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Changeset 149

Timestamp:

08/05/10 18:28:38 (18 months ago)

Author:

mauro

Message:

plone4

Location:

plone4bio.base/trunk

Files:

: 2 added
: 1 removed
: 12 modified

docs/CHANGES.txt (modified) (1 diff)
plone3.cfg (deleted)
setup.py (modified) (2 diffs)
src/plone4bio/base/browser/configure.zcml (modified) (1 diff)
src/plone4bio/base/browser/javascripts (added)
src/plone4bio/base/browser/javascripts/plone4bio.js (added)
src/plone4bio/base/browser/templates/annotations.pt (modified) (2 diffs)
src/plone4bio/base/browser/templates/features.pt (modified) (1 diff)
src/plone4bio/base/browser/templates/seqrecord.pt (modified) (5 diffs)
src/plone4bio/base/configure.zcml (modified) (1 diff)
src/plone4bio/base/content/configure.zcml (modified) (1 diff)
src/plone4bio/base/content/seqrecord.py (modified) (6 diffs)
src/plone4bio/base/png/seqrecord.py (modified) (2 diffs)
src/plone4bio/base/profiles/default/jsregistry.xml (modified) (1 diff)
src/plone4bio/base/profiles/default/metadata.xml (modified) (1 diff)

Legend:

: Unmodified
: Added
: Removed

plone4bio.base/trunk/docs/CHANGES.txt

r141	r149
2	2	plone4bio.base Changes
3	3	======================
	4
	5	plone4bio.base 1.1.0 (unreleased)
	6	=================================
	7
	8	Features
	9	--------
	10
	11	* works with Plone 4.x
	12
	13	* use plone4bio.graphics instead BioPerl's stuff
4	14
5	15	plone4bio.base 1.0.2 (2010-06-03)

plone4bio.base/trunk/setup.py

r128	r149
2	2	import os
3	3
4		version = '1.~~0.2~~'
	4	version = '1.1.0'
5	5
6	6	setup(name='plone4bio.base',
…	…
33	33	'setuptools',
34	34	# -- Extra requirements: --
	35	'plone.app.registry',
	36	'collective.js.jqueryui',
35	37	'numpy',
36	38	'biopython',

plone4bio.base/trunk/src/plone4bio/base/browser/configure.zcml

r78	r149
121	121	/>
122	122
	123	<browser:resourceDirectory
	124	name="plone4bio.javascripts"
	125	directory="javascripts"
	126	/>
	127
123	128	<browser:resource
124	129	name="plone4bio.css"

plone4bio.base/trunk/src/plone4bio/base/browser/templates/annotations.pt

r45	r149
1		<tal:annotations tal:define="annotations context/annotations;
2		keys python:annotations.keys();
3		keystoignore python:[x for x in keys if x[-7:] == 'protein' ];
4		keys python:list(set(keys).difference(['references','dbxref','dates','gi','id']+keystoignore));
5		keysgroups python:[x.split('_')[0] for x in keys];
6		keysgroups python:list(set(keysgroups));
7		sorting python:keysgroups.sort()"
8		tal:repeat="keygroup keysgroups">
9		<dl tal:attributes="id string:group-${keygroup}" class="collapsible inline collapsedOnLoad">
10		<dt class="collapsibleHeader" tal:content="keygroup">keygroup</dt>
11		<dd class="collapsibleContent">
12		<table class="listing" summary="Annotations" style="width:100%">
13		<tr><th colspan="2" tal:content="keygroup" style="text-align:left" style="width:100%"/></tr>
14		<tal:annotgroup tal:define="subannots python:[key for key in keys if key.startswith(keygroup)];
15		sorting python:subannots.sort();"
16		tal:repeat="subannot subannots">
17		<tr style="width:100%"
18		tal:define="oddrow repeat/subannot/odd;
	1	<div id="accordion-annotations">
	2	<tal:annotations tal:define="annotations context/annotations;
	3	keys python:annotations.keys();
	4	keystoignore python:[x for x in keys if x[-7:] == 'protein' ];
	5	keys python:list(set(keys).difference(['references','dbxref','dates','gi','id']+keystoignore));
	6	keysgroups python:[x.split('_')[0] for x in keys];
	7	keysgroups python:list(set(keysgroups));
	8	sorting python:keysgroups.sort()"
	9	tal:repeat="keygroup keysgroups">
	10	<h3><a href="#" tal:content="keygroup">keygroup</a></h3>
	11	<div>
	12	<table class="listing" summary="Annotations" style="width:100%">
	13	<tal:annotgroup tal:define="subannots python:[key for key in keys if key.startswith(keygroup)];
	14	sorting python:subannots.sort();"
	15	tal:repeat="subannot subannots">
	16	<tr tal:define="oddrow repeat/subannot/odd;
19	17	annotdatas python:annotations[subannot];"
20		tal:attributes="class python:(oddrow and 'even' or 'odd');">
21		<td tal:content="subannot" style="width:200px; max-width:200px"/>
22		<td
23		tal:condition="python:isinstance(annotdatas,list) and annotdatas">
24		<ul>
	18	tal:attributes="class python:(oddrow and 'even' or 'odd');">
	19	<td tal:content="subannot" />
	20	<td tal:condition="python:isinstance(annotdatas,list) and annotdatas">
	21	<ul>
25	22	<tal:annotdata tal:define="annotlist python:[];
26	23	annotlistspace python:[];
…	…
28	25	insertspace python:[annotlistspace.append(', '.join(x.split(','))) for x in annotlist]"
29	26	tal:repeat="annotdata annotlistspace">
30		~~<li><span tal:content="annotdata" />~~</li>
	27	<li tal:content="annotdata">annotation data</li>
31	28	</tal:annotdata>
32		</ul>
	29	</ul>
33	30	</td>
34		<td
35		tal:condition="python:isinstance(annotdatas,str) and annotdatas" >
36		<ul>
	31	<td tal:condition="python:isinstance(annotdatas,str) and annotdatas">
	32	<ul>
37	33	<tal:annotdata tal:define="annotlistspace python:[];
38	34	annotdatas python:annotdatas.split('###');
39	35	insertspace python:[annotlistspace.append(', '.join(x.split(','))) for x in annotdatas]"
40	36	tal:repeat="annotdata annotlistspace">
41		~~<li><span tal:content="annotdata" />~~</li>
	37	<li tal:content="annotdata">annotation data</li>
42	38	</tal:annotdata>
43		</ul>
44		</td>
	39	</ul>
	40	</td>
45	41	</tr>
46		</tal:annotgroup>
47		</table>
48		</dd>
49		</dl>
50
51		</tal:annotations>
	42	</tal:annotgroup>
	43	</table>
	44	</div>
	45	</tal:annotations>
	46	</div>

plone4bio.base/trunk/src/plone4bio/base/browser/templates/features.pt

r119	r149
1	1	<div tal:define="featuredict context/features_dict">
2		<tal:imagemap tal:content="structure context/@@imagemap" />
3		<dl>
4		<dd>
5		<div align="center" >
6		<img usemap="#graphicsmap" src="" tal:attributes="src string:${here/absolute_url}/features.png" />
7		</div>
8		</dd>
9		</dl>
10		<tal:features tal:repeat="featuretype featuredict">
11		<dl tal:attributes="id string:group-${featuretype}" class="collapsible inline collapsedOnLoad">
12		<dt class="collapsibleHeader" tal:content="featuretype" >Feature</dt>
13		<dd class="collapsibleContent" >
14		<div tal:define="featureaccessiondict python:featuredict[featuretype];"
15		class="listing" summary="Features" style="width:100%">
16		<tal:featuregroup tal:repeat="featureaccession featureaccessiondict">
17		<table class="listing" summary="FeaturesAccession" style="width:100%"
	2	<tal:imagemap tal:content="structure here/@@imagemap" />
	3	<div align="center" style="overflow: auto; ">
	4	<img style="max-width: none;" usemap="#graphicsmap" src="" tal:attributes="src string:${here/absolute_url}/features.png" />
	5	</div>
	6	<div id="accordion-features">
	7	<tal:features tal:repeat="featuretype featuredict">
	8	<h3><a href="#" tal:content="featuretype">group featuretype</a></h3>
	9	<div tal:define="featureaccessiondict python:featuredict[featuretype];"
	10	class="listing" summary="Features" style="width:100%">
	11	<tal:featuregroup tal:repeat="featureaccession featureaccessiondict">
	12	<table class="listing" summary="FeaturesAccession" style="width:100%"
18	13	tal:define="features python:featureaccessiondict[featureaccession]">
19		<thead>
20		~~<tr><th colspan="3" style="text-align:left" style="width:100%"><b tal:content="featureaccession"/>~~</th></tr>
21		<tr>
	14	<thead>
	15	<tr><th class="nosort" colspan="3" tal:content="featureaccession">feature accession</th></tr>
	16	<tr>
22	17	<th class="nosort">type</th>
23	18	<th class="nosort">location</th>
24	19	<th class="nosort">qualifiers</th>
25		</tr>
26		</thead>
27		<tbody>
28		<tal:features tal:repeat="feature features">
29		<tr
30		tal:define="oddrow repeat/feature/odd;
31		start python:'Start: ' + str(feature.location.start.position + 1);
32		end python:'End: ' + str(feature.location.end.position);"
33		tal:attributes="class python:(oddrow and 'even' or 'odd')">
34		<td><b tal:content="feature/type" /></td>
35		<td tal:content="python:start + ' : ' + end" />
36		<td>
37		<ul>
38		<tal:qualifiers tal:repeat="key feature/qualifiers/keys">
39		<li tal:condition="python:isinstance(feature.qualifiers[key],list)">
40		<b tal:content="key" />: <span tal:content="python:feature.qualifiers[key][0]" />
41		</li>
42		<li tal:condition="python:isinstance(feature.qualifiers[key],str)">
43		<b tal:content="key" />: <span tal:content="python:feature.qualifiers[key]" />
44		</li>
45		</tal:qualifiers>
46		</ul>
47		</td>
48		</tr>
49		</tal:features>
	20	</tr>
	21	</thead>
	22	<tbody>
	23	<tal:features tal:repeat="feature features">
	24	<tr tal:define="oddrow repeat/feature/odd;
	25	start python:'Start: ' + str(feature.location.start.position + 1);
	26	end python:'End: ' + str(feature.location.end.position);"
	27	tal:attributes="class python:(oddrow and 'even' or 'odd')">
	28	<td><strong tal:content="feature/type" /></td>
	29	<td tal:content="python:start + ' : ' + end" />
	30	<td>
	31	<ul>
	32	<tal:qualifiers tal:repeat="key feature/qualifiers/keys">
	33	<li tal:condition="python:isinstance(feature.qualifiers[key],list)">
	34	<strong tal:content="key" />: <span tal:content="python:feature.qualifiers[key][0]" />
	35	</li>
	36	<li tal:condition="python:isinstance(feature.qualifiers[key],str)">
	37	<strong tal:content="key" />: <span tal:content="python:feature.qualifiers[key]" />
	38	</li>
	39	</tal:qualifiers>
	40	</ul>
	41	</td>
	42	</tr>
	43	</tal:features>
50	44	</tbody>
51		</table>
52		</tal:featuregroup>
53		</div>
54		</dd>
55		</dl>
56		</tal:features>
57
	45	</table>
	46	</tal:featuregroup>
	47	</div>
	48	</tal:features>
	49	</div>
58	50	</div>

plone4bio.base/trunk/src/plone4bio/base/browser/templates/seqrecord.pt

r78	r149
1		<html xmlns="http://www.w3.org/1999/xhtml"
2		xmlns:metal="http://xml.zope.org/namespaces/metal"
3		xmlns:tal="http://xml.zope.org/namespaces/tal"
4		xmlns:i18n="http://xml.zope.org/namespaces/i18n"
5		metal:use-macro="context/@@standard_macros/page"
	1	<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"
	2	lang="en"
	3	metal:use-macro="here/main_template/macros/master"
6	4	i18n:domain="plone4bio">
7	5	<head>
…	…
9	7
10	8	<body>
11		<div metal:fill-slot="body">
12
13		<h1 class="documentFirstHeading" tal:content="context/title" />
	9	<div metal:fill-slot="main">
	10	<metal:main-macro define-macro="main">
14	11
	12	<div tal:replace="structure provider:plone.abovecontenttitle" />
	13
	14	<h1 tal:content="object_title\|nothing" class="documentFirstHeading">
	15	Title or id
	16	</h1>
	17
	18	<div tal:replace="structure provider:plone.belowcontenttitle" />
	19
	20	<a href=""
	21	class="link-parent"
	22	tal:define="parent_url python:here.navigationParent(here)"
	23	tal:condition="parent_url"
	24	tal:attributes="href parent_url"
	25	i18n:translate="go_to_parent_url">
	26	Up one level
	27	</a>
	28
	29	<div tal:replace="structure provider:plone.abovecontentbody" />
15	30
16	31	<table class="listing vertical" summary="Main" style="width:100%">
…	…
48	63	<dl class="enableFormTabbing">
49	64	<dt id="fieldsetlegend-annotations" tal:condition="context/annotations">Annotations</dt>
50		<dd id="fieldset-annotations" tal:condition="context/annotations" tal:content="structure ~~context~~/@@annotations" />
	65	<dd id="fieldset-annotations" tal:condition="context/annotations" tal:content="structure here/@@annotations" />
51	66	<dt id="fieldsetlegend-features" tal:condition="context/features">Features</dt>
52		<dd id="fieldset-features" tal:condition="context/features" tal:content="structure ~~context~~/@@features" />
	67	<dd id="fieldset-features" tal:condition="context/features" tal:content="structure here/@@features" />
53	68	<dt id="fieldsetlegend-dbxrefs" tal:condition="context/dbxrefs">Dbxrefs</dt>
54		<dd id="fieldset-dbxrefs" tal:condition="context/dbxrefs" tal:content="structure ~~context~~/@@dbxrefs" />
	69	<dd id="fieldset-dbxrefs" tal:condition="context/dbxrefs" tal:content="structure here/@@dbxrefs" />
55	70	<dt id="fieldsetlegend-sequence">Sequences</dt>
56	71	<dd id="fieldset-sequence">
…	…
85	100
86	101	</dd>
87		~~<dt id="fieldsetlegend-references" tal:condition="context/annotations/references\|python:False~~">References</dt>
88		<dd id="fieldset-references" tal:condition="context/annotations/references\|~~python:False~~">
89		~~<ul~~ tal:define="annotations context/annotations;"
90		tal:condition="python:annotations.has_key('references')">
91		<tal:reference tal:define="references python:annotations['references'];"
92		tal:repeat="ref references">
93		~~<li~~ tal:define="title python:ref.title;
94		refdict python:{};
95		authors python:refdict.update({'Authors' : ref.authors});
96		journal python:refdict.update({'Journal' : ref.journal});
97		location python:refdict.update({'Location' : ref.location});
98		medline python:refdict.update({'Medline' : ref.medline_id});
99		pubmed python:refdict.update({'Pubmed' : ref.pubmed_id});
100		comment python:refdict.update({'Comment' : ref.comment});
101		crc python:refdict.update({'CRC' : ref.consrtm});
102		fields python:['Authors','Journal','Comment','Medline','Pubmed','Location','CRC'];
103		fields python:[x for x in fields if refdict[x]];">
104		<table class="listing" summary="References" style="width:100%">
105		<tr><th colspan="2" tal:content="python:'Title: ' + title" style="text-align:left" style="width:100%"/></tr>
	102	<dt id="fieldsetlegend-references" tal:condition="context/annotations/references\|nothing">References</dt>
	103	<dd id="fieldset-references" tal:condition="context/annotations/references\|nothing">
	104	<tal:annotations tal:define="annotations context/annotations;"
	105	tal:condition="python:annotations.has_key('references')">
	106	<tal:reference tal:define="references python:annotations['references'];"
	107	tal:repeat="ref references">
	108	<div tal:define="title python:ref.title;
	109	refdict python:{};
	110	authors python:refdict.update({'Authors' : ref.authors});
	111	journal python:refdict.update({'Journal' : ref.journal});
	112	location python:refdict.update({'Location' : ref.location});
	113	medline python:refdict.update({'Medline' : ref.medline_id});
	114	pubmed python:refdict.update({'Pubmed' : ref.pubmed_id});
	115	comment python:refdict.update({'Comment' : ref.comment});
	116	crc python:refdict.update({'CRC' : ref.consrtm});
	117	fields python:['Authors','Journal','Comment','Medline','Pubmed','Location','CRC'];
	118	fields python:[x for x in fields if refdict[x]];">
	119	<table class="listing" summary="References" style="width:100%">
	120	<tr><th colspan="2" tal:content="python:'Title: ' + title" style="text-align:left" style="width:100%"/></tr>
106	121	<tal:refdields tal:repeat="field fields">
107	122	<tr tal:define="oddrow repeat/field/odd;"
…	…
134	149	</table>
135	150
136		</li>
	151	</div>
137	152	</tal:reference>
138		~~</ul~~>
	153	</tal:annotations>
139	154	</dd>
140	155	</dl>
	156	</metal:main-macro>
	157
141	158	</div>
142	159	</body>

plone4bio.base/trunk/src/plone4bio/base/configure.zcml

r45	r149
8	8
9	9	<!-- Poke dependencies -->
	10	<include package="plone.app.registry" />
	11	<include package="collective.js.jqueryui" />
10	12
11	13	<!-- Include sub-packages -->

plone4bio.base/trunk/src/plone4bio/base/content/configure.zcml

r45	r149
16	16	name="plone4bio.base.SeqRecord"
17	17	/>
	18
	19	<!--
	20	<adapter factory=".seqrecord.SeqRecordSearchableText" />
	21	-->
18	22
19	23	<class class=".seqrecord.SeqRecord">

plone4bio.base/trunk/src/plone4bio/base/content/seqrecord.py

r45	r149
6	6
7	7	from zope.interface import implements
	8	from zope.component import adapts
8	9	from zope.component.factory import Factory
9	10	from zope.schema.fieldproperty import FieldProperty
	11	# from zope.index.text.interfaces import ISearchableText
10	12
11	13	from plone.locking.interfaces import ITTWLockable
…	…
43	45	def __init__(self, seq=None):
44	46	super(SeqRecordProxy, self).__init__(seq)
45
	47
	48	"""
	49	class SeqRecordSearchableText(object):
	50	adapts(ISeqRecord)
	51	implements(ISearchableText)
	52
	53	def __init__(self, seqrecord):
	54	self.seqrecord = seqrecord
	55
	56	def getSearchableText(self):
	57	return u' '.join(
	58	unicode(v) for v in self.seqrecord.dbxrefs)
	59	"""
	60
46	61	# TODO
47	62	class SeqRecord(Item):
…	…
61	76
62	77	def __init__(self, args, *kwargs):
	78	import pdb; pdb.set_trace()
63	79	seqrecord = None
64	80	if kwargs.has_key('seqrecord'):
65	81	seqrecord = kwargs['seqrecord']
66	82	del(kwargs['seqrecord'])
	83	if kwargs.has_key('parent'):
	84	parent = kwargs['parent']
	85	del(kwargs['parent'])
	86	kwargs['title'] = unicode(kwargs.get('title', ''))
67	87	super(SeqRecord, self).__init__(args, *kwargs)
68	88	if seqrecord:
…	…
73	93	def Accession(self):
74	94	return self.id
75
	95
76	96	def Name(self):
77	97	return self.title
…	…
82	102	else:
83	103	return None
84
	104
85	105	@property
86	106	def seqrecord(self):
…	…
288	308	return {}
289	309	"""
290
	310
291	311	seqRecordFactory = Factory(SeqRecord, title=_(u"Create a new SeqRecord"))

plone4bio.base/trunk/src/plone4bio/base/png/seqrecord.py

r119	r149
11	11	from plone4bio.base.png.interfaces import IImagemapPresentation
12	12
13		from StringIO import StringIO
	13	from Bio import SeqIO
	14	from cStringIO import StringIO
	15	import logging
14	16
15		# BioPerl
16		import subprocess
17		import os
18		from Bio import SeqIO
	17	logger = logging.getLogger('plone4bio.base')
	18
	19	try:
	20	from plone4bio.graphics.seqrecord import SeqRecordDrawer
	21	has_plone4bio_graphics = True
	22	except ImportError:
	23	logger.warning("missing plone4bio.graphics")
	24	# BioPerl
	25	import subprocess
	26	import os
	27	has_plone4bio_graphics = False
	28
	29
	30	@adapter(ISeqRecord, IRequest)
	31	@implementer(IImagemapPresentation)
	32	def seqrecordImagemap(context, request):
	33	# FIXME: XXX
	34	context.Description()
	35	seqrecord = context.seqrecord
	36	if has_plone4bio_graphics:
	37	imagemap = """<map name="graphicsmap" id="graphicsmap">\n"""
	38	for box in SeqRecordDrawer(seqrecord, fig_width=1500).boxes():
	39	box['start'] = box['feature'].start
	40	box['end'] = box['feature'].end
	41	box['tag'] = box['feature'].name
	42	# my $tag = eval {$feature->method} \|\| $feature->primary_tag;
	43	# $left += $pad_left;
	44	# $right += $pad_left;
	45	# next unless $tag;
	46	imagemap = imagemap + \
	47	"""<area class="tips" shape="rect" """ \
	48	"""coords="%(left)i,%(top)i,%(right)i,%(bottom)i" href="#" """ \
	49	"""rel="#%(tag)sX%(start)sX$%(end)s" title="%(tag)s %(start)s:%(end)s" alt="" />""" \
	50	% box
	51	imagemap = imagemap + "</map>\n"
	52	return imagemap
	53	else:
	54	# BIOPERL
	55	perlpath = os.sep.join((os.path.dirname(__file__), "perl"))
	56	cmd = ["perl", "-I"+ perlpath, os.sep.join((perlpath, "graphics-imagemap-cmd.pl")), "-"]
	57	graphics = subprocess.Popen(cmd, stdout=subprocess.PIPE, stdin=subprocess.PIPE)
	58	genbank=StringIO()
	59	seqrecord.name = seqrecord.name[:16]
	60	for f in seqrecord.features:
	61	f.type = f.type.replace(" ", "_")
	62	SeqIO.write([seqrecord, ], genbank, "genbank")
	63	(stdoutdata, stderrdata) = graphics.communicate(genbank.getvalue())
	64	return stdoutdata
	65
	66	@adapter(ISeqRecord, IRequest)
	67	@implementer(IPNGPresentation)
	68	def seqrecordPNG(context, request):
	69	# FIXME: XXX
	70	context.Description()
	71	seqrecord = context.seqrecord
	72	if has_plone4bio_graphics:
	73	imgdata=StringIO()
	74	SeqRecordDrawer(seqrecord, fig_width=1500).save(imgdata, format='PNG')
	75	return imgdata.getvalue()
	76	else:
	77	# BioPerl
	78	# prediction.getDataCharts() =
	79	# [{'chart':(line,bar,...),'data':[(x,y),(x,y),...}, ...]
	80	perlpath = os.sep.join((os.path.dirname(__file__), "perl"))
	81	cmd = ["perl", "-I"+ perlpath, os.sep.join((perlpath, "graphics-cmd.pl")), "-"]
	82	graphics = subprocess.Popen(cmd, stdout=subprocess.PIPE, stdin=subprocess.PIPE)
	83	genbank=StringIO()
	84	seqrecord.name = seqrecord.name[:16]
	85	for f in seqrecord.features:
	86	f.type = f.type.replace(" ", "_")
	87	SeqIO.write([seqrecord, ], genbank, "genbank")
	88	(stdoutdata, stderrdata) = graphics.communicate(genbank.getvalue())
	89	return stdoutdata
19	90
20	91	class PNGFeaturesView(BrowserPage):
…	…
27	98	class ImagemapFeaturesView(BrowserView):
28	99	def __call__(self):
29		return getMultiAdapter((self.context, self.request), IImagemapPresentation)
	100	return seqrecordImagemap(self.context, self.request)
	101	# return getMultiAdapter((self.context, self.request), IImagemapPresentation)
30	102
31		~~# TODO: refactoring with genometools (?)~~
32		~~@adapter(ISeqRecord, IRequest)~~
33		~~@implementer(IImagemapPresentation)~~
34		~~def seqrecordImagemap(context, request):~~
35		~~perlpath = os.sep.join((os.path.dirname(__file__), "perl"))~~
36		~~cmd = ["perl", "-I"+ perlpath, os.sep.join((perlpath, "graphics-imagemap-cmd.pl")), "-"]~~
37		~~graphics = subprocess.Popen(cmd, stdout=subprocess.PIPE, stdin=subprocess.PIPE)~~
38		~~# FIXME: XXX~~
39		~~context.Description()~~
40		~~genbank=StringIO()~~
41		~~seqrecord = context.seqrecord~~
42		~~seqrecord.name = seqrecord.name[:16]~~
43		~~for f in seqrecord.features:~~
44		~~f.type = f.type.replace(" ", "_")~~
45		~~SeqIO.write([seqrecord, ], genbank, "genbank")~~
46		~~(stdoutdata, stderrdata) = graphics.communicate(genbank.getvalue())~~
47		~~return stdoutdata~~
48
49		~~# TODO: refactoring with genometools (?)~~
50		~~@adapter(ISeqRecord, IRequest)~~
51		~~@implementer(IPNGPresentation)~~
52		~~def seqrecordPNG(context, request):~~
53		~~# prediction.getDataCharts() = [{'chart':(line,bar,...),'data':[(x,y),(x,y),...}, ...]~~
54
55		~~# BioPerl~~
56		~~perlpath = os.sep.join((os.path.dirname(__file__), "perl"))~~
57		~~cmd = ["perl", "-I"+ perlpath, os.sep.join((perlpath, "graphics-cmd.pl")), "-"]~~
58		~~graphics = subprocess.Popen(cmd, stdout=subprocess.PIPE, stdin=subprocess.PIPE)~~
59		~~# FIXME: XXX~~
60		~~context.Description()~~
61		~~genbank=StringIO()~~
62		~~seqrecord = context.seqrecord~~
63		~~seqrecord.name = seqrecord.name[:16]~~
64		~~for f in seqrecord.features:~~
65		~~f.type = f.type.replace(" ", "_")~~
66		~~SeqIO.write([seqrecord, ], genbank, "genbank")~~
67		~~(stdoutdata, stderrdata) = graphics.communicate(genbank.getvalue())~~
68		~~return stdoutdata~~

plone4bio.base/trunk/src/plone4bio/base/profiles/default/jsregistry.xml

r45	r149
10	10	enabled="1" expression="" id="++resource++plone4bio-imagemap.js"
11	11	insert-after="jquery.js" />
	12	<javascript cacheable="True" compression="safe" cookable="True"
	13	enabled="1" expression="" id="++resource++plone4bio.javascripts/plone4bio.js"
	14	insert-after="jquery.js" />
12	15	</object>
13	16

plone4bio.base/trunk/src/plone4bio/base/profiles/default/metadata.xml

r45	r149
2	2	<metadata>
3	3	<version>1.0.1</version>
	4	<dependencies>
	5	<dependency>profile-plone.app.registry:default</dependency>
	6	</dependencies>
4	7	</metadata>
5	8

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