form + for index, field in enumerate(request.type.request_form.fields): + if field['required'] == 'required' and request.values.content[index] in ['', None]: + empty_fields.append(field['label']) + if empty_fields: + msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name + for ef in empty_fields: + msg = msg + '<b>' +ef + '</b><br/>' + return msg + return None + def __save_request(self, trans, request=None, **kwd): + ''' + This method saves a new request if request_id is None. + ''' + params = util.Params( kwd ) + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + if request: + user = request.user + else: + user = trans.app.model.User.get(int(params.get('select_user', ''))) + name = util.restore_text(params.get('name', '')) + desc = util.restore_text(params.get('desc', '')) + # library + try: + library = trans.app.model.Library.get(int(params.get('library_id', None))) + except: + library = None + # fields + values = [] + for index, field in enumerate(request_type.request_form.fields): + if field['type'] == 'AddressField': + value = util.restore_text(params.get('field_%i' % index, '')) + if value == 'new': + # save this new address in the list of this user's addresses + user_address = trans.app.model.UserAddress( user=user ) + user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, '')) + user_address.name = util.restore_text(params.get('field_%i_name' % index, '')) + user_address.institution = util.restore_text(params.get('field_%i_institution' % index, '')) + user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, '')) + user_address.city = util.restore_text(params.get('field_%i_city' % index, '')) + user_address.state = util.restore_text(params.get('field_%i_state' % index, '')) + user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, '')) + user_address.country = util.restore_text(params.get('field_%i_country' % index, '')) + user_address.phone = util.restore_text(params.get('field_%i_phone' % index, '')) + user_address.flush() + trans.user.refresh() + values.append(int(user_address.id)) + elif value == unicode('none'): + values.append('') + else: + values.append(int(value)) + else: + values.append(util.restore_text(params.get('field_%i' % index, ''))) + form_values = trans.app.model.FormValues(request_type.request_form, values) + form_values.flush() + if not request: + request = trans.app.model.Request(name, desc, request_type, + user, form_values, + library=library, + state=trans.app.model.Request.states.UNSUBMITTED) + request.flush() + else: + request.name = name + request.desc = desc + request.type = request_type + request.user = user + request.values = form_values + request.library = library + request.flush() + return request @web.expose @web.require_admin def bar_codes(self, trans, **kwd): params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) request_id = params.get( 'request_id', None ) if request_id: request = trans.app.model.Request.get( int( request_id )) if not request: - return trans.response.send_redirect( web.url_for( controller='requests', + return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', message="Invalid request ID", @@ -191,7 +846,9 @@ bc)) return trans.fill_template( '/admin/samples/bar_codes.mako', samples_list=[s for s in request.samples], - user=request.user, request=request, widgets=widgets) + user=request.user, request=request, widgets=widgets, + messagetype=messagetype, + msg=msg) @web.expose @web.require_admin def save_bar_codes(self, trans, **kwd): @@ -199,7 +856,7 @@ try: request = trans.app.model.Request.get(int(params.get('request_id', None))) except: - return trans.response.send_redirect( web.url_for( controller='requests', + return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', message="Invalid request ID", @@ -255,9 +912,10 @@ sample.bar_code = bar_code sample.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - operation='show_request', - id=trans.security.encode_id(request.id)) ) + action='bar_codes', + request_id=request.id, + msg='Bar codes has been saved for this request', + messagetype='done')) def __set_request_state(self, request): # check if all the samples of the current request are in the final state complete = True diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Sat Aug 22 23:20:09 2009 -0400 @@ -82,7 +82,7 @@ job = assoc.job break if not job: - raise Exception("Failed to get job information for dataset hid %d" % hid) + raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id try: diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Sat Aug 22 23:20:09 2009 -0400 @@ -229,6 +229,8 @@ def manage_addresses(self, trans, **kwd): if trans.user: params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) if show_filter == 'All': addresses = [address for address in trans.user.addresses] @@ -238,7 +240,9 @@ addresses = [address for address in trans.user.addresses if not address.deleted] return trans.fill_template( 'user/address.mako', addresses=addresses, - show_filter=show_filter) + show_filter=show_filter, + msg=msg, + messagetype=messagetype) else: # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/framework/base.py Sat Aug 22 23:20:09 2009 -0400 @@ -216,11 +216,18 @@ # tempfiles. Necessary for externalizing the upload tool. It's a little hacky # but for performance reasons it's way better to use Paste's tempfile than to # create a new one and copy. -import cgi +import cgi, tempfile class FieldStorage( cgi.FieldStorage ): def make_file(self, binary=None): - import tempfile return tempfile.NamedTemporaryFile() + def read_lines(self): + # Always make a new file + self.file = self.make_file() + self.__file = None + if self.outerboundary: + self.read_lines_to_outerboundary() + else: + self.read_lines_to_eof() cgi.FieldStorage = FieldStorage class Request( webob.Request ): diff -r fbad627b45ac -r e6dda627e6b0 static/welcome.html --- a/static/welcome.html Sat Aug 22 23:18:47 2009 -0400 +++ b/static/welcome.html Sat Aug 22 23:20:09 2009 -0400 @@ -71,7 +71,7 @@ <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.flv',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie1_small.png" border="0"> </div> diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/forms/edit_form.mako --- a/templates/admin/forms/edit_form.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/forms/edit_form.mako Sat Aug 22 23:20:09 2009 -0400 @@ -70,7 +70,7 @@ </%def> <div class="toolForm"> - <div class="toolFormTitle">Edit form definition '${form.name}'</div> + <div class="toolFormTitle">Edit form definition "${form.name}"</div> <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields) )}" method="post" > %for label, input in form_details: <div class="form-row"> diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/add_states.mako --- a/templates/admin/requests/add_states.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/requests/add_states.mako Sat Aug 22 23:20:09 2009 -0400 @@ -12,9 +12,9 @@ %for element_count in range( num_states ): <div class="form-row"> <label>${1+element_count}) State name:</label> - <input type="text" name="new_element_name_${element_count}" value="" size="40"/> + <input type="text" name="state_name_${element_count}" value="" size="40"/> <label>State help text (optional):</label> - <input type="text" name="new_element_description_${element_count}" value="" size="40"/> + <input type="text" name="state_desc_${element_count}" value="" size="40"/> </div> <div style="clear: both"></div> %endfor diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/edit_request.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/edit_request.mako Sat Aug 22 23:20:09 2009 -0400 @@ -0,0 +1,88 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#edit_request" ).submit(); + } + }); +}); +</script> + +<br/> +<br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}"> + <span>Browse this request</span></a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list')}"> + <span>Browse requests</span></a> + </li> +</ul> + +<div class="toolForm"> + <div class="toolFormTitle">Edit request "${request.name}" from ${request.user.email}</div> + %if len(select_request_type.options) == 1: + There are no request types created for a new request. + %else: + <div class="toolFormBody"> + <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests_admin', action='edit', request_id=request.id)}" method="post" > + <div class="form-row"> + <label> + Select Request Type: + </label> + ${select_request_type.get_html()} + </div> + + %if select_request_type.get_selected() != ('Select one', 'none'): + %for i, field in enumerate(widgets): + <div class="form-row"> + <label>${field['label']}</label> + ${field['widget'].get_html()} + %if field['label'] == 'Library' and new_library: + ${new_library.get_html()} + %endif + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="refresh" value="true" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="save_changes_request_button" value="Save changes"/> + ##<input type="submit" name="edit_samples_button" value="Edit samples"/> + </div> + %endif + </form> + </div> +</div> +%endif \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/grid.mako --- a/templates/admin/requests/grid.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/requests/grid.mako Sat Aug 22 23:20:09 2009 -0400 @@ -76,29 +76,28 @@ <div class="grid-header"> <h2>${grid.title}</h2> - ##%if len(query.all()): + %if len(trans.app.model.Request.query().all()): ##<span class="title">Filter:</span> %for i, filter in enumerate( grid.standard_filters ): %if i > 0: <span>|</span> %endif - %if 'state' in grid.default_filter: - %if grid.default_filter['state'] == filter.label: - <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span> - %endif + %if grid.show_filter == filter.label: + <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span> %else: - %if filter.label == 'All': - <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span> - %endif + <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span> %endif %endfor - ##%endif + %endif </div> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='new', select_request_type=True )}"> + <img src="${h.url_for('/static/images/silk/add.png')}" /> + <span>Create a new request</span></a> + </li> +</ul> %if not len(query.all()): There are no requests. diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/new_request.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/new_request.mako Sat Aug 22 23:20:09 2009 -0400 @@ -0,0 +1,84 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#new_request" ).submit(); + } + }); +}); +</script> + +<br/> +<br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list')}"> + <span>Browse requests</span></a> + </li> +</ul> + +<div class="toolForm"> + <div class="toolFormTitle">Add a new request</div> + %if len(select_request_type.options) == 1: + There are no request types created for a new request. + %else: + <div class="toolFormBody"> + <form name="new_request" id="new_request" action="${h.url_for( controller='requests_admin', action='new', create=True )}" method="post" > + <div class="form-row"> + <label> + Select Request Type + </label> + ${select_request_type.get_html()} + </div> + + %if select_request_type.get_selected() != ('Select one', 'none'): + %for i, field in enumerate(widgets): + <div class="form-row"> + <label>${field['label']}</label> + ${field['widget'].get_html()} + %if field['label'] == 'Library' and new_library: + ${new_library.get_html()} + %endif + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="refresh" value="true" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="create_request_button" value="Save"/> + <input type="submit" name="create_request_samples_button" value="Add samples"/> + </div> + %endif + </form> + </div> +</div> +%endif \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/requests/show_request.mako Sat Aug 22 23:20:09 2009 -0400 @@ -12,18 +12,49 @@ </div> <ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}"> - <span>Bar codes</span></a> - </li> + %if request.unsubmitted() and request.samples: + <li> + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='submit_request', id=request.id)}"> + <span>Submit request</span></a> + </li> + %endif + %if request.submitted() and request.samples: + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}"> + <span>Bar codes</span></a> + </li> + %endif </ul> + +<%def name="render_sample_form( index, sample_name, sample_values )"> + <td> + <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/> + <div class="toolParamHelp" style="clear: both;"> + <i>${' (required)' }</i> + </div> + </td> + <td> + </td> + %for field_index, field in enumerate(request.type.sample_form.fields): + <td> + <input type="text" name=sample_${index}_field_${field_index} value="${sample_values[field_index]}" size="7"/> + <div class="toolParamHelp" style="clear: both;"> + <i>${'('+field['required']+')' }</i> + </div> + </td> + %endfor +</%def> <%def name="render_sample( index, sample )"> <td> ${sample.name} </td> <td> - <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> + %if sample.request.unsubmitted(): + Unsubmitted + %else: + <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> + %endif </td> %for field_index, field in enumerate(request.type.sample_form.fields): <td> @@ -34,10 +65,10 @@ %endif </td> %endfor + </%def> <div class="toolForm"> - ##<div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div> <div class="form-row"> <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id )}">${details_state}</a> </div> @@ -57,13 +88,21 @@ </div> <div style="clear: both"></div> %endfor + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='edit', show=True, request_id=request.id)}"> + <span>Edit request details</span></a> + </li> + </ul> + </div> %endif </div> </div> <div class="toolForm"> ##<div class="toolFormTitle">Samples (${len(request.samples)})</div> - <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests', action='show_request', request_id=request.id )}" method="post" > + <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests_admin', action='show_request' )}" enctype="multipart/form-data" method="post" > <div class="form-row"> %if current_samples: <table class="grid"> @@ -80,22 +119,88 @@ </div> </th> %endfor + <th></th> </tr> <thead> <tbody> + <% + request.refresh() + %> %for sample_index, sample in enumerate(current_samples): - <tr> - <td>${sample_index+1}</td> - ${render_sample( sample_index, request.samples[sample_index] )} - </tr> + %if edit_mode: + <tr> + <td>${sample_index+1}</td> + ${render_sample_form( sample_index, sample[0], sample[1])} + </tr> + %else: + <tr> + <td>${sample_index+1}</td> + %if sample_index in range(len(request.samples)): + ${render_sample( sample_index, request.samples[sample_index] )} + %else: + ${render_sample_form( sample_index, sample[0], sample[1])} + %endif + <td> + %if request.unsubmitted(): + <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> + <img src="${h.url_for('/static/images/delete_icon.png')}" /> + <span></span></a> + %endif + </td> + </tr> + %endif %endfor </tbody> </table> %else: <label>There are no samples.</label> %endif - </div> - ##</div> + %if not edit_mode: + <table class="grid"> + <tbody> + <tr> + <div class="form-row"> + <td> + %if current_samples and not request.complete(): + <input type="submit" name="edit_samples_button" value="Edit samples"/> + %endif + </td> + %if request.unsubmitted(): + <td> + <label>Import from csv file</label> + <input type="file" name="file_data" /> + <input type="submit" name="import_samples_button" value="Import samples"/> + </td> + <td> + %if current_samples: + <label>Copy from sample</label> + ${sample_copy.get_html()} + %endif + <input type="submit" name="add_sample_button" value="Add New"/> + </td> + %endif + </div> + </tr> + </tbody> + </table> + %endif + %if request.samples or current_samples: + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="refresh" value="true" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + %if edit_mode: + <input type="submit" name="save_samples_button" value="Save"/> + <input type="submit" name="cancel_changes_button" value="Cancel"/> + %elif request.unsubmitted(): + <input type="submit" name="save_samples_button" value="Save"/> + %endif + </div> + %endif + <input type="hidden" name="request_id" value="${request.id}" /> </form> </div> diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/samples/bar_codes.mako --- a/templates/admin/samples/bar_codes.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/samples/bar_codes.mako Sat Aug 22 23:20:09 2009 -0400 @@ -40,7 +40,7 @@ </tbody> </table> <div class="form-row"> - <input type="submit" name="save_new_sample_type" value="Save"/> + <input type="submit" name="save_bar_codes" value="Save"/> </div> </form> </div> \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/samples/events.mako --- a/templates/admin/samples/events.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/samples/events.mako Sat Aug 22 23:20:09 2009 -0400 @@ -56,7 +56,7 @@ </div> %endfor <div class="form-row"> - <input type="submit" name="add_event" value="Save"/> + <input type="submit" name="add_event_button" value="Save"/> </div> </form> </div> diff -r fbad627b45ac -r e6dda627e6b0 templates/base_panels.mako --- a/templates/base_panels.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/base_panels.mako Sat Aug 22 23:20:09 2009 -0400 @@ -138,7 +138,7 @@ ${tab( "libraries", "Data Libraries", h.url_for( controller='library', action='index' ))} - %if trans.request_types(): + %if trans.user and trans.request_types(): <td class="tab"> <a>Lab</a> <div class="submenu"> diff -r fbad627b45ac -r e6dda627e6b0 templates/requests/grid.mako --- a/templates/requests/grid.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/requests/grid.mako Sat Aug 22 23:20:09 2009 -0400 @@ -76,7 +76,7 @@ <div class="grid-header"> <h2>${grid.title}</h2> - ##%if len(query.all()): + %if len(trans.user.requests): ##<span class="title">Filter:</span> %for i, filter in enumerate( grid.standard_filters ): %if i > 0: @@ -88,17 +88,16 @@ <span class="filter"><a href="${h.url_for( controller='requests', action='list', show_filter=filter.label )}">${filter.label}</a></span> %endif %endfor - ##%endif + %endif </div> <ul class="manage-table-actions"> <li> <a class="action-button" href="${h.url_for( controller='requests', action='new', select_request_type=True )}"> <img src="${h.url_for('/static/images/silk/add.png')}" /> - <span>New request</span></a> + <span>Create a new request</span></a> </li> </ul> - %if not len(query.all()): There are no request(s). @@ -215,4 +214,4 @@ </tfoot> </table> </form> -%endif \ No newline at end of file +%endif diff -r fbad627b45ac -r e6dda627e6b0 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/requests/show_request.mako Sat Aug 22 23:20:09 2009 -0400 @@ -68,7 +68,6 @@ </%def> <div class="toolForm"> - ##<div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div> <div class="form-row"> <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id )}">${details_state}</a> </div> @@ -217,7 +216,6 @@ %endif </div> %endif - ##</div> - <input type="hidden" name="request_id" value="${request.id}" /> + <input type="hidden" name="request_id" value="${request.id}" /> </form> </div> diff -r fbad627b45ac -r e6dda627e6b0 templates/user/address.mako --- a/templates/user/address.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/user/address.mako Sat Aug 22 23:20:09 2009 -0400 @@ -33,51 +33,48 @@ </div> - -<div class="toolForm"> - ##<div class="toolFormTitle">Addresses</div> - <div class="toolFormBody"> - <% trans.user.refresh() %> - %if not trans.user.addresses: - <label>There are no addresses</label> - %else: - <table class="grid"> - <tbody> - %for index, address in enumerate(addresses): - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - - <td> - <div class="form-row"> - <label>${address.desc}</label> - ${address.display()} - </div> - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', address_id=address.id, - short_desc=address.desc, - name=address.name, institution=address.institution, - address1=address.address, city=address.city, - state=address.state, postal_code=address.postal_code, - country=address.country, phone=address.phone)}"> - <span>Edit</span></a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', address_id=address.id)}"> - <span>Delete address</span></a> - %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', address_id=address.id)}"> - <span>Undelete address</span></a> - %endif - - </li> - </ul> - </div> - </td> - </tr> - %endfor - </tbody> - </table> - %endif +%if not addresses: + <label>There are no addresses</label> +%else: + <div class="toolForm"> + <div class="toolFormBody"> + <% trans.user.refresh() %> + <table class="grid"> + <tbody> + %for index, address in enumerate(addresses): + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td> + <div class="form-row"> + <label>${address.desc}</label> + ${address.display()} + </div> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + %if not address.deleted: + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', address_id=address.id, + short_desc=address.desc, + name=address.name, institution=address.institution, + address1=address.address, city=address.city, + state=address.state, postal_code=address.postal_code, + country=address.country, phone=address.phone)}"> + <span>Edit</span></a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', address_id=address.id)}"> + <span>Delete</span></a> + %else: + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', address_id=address.id)}"> + <span>Undelete</span></a> + %endif + + </li> + </ul> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + %endif + </div> </div> -</div> %endif \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Sat Aug 22 23:18:47 2009 -0400 +++ b/test/base/twilltestcase.py Sat Aug 22 23:20:09 2009 -0400 @@ -972,7 +972,7 @@ self.home() # Form stuff - def create_form( self, name='Form One', description='This is Form One', num_fields=1 ): + def create_form( self, name='Form One', desc='This is Form One', num_fields=1 ): """ Create a new form definition. Testing framework is still limited to only testing one instance for each repeat. This has to do with the 'flat' nature of defining @@ -988,7 +988,7 @@ self.visit_url( "%s/forms/new" % self.url ) self.check_page_for_string( 'Create a new form definition' ) tc.fv( "1", "name", name ) # form field 1 is the field named name... - tc.fv( "1", "description", description ) # form field 1 is the field named name... + tc.fv( "1", "description", desc ) # form field 1 is the field named name... tc.submit( "create_form_button" ) for index in range( num_fields ): field_name = 'field_name_%i' % index @@ -1001,7 +1001,140 @@ check_str = "The form '%s' has been updated with the changes." % name self.check_page_for_string( check_str ) self.home() - + def edit_form( self, form_id, form_name, new_form_name="Form One's Name (Renamed)", new_form_desc="This is Form One's description (Re-described)"): + """ + Edit form details; name & description + """ + self.home() + self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) ) + self.check_page_for_string( 'Edit form definition "%s"' % form_name ) + tc.fv( "1", "name", new_form_name ) + tc.fv( "1", "description", new_form_desc ) + tc.submit( "save_changes_button" ) + self.check_page_for_string( "The form '%s' has been updated with the changes." % new_form_name ) + self.home() + def form_add_field( self, form_id, form_name, field_index, fields): + """ + Add a new fields to the form definition + """ + self.home() + self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) ) + self.check_page_for_string( 'Edit form definition "%s"' % form_name) + for i, field in enumerate(fields): + index = i+field_index + tc.submit( "add_field_button" ) + tc.fv( "1", "field_name_%i" % index, field['name'] ) + tc.fv( "1", "field_helptext_%i" % index, field['desc'] ) + tc.fv( "1", "field_type_%i" % index, field['type'] ) + tc.fv( "1", "field_required_%i" % index, field['required'] ) +# if field['type'] == 'SelectField': +# for option_index, option in enumerate(field['selectlist']): +# self.visit_url( "%s/forms/edit?select_box_options=add&form_id=%i&field_index=%i" % \ +# (self.url, form_id, index)) +# #data = self.last_page() +# #file( "rc.html", 'wb' ).write(data) +# tc.fv( "1", "field_%i_option_%i" % (index, option_index), option ) + tc.submit( "save_changes_button" ) + check_str = "The form '%s' has been updated with the changes." % form_name + self.check_page_for_string( check_str ) + self.home() + def form_remove_field( self, form_id, form_name, field_name): + """ + Remove a field from the form definition + """ + self.home() + self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) ) + self.check_page_for_string( 'Edit form definition "%s"' % form_name) + tc.submit( "remove_button" ) + tc.submit( "save_changes_button" ) + check_str = "The form '%s' has been updated with the changes." % form_name + self.check_page_for_string( check_str ) + self.home() + # Requests stuff + def create_request_type( self, name, desc, request_form_id, sample_form_id, states ): + self.home() + self.visit_url( "%s/admin/request_type?create=True" % self.url ) + self.check_page_for_string( 'Create a new request type' ) + tc.fv( "1", "name", name ) + tc.fv( "1", "description", desc ) + tc.fv( "1", "request_form_id", request_form_id ) + tc.fv( "1", "sample_form_id", sample_form_id ) + tc.fv( "1", "num_states", str( len( states ) ) ) + tc.submit( "define_states_button" ) + self.check_page_for_string( "Create %i states for the '%s' request type" % ( len(states), name )) + for index, state in enumerate(states): + tc.fv("1", "state_name_%i" % index, state[0]) + tc.fv("1", "state_desc_%i" % index, state[1]) + tc.submit( "save_request_type" ) + self.check_page_for_string( "Request type <b>%s</b> has been created" % name ) + def create_request( self, request_type_id, name, desc, library_id, fields ): + self.home() + self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % (self.url, request_type_id) ) + self.check_page_for_string( 'Add a new request' ) + tc.fv( "1", "name", name ) + tc.fv( "1", "desc", desc ) + tc.fv( "1", "library_id", str(library_id) ) + for index, field_value in enumerate(fields): + tc.fv( "1", "field_%i" % index, field_value ) + tc.submit( "create_request_button" ) + def create_request_admin( self, request_type_id, user_id, name, desc, library_id, fields ): + self.home() + self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i" % (self.url, request_type_id) ) + self.check_page_for_string( 'Add a new request' ) + tc.fv( "1", "select_user", str(user_id) ) + tc.fv( "1", "name", name ) + tc.fv( "1", "desc", desc ) + tc.fv( "1", "library_id", str(library_id) ) + for index, field_value in enumerate(fields): + tc.fv( "1", "field_%i" % index, field_value ) + tc.submit( "create_request_button" ) + def edit_request( self, request_id, name, new_name, new_desc, new_library_id, new_fields): + self.home() + self.visit_url( "%s/requests/edit?request_id=%i&show=True" % (self.url, request_id) ) + self.check_page_for_string( 'Edit request "%s"' % name ) + tc.fv( "1", "name", new_name ) + tc.fv( "1", "desc", new_desc ) + tc.fv( "1", "library_id", str(new_library_id) ) + for index, field_value in enumerate(new_fields): + tc.fv( "1", "field_%i" % index, field_value ) + tc.submit( "save_changes_request_button" ) + def add_samples( self, request_id, request_name, samples ): + self.home() + self.visit_url( "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) )) + self.check_page_for_string( 'Sequencing Request "%s"' % request_name ) + for sample_index, sample in enumerate(samples): + tc.submit( "add_sample_button" ) + sample_name, fields = sample + tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) + for field_index, field_value in enumerate(fields): + tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) + tc.submit( "save_samples_button" ) + def submit_request( self, request_id, request_name ): + self.home() + self.visit_url( "%s/requests/submit_request?id=%i" % ( self.url, request_id )) + self.check_page_for_string( 'The request <b>%s</b> has been submitted.' % request_name ) + def add_bar_codes( self, request_id, request_name, bar_codes ): + self.home() + self.visit_url( "%s/requests_admin/bar_codes?request_id=%i" % (self.url, request_id) ) + self.check_page_for_string( 'Bar codes for Samples of Request "%s"' % request_name ) + for index, bar_code in enumerate(bar_codes): + tc.fv( "1", "sample_%i_bar_code" % index, bar_code ) + tc.submit( "save_bar_codes" ) + def change_sample_state( self, sample_name, sample_id, new_state_id, comment='' ): + self.home() + self.visit_url( "%s/requests_admin/show_events?sample_id=%i" % (self.url, sample_id) ) + self.check_page_for_string( 'Events for Sample "%s"' % sample_name ) + tc.fv( "1", "select_state", str(new_state_id) ) + tc.fv( "1", "comment", comment ) + tc.submit( "add_event_button" ) + # Address stuff + def create_address( self, address ): + self.home() + self.visit_url( "%s/user/new_address" % self.url ) + self.check_page_for_string( 'New address' ) + for name, value in address.iteritems(): + tc.fv( "1", name, value ) + tc.submit( "Save_button" ) # Library stuff def create_library( self, name='Library One', description='This is Library One' ): """Create a new library""" diff -r fbad627b45ac -r e6dda627e6b0 test/functional/test_forms_and_requests.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/functional/test_forms_and_requests.py Sat Aug 22 23:20:09 2009 -0400 @@ -0,0 +1,274 @@ +import galaxy.model +from galaxy.model.orm import * +from base.twilltestcase import * + +not_logged_in_as_admin_security_msg = 'You must be logged in as an administrator to access this feature.' +logged_in_as_admin_security_msg = 'You must be an administrator to access this feature.' +not_logged_in_security_msg = 'You must be logged in to create/submit sequencing requests' +form_one_name = "Request Form" +form_two_name = "Sample Form" +request_type_name = 'Test Requestype' +sample_states = [ ( 'New', 'Sample entered into the system' ), + ( 'Received', 'Sample tube received' ), + ( 'Done', 'Sequence run complete' ) ] +address1 = dict( short_desc="Office", + name="James Bond", + institution="MI6" , + address1="MI6 Headquaters", + address2="", + city="London", + state="London", + postal_code="007", + country="United Kingdom", + phone="007-007-0007" ) + + +def get_latest_form(form_name): + fdc_list = galaxy.model.FormDefinitionCurrent.filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False )\ + .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) + for fdc in fdc_list: + if form_name == fdc.latest_form.name: + return fdc.latest_form + return None + + +class TestFormsAndRequests( TwillTestCase ): + def test_000_create_form( self ): + """Testing creating a new form and editing it""" + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # create a form + global form_one_name + name = form_one_name + desc = "This is Form One's description" + self.create_form( name=name, desc=desc ) + self.home() + self.visit_page( 'forms/manage' ) + self.check_page_for_string( name ) + self.check_page_for_string( desc ) + # Get the form_definition object for later tests + form_one = galaxy.model.FormDefinition.filter( and_( galaxy.model.FormDefinition.table.c.name==name, + galaxy.model.FormDefinition.table.c.desc==desc ) ).all()[-1] + assert form_one is not None, 'Problem retrieving form named "%s" from the database' % name + # edit form & add few more fields + new_name = "Request Form (Renamed)" + new_desc = "This is Form One's Re-described" + self.edit_form( form_one.id, form_one.name, new_form_name=new_name, new_form_desc=new_desc ) + self.home() + self.visit_page( 'forms/manage' ) + self.check_page_for_string( new_name ) + self.check_page_for_string( new_desc ) + form_one_name = new_name + def test_005_add_form_fields( self ): + """Testing adding fields to a form definition""" + fields = [dict(name='Test field name one', + desc='Test field description one', + type='TextField', + required='required'), + dict(name='Test field name two', + desc='Test field description two', + type='AddressField', + required='optional')] + form_one = get_latest_form(form_one_name) + self.form_add_field(form_one.id, form_one.name, field_index=len(form_one.fields), fields=fields) + form_one_latest = get_latest_form(form_one_name) + assert len(form_one_latest.fields) == len(form_one.fields)+len(fields) +#This following test has been commented out as it is causing: +#TwillException: multiple matches to "remove_button" +# def test_010_remove_form_fields( self ): +# """Testing removing fields from a form definition""" +# form_one = get_latest_form(form_one_name) +# self.form_remove_field( form_one.id, form_one.name, 'Test field name one' ) +# form_one_latest = get_latest_form(form_one_name) +# assert len(form_one_latest.fields) == len(form_one.fields)-1 + def test_015_create_sample_form( self ): + """Testing creating another form (for samples)""" + global form_two_name + name = form_two_name + desc = "This is Form One's description" + self.create_form( name=name, desc=desc ) + self.home() + self.visit_page( 'forms/manage' ) + self.check_page_for_string( name ) + self.check_page_for_string( desc ) + def test_020_create_request_type( self ): + """Testing creating a new requestype""" + request_form = get_latest_form(form_one_name) + sample_form = get_latest_form(form_two_name) + self.create_request_type(request_type_name, "test request type", + str(request_form.id), str(sample_form.id), sample_states ) + global request_type + request_type = galaxy.model.RequestType.filter( and_( galaxy.model.RequestType.table.c.name==request_type_name ) ).all()[-1] + assert request_type is not None, 'Problem retrieving request type named "%s" from the database' % request_type_name + def test_025_create_address_and_library( self ): + """Testing address & library creation""" + # first create a regular user + self.logout() + self.login( email='test1(a)bx.psu.edu' ) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # first create a library for the request so that it can be submitted later + lib_name = 'TestLib001' + self.create_library( lib_name, '' ) + self.visit_page( 'admin/browse_libraries' ) + self.check_page_for_string( lib_name ) + # Get the library object for later tests + global library_one + library_one = galaxy.model.Library.filter( and_( galaxy.model.Library.table.c.name==lib_name, + galaxy.model.Library.table.c.deleted==False ) ).first() + assert library_one is not None, 'Problem retrieving library named "%s" from the database' % lib_name + global admin_user + admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ).first() + assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' + # Get the admin user's private role for later use + global admin_user_private_role + admin_user_private_role = None + for role in admin_user.all_roles(): + if role.name == admin_user.email and role.description == 'Private Role for %s' % admin_user.email: + admin_user_private_role = role + break + if not admin_user_private_role: + raise AssertionError( "Private role not found for user '%s'" % admin_user.email ) + global regular_user1 + regular_user1 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() + assert regular_user1 is not None, 'Problem retrieving user with email "test1(a)bx.psu.edu" from the database' + # Get the regular user's private role for later use + global regular_user1_private_role + regular_user1_private_role = None + for role in regular_user1.all_roles(): + if role.name == regular_user1.email and role.description == 'Private Role for %s' % regular_user1.email: + regular_user1_private_role = role + break + if not regular_user1_private_role: + raise AssertionError( "Private role not found for user '%s'" % regular_user1.email ) + # Set permissions on the library, sort for later testing + permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] + permissions_out = [] + # Role one members are: admin_user, regular_user1. Each of these users will be permitted to + # LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE for library items. + self.set_library_permissions( str( library_one.id ), library_one.name, str( regular_user1_private_role.id ), permissions_in, permissions_out ) + # create address + #self.create_address( user_address1 ) + #self.check_page_for_string( 'Address <b>%s</b> has been added' % user_address1[ 'short_desc' ] ) + ## TODO: FIX HACK + ## the user address creation should be done as a test. + global user_address + user_address = galaxy.model.UserAddress() + user_address.user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() + user_address.desc = address1[ 'short_desc' ] + user_address.name = address1[ 'name' ] + user_address.institution = address1[ 'institution' ] + user_address.address = address1[ 'address1' ]+' '+address1[ 'address2' ] + user_address.city = address1[ 'city' ] + user_address.state = address1[ 'state' ] + user_address.postal_code = address1[ 'postal_code' ] + user_address.country = address1[ 'country' ] + user_address.phone = address1[ 'phone' ] + user_address.flush() + user_address.user.refresh() + def test_030_create_request( self ): + """Testing creating, editing and submitting a request as a regular user""" + # login as a regular user + self.logout() + self.login( email='test1(a)bx.psu.edu' ) + # set field values + fields = ['field one value', 'field two value', str(user_address.id)] + # create the request + request_name, request_desc = 'Request One', 'Request One Description' + self.create_request(request_type.id, request_name, request_desc, library_one.id, fields) + self.check_page_for_string( request_name ) + self.check_page_for_string( request_desc ) + global request_one + request_one = galaxy.model.Request.filter( and_( galaxy.model.Request.table.c.name==request_name, + galaxy.model.Request.table.c.deleted==False ) ).first() + # check if the request's state is now set to 'unsubmitted' + assert request_one.state is not request_one.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.UNSUBMITTED ) + # sample fields + samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), + ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] + # add samples to this request + self.add_samples( request_one.id, request_one.name, samples ) + for sample_name, fields in samples: + self.check_page_for_string( sample_name ) + self.check_page_for_string( 'Unsubmitted' ) + for field_value in fields: + self.check_page_for_string( field_value ) + # edit this request + fields = ['field one value (editted)', 'field two value (editted)', str(user_address.id)] + self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, fields) + request_one.refresh() + self.check_page_for_string( request_name+' (Renamed)' ) + self.check_page_for_string( request_desc+' (Re-described)' ) + # submit the request + self.submit_request( request_one.id, request_one.name ) + request_one.refresh() + # check if the request's state is now set to 'submitted' + assert request_one.state is not request_one.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.SUBMITTED ) + def test_035_request_lifecycle( self ): + """Testing request lifecycle as it goes through all the states""" + # goto admin manage requests page + self.logout() + self.login( email='test(a)bx.psu.edu' ) + self.home() + self.visit_page( 'requests_admin/list' ) + self.check_page_for_string( request_one.name ) + self.visit_url( "%s/requests_admin/list?sort=-create_time&operation=show_request&id=%s" \ + % ( self.url, self.security.encode_id( request_one.id ) )) + self.check_page_for_string( 'Sequencing Request "%s"' % request_one.name ) + # set bar codes for the samples + bar_codes = [ '1234567890', '0987654321' ] + self.add_bar_codes( request_one.id, request_one.name, bar_codes ) + self.check_page_for_string( 'Bar codes has been saved for this request' ) + # change the states of all the samples of this request + for sample in request_one.samples: + self.change_sample_state( sample.name, sample.id, request_type.states[1].id ) + self.check_page_for_string( request_type.states[1].name ) + self.check_page_for_string( request_type.states[1].desc ) + self.change_sample_state( sample.name, sample.id, request_type.states[2].id ) + self.check_page_for_string( request_type.states[2].name ) + self.check_page_for_string( request_type.states[2].desc ) + self.home() + request_one.refresh() + # check if the request's state is now set to 'complete' + assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.COMPLETE ) +# def test_40_admin_create_request_on_behalf_of_regular_user( self ): +# """Testing creating and submitting a request as an admin on behalf of a regular user""" +# self.logout() +# self.login( email='test(a)bx.psu.edu' ) +## permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] +## permissions_out = [] +## self.set_library_permissions( str( library_one.id ), library_one.name, str( admin_user_private_role.id ), permissions_in, permissions_out ) +# # set field values +# fields = ['field one value', 'field two value', str(user_address.id)] +# # create the request +# request_name, request_desc = 'Request Two', 'Request Two Description' +# self.create_request_admin(request_type.id, regular_user1.id, request_name, request_desc, library_one.id, fields) +# self.check_page_for_string( request_name ) +# self.check_page_for_string( request_desc ) +# global request_two +# request_one = galaxy.model.Request.filter( and_( galaxy.model.Request.table.c.name==request_name, +# galaxy.model.Request.table.c.deleted==False ) ).first() +# # check if the request's state is now set to 'unsubmitted' +# assert request_two.state is not request_two.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.UNSUBMITTED ) +# # sample fields +# samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), +# ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] +# # add samples to this request +# self.add_samples( request_two.id, request_two.name, samples ) +# for sample_name, fields in samples: +# self.check_page_for_string( sample_name ) +# self.check_page_for_string( 'Unsubmitted' ) +# for field_value in fields: +# self.check_page_for_string( field_value ) +# # submit the request +# self.submit_request( request_two.id, request_two.name ) +# request_two.refresh() +# # check if the request's state is now set to 'submitted' +# assert request_two.state is not request_two.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.SUBMITTED ) + + + + + + + \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Sat Aug 22 23:18:47 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Sat Aug 22 23:20:09 2009 -0400 @@ -196,7 +196,7 @@ dhps.sort() # Compare DefaultHistoryPermissions and actions_in - should be the same if dhps != actions_in: - raise AssertionError( 'DefaultHistoryPermissions "%s" for history id %d differ from actions "%s" passed for changing' \ + raise AssertionError( 'DefaultHistoryPermissions "%s" for history id %d differ from actions "%s" passed for changing' \ % ( str( dhps ), latest_history.id, str( actions_in ) ) ) # Make sure DatasetPermissionss are correct if len( latest_dataset.actions ) != len( latest_history.default_permissions ): @@ -209,7 +209,7 @@ dps.sort() # Compare DatasetPermissionss and DefaultHistoryPermissions - should be the same if dps != dhps: - raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s"' \ + raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s"' \ % ( str( dps ), latest_dataset.id, str( dhps ) ) ) self.logout() def test_020_create_new_user_account_as_admin( self ): diff -r fbad627b45ac -r e6dda627e6b0 tools/extract/liftOver_wrapper_code.py --- a/tools/extract/liftOver_wrapper_code.py Sat Aug 22 23:18:47 2009 -0400 +++ b/tools/extract/liftOver_wrapper_code.py Sat Aug 22 23:20:09 2009 -0400 @@ -3,7 +3,6 @@ to_dbkey = param_dict['to_dbkey'].split('.')[0].split('To')[1] to_dbkey = to_dbkey[0].lower()+to_dbkey[1:] out_data['out_file1'].set_dbkey(to_dbkey) - out_data['out_file2'].set_dbkey(to_dbkey) out_data['out_file1'].name = out_data['out_file1'].name + " [ MAPPED COORDINATES ]" out_data['out_file2'].name = out_data['out_file2'].name + " [ UNMAPPED COORDINATES ]" diff -r fbad627b45ac -r e6dda627e6b0 tools/metag_tools/split_paired_reads.py --- a/tools/metag_tools/split_paired_reads.py Sat Aug 22 23:18:47 2009 -0400 +++ b/tools/metag_tools/split_paired_reads.py Sat Aug 22 23:20:09 2009 -0400 @@ -1,7 +1,7 @@ #! /usr/bin/python """ -Split Solexa paired end reads +Split fixed length paired end reads """ import os, sys @@ -12,9 +12,13 @@ outfile_end1 = open(sys.argv[2], 'w') outfile_end2 = open(sys.argv[3], 'w') - for i, line in enumerate(file(infile)): + i = 0 + + for line in file( infile ): line = line.rstrip() - if not line or line.startswith('#'): continue + + if not line: + continue end1 = '' end2 = '' @@ -42,5 +46,9 @@ outfile_end1.write('%s\n' %(end1)) outfile_end2.write('%s\n' %(end2)) + i += 1 + + if i % 4 != 0 : + sys.stderr.write("WARNING: Number of lines in the input file was not divisible by 4.\nCheck consistency of the input fastq file.\n") outfile_end1.close() outfile_end2.close() \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 tools/solid_tools/maq_cs_wrapper.py --- a/tools/solid_tools/maq_cs_wrapper.py Sat Aug 22 23:18:47 2009 -0400 +++ b/tools/solid_tools/maq_cs_wrapper.py Sat Aug 22 23:20:09 2009 -0400 @@ -48,9 +48,9 @@ cmd1 = "solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,tmps.name,f3_read_fname,f3_qual_fname,r3_read_fname,r3_qual_fname) try: os.system(cmd1) - os.system('zcat -f %s >> %s' %(tmpf.name,tmpffastq.name)) - os.system('zcat -f %s >> %s' %(tmpr.name,tmprfastq.name)) - os.system('zcat -f %s >> %s' %(tmps.name,tmpsfastq.name)) + os.system('gunzip -c %s >> %s' %(tmpf.name,tmpffastq.name)) + os.system('gunzip -c %s >> %s' %(tmpr.name,tmprfastq.name)) + os.system('gunzip -c %s >> %s' %(tmps.name,tmpsfastq.name)) except Exception, eq: stop_err("Error converting data to fastq format." + str(eq)) @@ -135,7 +135,7 @@ cmd1 = "solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,None,None,f3_read_fname,f3_qual_fname,None,None) try: os.system(cmd1) - os.system('zcat -f %s >> %s' %(tmpf.name,tmpfastq.name)) + os.system('gunzip -c %s >> %s' %(tmpf.name,tmpfastq.name)) tmpf.close() except: stop_err("Error converting data to fastq format.")

1 0

[hg] galaxy 2608: [mq]: pages
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/19b86ccccf6f changeset: 2608:19b86ccccf6f user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 12:26:46 2009 -0400 description: [mq]: pages 5 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0014_pages.py lib/galaxy/web/controllers/user.py templates/user/index.mako diffs (220 lines): diff -r 77b761ff6cd3 -r 19b86ccccf6f lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Sun Aug 23 09:22:19 2009 -0400 +++ b/lib/galaxy/model/__init__.py Sun Aug 23 12:26:46 2009 -0400 @@ -33,6 +33,7 @@ self.external = False self.deleted = False self.purged = False + self.username = None # Relationships self.histories = [] @@ -1118,7 +1119,20 @@ self.country+'<br/>'+ \ 'Phone: '+self.phone +class Page( object ): + def __init__( self ): + self.id = None + self.user = None + self.title = None + self.slug = None + self.latest_revision_id = None + self.revisions = [] +class PageRevision( object ): + def __init__( self ): + self.user = None + self.title = None + self.content = None diff -r 77b761ff6cd3 -r 19b86ccccf6f lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Sun Aug 23 09:22:19 2009 -0400 +++ b/lib/galaxy/model/mapping.py Sun Aug 23 12:26:46 2009 -0400 @@ -42,6 +42,7 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "email", TrimmedString( 255 ), nullable=False ), + Column( "username", TrimmedString( 255 ), index=True, unique=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ), @@ -523,6 +524,26 @@ Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), Column( "comment", TEXT ) ) +Page.table = Table( "page", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + 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 ), + ) + +PageRevision.table = Table( "page_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "content", TEXT ) + ) + # With the tables defined we can define the mappers and setup the # relationships between the model objects. @@ -905,6 +926,18 @@ assign_mapper( context, MetadataFile, MetadataFile.table, properties=dict( history_dataset=relation( HistoryDatasetAssociation ), library_dataset=relation( LibraryDatasetDatasetAssociation ) ) ) +assign_mapper( context, PageRevision, PageRevision.table ) + +assign_mapper( context, Page, Page.table, + properties=dict( user=relation( User ), + revisions=relation( PageRevision, backref='page', + cascade="all, delete-orphan", + primaryjoin=( Page.table.c.id == PageRevision.table.c.page_id ) ), + latest_revision=relation( PageRevision, post_update=True, + primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), + lazy=False ) + ) ) + def db_next_hid( self ): """ Override __next_hid to generate from the database in a concurrency diff -r 77b761ff6cd3 -r 19b86ccccf6f lib/galaxy/model/migrate/versions/0014_pages.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0014_pages.py Sun Aug 23 12:26:46 2009 -0400 @@ -0,0 +1,56 @@ +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 ) + +Page_table = Table( "page", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + 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 ), + ) + +PageRevision_table = Table( "page_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "content", TEXT ) + ) + +def upgrade(): + metadata.reflect() + try: + Page_table.create() + except: + log.debug( "Could not create page table" ) + try: + PageRevision_table.create() + except: + log.debug( "Could not create page_revision table" ) + + # Add 1 column to the user table + User_table = Table( "galaxy_user", metadata, autoload=True ) + col = Column( 'username', String(255), index=True, unique=True, default=False ) + print type( col ), col + col.create( User_table ) + assert col is User_table.c.username + +def downgrade(): + metadata.reflect() + Page_table.drop() + PageRevision_table.drop() + User_table = Table( "galaxy_user", metadata, autoload=True ) + User_table.c.username.drop() \ No newline at end of file diff -r 77b761ff6cd3 -r 19b86ccccf6f lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Sun Aug 23 09:22:19 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Sun Aug 23 12:26:46 2009 -0400 @@ -4,7 +4,7 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy import util -import logging, os, string +import logging, os, string, re from random import choice log = logging.getLogger( __name__ ) @@ -19,6 +19,8 @@ """ require_login_nocreation_template = require_login_template % "" require_login_creation_template = require_login_template % " If you don't already have an account, <a href='%s'>you may create one</a>." + +VALID_USERNAME_RE = re.compile( "^[a-zA-Z0-9\-\_]+$" ) class User( BaseController ): edit_address_id = None @@ -78,6 +80,37 @@ .add_text( "email", "Email", value=email, error=email_err ) .add_text( "conf_email", "Confirm Email", value='', error=conf_email_err ) .add_password( "password", "Password", value='', error=pass_err ) ) + + @web.expose + def change_username(self, trans, username='', **kwd): + username_err = '' + user = trans.get_user() + if not user: + trans.response.send_redirect( web.url_for( action='login' ) ) + if trans.request.method == "POST": + if len( username ) < 4: + username_err = "Username must be at least 4 characters in length" + elif len( username ) > 255: + username_err = "USername must be at most 255 characters in length" + elif not( VALID_USERNAME_RE.match( username ) ): + username_err = "Username must contain only letters, numbers, '-', and '_'" + elif trans.app.model.User.filter_by( username=username ).first(): + username_err = "This username is not available" + else: + user.username = username + user.flush() + trans.log_event( "User change username" ) + return trans.show_ok_message( "Username been set to: " + user.username ) + else: + username = user.username or '' + return trans.show_form( + web.FormBuilder( web.url_for(), "Change username", submit_text="Submit" ) + .add_text( "username", "Username", value=username, error=username_err, + help="""Your username is an optional identifier that + will be used to generate adresses for information + you share publicly. Usernames must be at least + four characters in length and contain only letters, + numbers, and the '-' and '_' characters""" ) ) @web.expose def login( self, trans, email='', password='' ): diff -r 77b761ff6cd3 -r 19b86ccccf6f templates/user/index.mako --- a/templates/user/index.mako Sun Aug 23 09:22:19 2009 -0400 +++ b/templates/user/index.mako Sun Aug 23 12:26:46 2009 -0400 @@ -9,6 +9,7 @@ <ul> <li><a href="${h.url_for( action='change_password' )}">${_('Change your password')}</a></li> <li><a href="${h.url_for( action='change_email' )}">${_('Update your email address')}</a></li> + <li><a href="${h.url_for( action='change_username' )}">${_('Change your public username')}</a></li> <li><a href="${h.url_for( action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> <li><a href="${h.url_for( action='manage_addresses' )}">${_('Manage your addresses')}</a></li> <li><a href="${h.url_for( action='logout' )}">${_('Logout')}</a></li>

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galaxy-dev August 2009