mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
@@ -726,6 +726,8 @@
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<datatype extension="ideaspre" type="galaxy.datatypes.genetics:IdeasPre" display_in_upload="true"/>
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<!-- End IDEAS datatypes -->
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<datatype extension="sbml" type="galaxy.datatypes.xml:Sbml" mimetype="application/xml" display_in_upload="true"/>
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<datatype extension="spalndbnp" type="galaxy.datatypes.spaln:SpalnNuclDb" display_in_upload="true" />
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<datatype extension="spalndba" type="galaxy.datatypes.spaln:SpalnProtDb" display_in_upload="true" />
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</registration>
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<sniffers>
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<!--
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@@ -0,0 +1,213 @@
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"""
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spaln Composite Dataset
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"""
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import io
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import logging
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import os.path
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from galaxy.datatypes.data import Data
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from galaxy.datatypes.metadata import MetadataElement
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from galaxy.util import smart_str
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log = logging.getLogger(__name__)
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verbose = True
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class _SpalnDb(Data):
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allow_datatype_change = False
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composite_type = "auto_primary_file"
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MetadataElement(
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name="spalndb_name",
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default="spalndb",
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desc="DB name",
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readonly=True,
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visible=True,
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set_in_upload=True,
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)
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def __init__(self, **kwd):
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super(_SpalnDb, self).__init__(**kwd)
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self.add_composite_file(
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"%s.ent",
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is_binary=True,
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description="spalndb.ent",
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substitute_name_with_metadata="spalndb_name",
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)
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self.add_composite_file(
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"%s.grp",
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is_binary=True,
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description="spalndb.grp",
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substitute_name_with_metadata="spalndb_name",
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)
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self.add_composite_file(
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"%s.idx",
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is_binary=True,
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description="spalndb.idx",
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substitute_name_with_metadata="spalndb_name",
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)
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self.add_composite_file(
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"%s.seq",
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is_binary=True,
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description="spalndb.seq",
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substitute_name_with_metadata="spalndb_name",
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)
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def generate_primary_file(self, dataset=None):
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rval = ["<html><head><title>Spaln Database</title></head><p/>"]
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rval.append(
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"<div>This composite dataset is composed of the following files:<p/><ul>"
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)
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for composite_name, composite_file in self.get_composite_files(
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dataset=dataset
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).items():
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fn = composite_name
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opt_text = ""
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if composite_file.get("description"):
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rval.append(
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'<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>'
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% (fn, fn, composite_file.get("description"), opt_text)
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)
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else:
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rval.append(
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'<li><a href="%s" type="application/binary">%s</a>%s</li>'
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% (fn, fn, opt_text)
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)
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rval.append("</ul></div></html>")
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return "\n".join(rval)
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def regenerate_primary_file(self, dataset):
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"""
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cannot do this until we are setting metadata
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"""
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efp = dataset.extra_files_path
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flist = os.listdir(efp)
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rval = [
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"<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>"
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% (dataset.name, dataset.name)
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]
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for i, fname in enumerate(flist):
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sfname = os.path.split(fname)[-1]
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f, e = os.path.splitext(fname)
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rval.append('<li><a href="%s">%s</a></li>' % (sfname, sfname))
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rval.append("</ul></body></html>")
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with open(dataset.file_name, "w") as f:
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f.write("\n".join(rval))
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f.write("\n")
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def set_peek(self, dataset, is_multi_byte=False):
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"""Set the peek and blurb text."""
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if not dataset.dataset.purged:
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dataset.peek = "spaln database (multiple files)"
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dataset.blurb = "spaln database (multiple files)"
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else:
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dataset.peek = "file does not exist"
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dataset.blurb = "file purged from disk"
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def display_peek(self, dataset):
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"""Create HTML content, used for displaying peek."""
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try:
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return dataset.peek
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except Exception:
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return "spaln database (multiple files)"
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def display_data(
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self,
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trans,
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data,
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preview=False,
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filename=None,
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to_ext=None,
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size=None,
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offset=None,
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**kwd
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):
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"""
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If preview is `True` allows us to format the data shown in the central pane via the "eye" icon.
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If preview is `False` triggers download.
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"""
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if not preview:
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return super(_SpalnDb, self).display_data(
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trans,
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data=data,
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preview=preview,
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filename=filename,
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to_ext=to_ext,
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size=size,
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offset=offset,
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**kwd
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)
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if self.file_ext == "spalndbn":
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title = "This is a nucleotide-query spaln database"
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elif self.file_ext == "spalndbp":
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title = "This is a protein-query spaln database"
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elif self.file_ext == "spalndba":
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title = "This is a protein spaln database"
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else:
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# Error?
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title = "This is a spaln database (unknown format)."
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msg = ""
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try:
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# Try to use any text recorded in the dummy index file:
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with io.open(data.file_name, "rU", encoding="utf-8") as handle:
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msg = handle.read().strip()
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except Exception:
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pass
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if not msg:
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msg = title
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# Galaxy assumes HTML for the display of composite datatypes,
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return smart_str(
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"<html><head><title>%s</title></head><body><pre>%s</pre></body></html>"
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% (title, msg)
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)
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def merge(split_files, output_file):
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"""Merge spaln databases (not implemented)."""
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raise NotImplementedError("Merging spaln databases is not possible")
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def split(cls, input_datasets, subdir_generator_function, split_params):
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"""Split a spaln database (not implemented)."""
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if split_params is None:
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return None
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raise NotImplementedError("Can't split spaln database")
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def set_meta(self, dataset, **kwd):
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super(_SpalnDb, self).set_meta(dataset, **kwd)
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efp = dataset.extra_files_path
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for filename in os.listdir(efp):
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if filename.endswith(".ent"):
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dataset.metadata.spalndb_name = os.path.splitext(filename)[0]
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self.regenerate_primary_file(dataset)
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class SpalnNuclDb(_SpalnDb):
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file_ext = "spalndbnp"
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def __init__(self, **kwd):
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super(SpalnNuclDb, self).__init__(**kwd)
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self.add_composite_file(
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"%s.bkn",
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is_binary=True,
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description="spalndb.bkn",
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substitute_name_with_metadata="spalndb_name",
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)
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self.add_composite_file(
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"%s.bkp",
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is_binary=True,
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description="spalndb.bkp",
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substitute_name_with_metadata="spalndb_name",
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)
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class SpalnProtDb(_SpalnDb):
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file_ext = "spalndba"
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def __init__(self, **kwd):
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super(SpalnProtDb, self).__init__(**kwd)
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self.add_composite_file(
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"%s.bka",
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is_binary=True,
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description="spalndb.bka",
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substitute_name_with_metadata="spalndb_name",
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)
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