| Previous changeset 2:3d0a45a3100e (2018-10-19) Next changeset 4:4a9c1e73698e (2018-10-22) |
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Commit message:
Uploaded |
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modified:
datatypes_conf.xml |
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added:
pppmodel.py |
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removed:
ppp_model.py |
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| diff -r 3d0a45a3100e -r 6721b27c06b8 datatypes_conf.xml --- a/datatypes_conf.xml Fri Oct 19 17:35:45 2018 -0400 +++ b/datatypes_conf.xml Mon Oct 22 14:12:12 2018 -0400 |
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| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <datatypes> <datatype_files> - <datatype_file name="ppp_model.py"/> + <datatype_file name="pppmodel.py"/> </datatype_files> <registration> - <datatype extension="pppmodel" type="galaxy.datatypes.pppblah_model:Model" display_in_upload="True"/> + <datatype extension="pppmodel" type="galaxy.datatypes.pppmodel:pppmodel" display_in_upload="True"/> </registration> </datatypes> |
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| diff -r 3d0a45a3100e -r 6721b27c06b8 ppp_model.py --- a/ppp_model.py Fri Oct 19 17:35:45 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,59 +0,0 @@ -from __future__ import print_function - -import gzip -import logging -import os -import shutil -import subprocess -import tempfile -import json - -import pysam -from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE - -from galaxy.datatypes import metadata -from galaxy.datatypes.metadata import DictParameter, ListParameter, MetadataElement, MetadataParameter - -from binary import Binary -from text import Json - -log = logging.getLogger(__name__) - -class Model(Json): - file_ext = ".model" - #edam_format = "format_3746" - - MetadataElement(name="models", default=[], desc="Models", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[]) - MetadataElement(name="npop_dict", default={}, desc="Model population count", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value={}) - - # Update as format becomes more defined - def set_peek(self, dataset, is_multi_byte=False): - if not dataset.dataset.purged: - dataset.blurb = "Model File" - - # Update as format becomes more defined - ''' - def sniff(self, filename): - try: - json.loads(filename.file_name) - return True - except Exception: - return False - ''' - - def set_meta(self, dataset, **kwd): - if dataset.has_data(): - with open(dataset.file_name) as model_file: - try: - model_list = json.load(model_file) - except Exception: - return - - # Assign models - models = [model_dict['name'] for model_dict in model_list if 'name' in model_dict] - - # Assign population count per model - npop_dict = dict([(model_dict['name'], len(model_dict['pops'])) for model_dict in model_list if 'name' in model_dict]) - - dataset.metadata.models = models - dataset.metadata.npop_dict = npop_dict |
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| diff -r 3d0a45a3100e -r 6721b27c06b8 pppmodel.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pppmodel.py Mon Oct 22 14:12:12 2018 -0400 |
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| @@ -0,0 +1,59 @@ +from __future__ import print_function + +import gzip +import logging +import os +import shutil +import subprocess +import tempfile +import json + +import pysam +from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE + +from galaxy.datatypes import metadata +from galaxy.datatypes.metadata import DictParameter, ListParameter, MetadataElement, MetadataParameter + +from binary import Binary +from text import Json + +log = logging.getLogger(__name__) + +class pppmodel(Json): + file_ext = ".model" + #edam_format = "format_3746" + + MetadataElement(name="models", default=[], desc="Models", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[]) + MetadataElement(name="npop_dict", default={}, desc="Model population count", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value={}) + + # Update as format becomes more defined + def set_peek(self, dataset, is_multi_byte=False): + if not dataset.dataset.purged: + dataset.blurb = "Model File" + + # Update as format becomes more defined + ''' + def sniff(self, filename): + try: + json.loads(filename.file_name) + return True + except Exception: + return False + ''' + + def set_meta(self, dataset, **kwd): + if dataset.has_data(): + with open(dataset.file_name) as model_file: + try: + model_list = json.load(model_file) + except Exception: + return + + # Assign models + models = [model_dict['name'] for model_dict in model_list if 'name' in model_dict] + + # Assign population count per model + npop_dict = dict([(model_dict['name'], len(model_dict['pops'])) for model_dict in model_list if 'name' in model_dict]) + + dataset.metadata.models = models + dataset.metadata.npop_dict = npop_dict |