[2] | 1 | import sys, logging, copy, shutil, weakref, cPickle, tempfile, os |
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| 2 | |
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| 3 | from galaxy.util import string_as_bool, relpath, stringify_dictionary_keys, listify |
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| 4 | from galaxy.util.odict import odict |
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| 5 | from galaxy.web import form_builder |
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| 6 | import galaxy.model |
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| 7 | from sqlalchemy.orm import object_session |
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| 8 | |
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| 9 | import pkg_resources |
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| 10 | pkg_resources.require("simplejson") |
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| 11 | import simplejson |
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| 12 | |
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| 13 | log = logging.getLogger( __name__ ) |
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| 14 | |
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| 15 | STATEMENTS = "__galaxy_statements__" #this is the name of the property in a Datatype class where new metadata spec element Statements are stored |
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| 16 | |
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| 17 | DATABASE_CONNECTION_AVAILABLE = True #When False, certain metadata parameter types (see FileParameter) will behave differently |
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| 18 | |
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| 19 | class Statement( object ): |
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| 20 | """ |
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| 21 | This class inserts its target into a list in the surrounding |
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| 22 | class. the data.Data class has a metaclass which executes these |
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| 23 | statements. This is how we shove the metadata element spec into |
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| 24 | the class. |
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| 25 | """ |
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| 26 | def __init__( self, target ): |
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| 27 | self.target = target |
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| 28 | def __call__( self, *args, **kwargs ): |
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| 29 | class_locals = sys._getframe( 1 ).f_locals #get the locals dictionary of the frame object one down in the call stack (i.e. the Datatype class calling MetadataElement) |
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| 30 | statements = class_locals.setdefault( STATEMENTS, [] ) #get and set '__galaxy_statments__' to an empty list if not in locals dict |
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| 31 | statements.append( ( self, args, kwargs ) ) #add Statement containing info to populate a MetadataElementSpec |
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| 32 | @classmethod |
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| 33 | def process( cls, element ): |
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| 34 | for statement, args, kwargs in getattr( element, STATEMENTS, [] ): |
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| 35 | statement.target( element, *args, **kwargs ) #statement.target is MetadataElementSpec, element is a Datatype class |
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| 36 | |
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| 37 | |
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| 38 | class MetadataCollection( object ): |
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| 39 | """ |
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| 40 | MetadataCollection is not a collection at all, but rather a proxy |
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| 41 | to the real metadata which is stored as a Dictionary. This class |
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| 42 | handles processing the metadata elements when they are set and |
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| 43 | retrieved, returning default values in cases when metadata is not set. |
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| 44 | """ |
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| 45 | def __init__(self, parent ): |
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| 46 | self.parent = parent |
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| 47 | #initialize dict if needed |
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| 48 | if self.parent._metadata is None: |
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| 49 | self.parent._metadata = {} |
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| 50 | def get_parent( self ): |
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| 51 | if "_parent" in self.__dict__: |
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| 52 | return self.__dict__["_parent"]() |
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| 53 | return None |
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| 54 | def set_parent( self, parent ): |
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| 55 | self.__dict__["_parent"] = weakref.ref( parent ) # use weakref to prevent a circular reference interfering with garbage collection: hda/lda (parent) <--> MetadataCollection (self) ; needs to be hashable, so cannot use proxy. |
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| 56 | parent = property( get_parent, set_parent ) |
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| 57 | @property |
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| 58 | def spec( self ): |
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| 59 | return self.parent.datatype.metadata_spec |
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| 60 | def __iter__( self ): |
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| 61 | return self.parent._metadata.__iter__() |
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| 62 | def get( self, key, default=None ): |
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| 63 | try: |
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| 64 | return self.__getattr__( key ) or default |
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| 65 | except: |
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| 66 | return default |
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| 67 | def items(self): |
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| 68 | return iter( [ ( k, self.get( k ) ) for k in self.spec.iterkeys() ] ) |
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| 69 | def __str__(self): |
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| 70 | return dict( self.items() ).__str__() |
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| 71 | def __nonzero__( self ): |
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| 72 | return bool( self.parent._metadata ) |
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| 73 | def __getattr__( self, name ): |
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| 74 | if name in self.spec: |
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| 75 | if name in self.parent._metadata: |
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| 76 | return self.spec[name].wrap( self.parent._metadata[name] ) |
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| 77 | return self.spec[name].wrap( self.spec[name].default ) |
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| 78 | if name in self.parent._metadata: |
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| 79 | return self.parent._metadata[name] |
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| 80 | def __setattr__( self, name, value ): |
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| 81 | if name == "parent": |
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| 82 | return self.set_parent( value ) |
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| 83 | else: |
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| 84 | if name in self.spec: |
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| 85 | self.parent._metadata[name] = self.spec[name].unwrap( value ) |
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| 86 | else: |
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| 87 | self.parent._metadata[name] = value |
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| 88 | def element_is_set( self, name ): |
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| 89 | return bool( self.parent._metadata.get( name, False ) ) |
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| 90 | def get_html_by_name( self, name, **kwd ): |
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| 91 | if name in self.spec: |
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| 92 | rval = self.spec[name].param.get_html( value=getattr( self, name ), context=self, **kwd ) |
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| 93 | if rval is None: |
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| 94 | return self.spec[name].no_value |
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| 95 | return rval |
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| 96 | def make_dict_copy( self, to_copy ): |
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| 97 | """Makes a deep copy of input iterable to_copy according to self.spec""" |
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| 98 | rval = {} |
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| 99 | for key, value in to_copy.items(): |
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| 100 | if key in self.spec: |
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| 101 | rval[key] = self.spec[key].param.make_copy( value, target_context=self, source_context=to_copy ) |
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| 102 | return rval |
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| 103 | def from_JSON_dict( self, filename ): |
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| 104 | dataset = self.parent |
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| 105 | log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) ) |
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| 106 | JSONified_dict = simplejson.load( open( filename ) ) |
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| 107 | for name, spec in self.spec.items(): |
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| 108 | if name in JSONified_dict: |
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| 109 | dataset._metadata[ name ] = spec.param.from_external_value( JSONified_dict[ name ], dataset ) |
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| 110 | elif name in dataset._metadata: |
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| 111 | #if the metadata value is not found in our externally set metadata but it has a value in the 'old' |
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| 112 | #metadata associated with our dataset, we'll delete it from our dataset's metadata dict |
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| 113 | del dataset._metadata[ name ] |
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| 114 | def to_JSON_dict( self, filename ): |
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| 115 | #galaxy.model.customtypes.json_encoder.encode() |
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| 116 | meta_dict = {} |
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| 117 | dataset_meta_dict = self.parent._metadata |
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| 118 | for name, spec in self.spec.items(): |
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| 119 | if name in dataset_meta_dict: |
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| 120 | meta_dict[ name ] = spec.param.to_external_value( dataset_meta_dict[ name ] ) |
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| 121 | simplejson.dump( meta_dict, open( filename, 'wb+' ) ) |
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| 122 | def __getstate__( self ): |
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| 123 | return None #cannot pickle a weakref item (self._parent), when data._metadata_collection is None, it will be recreated on demand |
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| 124 | |
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| 125 | class MetadataSpecCollection( odict ): |
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| 126 | """ |
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| 127 | A simple extension of dict which allows cleaner access to items |
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| 128 | and allows the values to be iterated over directly as if it were a |
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| 129 | list. append() is also implemented for simplicity and does not |
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| 130 | "append". |
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| 131 | """ |
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| 132 | def __init__( self, dict = None ): |
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| 133 | odict.__init__( self, dict = None ) |
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| 134 | def append( self, item ): |
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| 135 | self[item.name] = item |
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| 136 | def iter( self ): |
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| 137 | return self.itervalues() |
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| 138 | def __getattr__( self, name ): |
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| 139 | return self.get( name ) |
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| 140 | |
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| 141 | class MetadataParameter( object ): |
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| 142 | def __init__( self, spec ): |
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| 143 | self.spec = spec |
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| 144 | |
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| 145 | def get_html_field( self, value=None, context={}, other_values={}, **kwd ): |
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| 146 | return form_builder.TextField( self.spec.name, value=value ) |
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| 147 | |
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| 148 | def get_html( self, value, context={}, other_values={}, **kwd ): |
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| 149 | """ |
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| 150 | The "context" is simply the metadata collection/bunch holding |
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| 151 | this piece of metadata. This is passed in to allow for |
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| 152 | metadata to validate against each other (note: this could turn |
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| 153 | into a huge, recursive mess if not done with care). For |
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| 154 | example, a column assignment should validate against the |
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| 155 | number of columns in the dataset. |
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| 156 | """ |
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| 157 | if self.spec.get("readonly"): |
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| 158 | return value |
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| 159 | if self.spec.get("optional"): |
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| 160 | checked = False |
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| 161 | if value: checked = "true" |
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| 162 | checkbox = form_builder.CheckboxField( "is_" + self.spec.name, checked=checked ) |
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| 163 | return checkbox.get_html() + self.get_html_field( value=value, context=context, other_values=other_values, **kwd ).get_html() |
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| 164 | else: |
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| 165 | return self.get_html_field( value=value, context=context, other_values=other_values, **kwd ).get_html() |
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| 166 | |
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| 167 | def to_string( self, value ): |
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| 168 | return str( value ) |
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| 169 | |
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| 170 | def make_copy( self, value, target_context = None, source_context = None ): |
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| 171 | return copy.deepcopy( value ) |
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| 172 | |
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| 173 | @classmethod |
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| 174 | def marshal ( cls, value ): |
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| 175 | """ |
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| 176 | This method should/can be overridden to convert the incoming |
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| 177 | value to whatever type it is supposed to be. |
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| 178 | """ |
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| 179 | return value |
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| 180 | |
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| 181 | def validate( self, value ): |
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| 182 | """ |
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| 183 | Throw an exception if the value is invalid. |
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| 184 | """ |
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| 185 | pass |
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| 186 | |
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| 187 | |
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| 188 | def unwrap( self, form_value ): |
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| 189 | """ |
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| 190 | Turns a value into its storable form. |
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| 191 | """ |
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| 192 | value = self.marshal( form_value ) |
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| 193 | self.validate( value ) |
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| 194 | return value |
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| 195 | |
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| 196 | def wrap( self, value ): |
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| 197 | """ |
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| 198 | Turns a value into its usable form. |
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| 199 | """ |
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| 200 | return value |
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| 201 | |
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| 202 | def from_external_value( self, value, parent ): |
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| 203 | """ |
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| 204 | Turns a value read from an external dict into its value to be pushed directly into the metadata dict. |
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| 205 | """ |
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| 206 | return value |
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| 207 | def to_external_value( self, value ): |
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| 208 | """ |
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| 209 | Turns a value read from a metadata into its value to be pushed directly into the external dict. |
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| 210 | """ |
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| 211 | return value |
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| 212 | |
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| 213 | class MetadataElementSpec( object ): |
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| 214 | """ |
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| 215 | Defines a metadata element and adds it to the metadata_spec (which |
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| 216 | is a MetadataSpecCollection) of datatype. |
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| 217 | """ |
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| 218 | |
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| 219 | def __init__( self, datatype, name=None, desc=None, param=MetadataParameter, default=None, no_value = None, visible=True, set_in_upload = False, **kwargs ): |
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| 220 | self.name = name |
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| 221 | self.desc = desc or name |
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| 222 | self.default = default |
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| 223 | self.no_value = no_value |
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| 224 | self.visible = visible |
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| 225 | self.set_in_upload = set_in_upload |
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| 226 | # Catch-all, allows for extra attributes to be set |
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| 227 | self.__dict__.update(kwargs) |
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| 228 | #set up param last, as it uses values set above |
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| 229 | self.param = param( self ) |
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| 230 | datatype.metadata_spec.append( self ) #add spec element to the spec |
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| 231 | def get( self, name ): |
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| 232 | return self.__dict__.get(name, None) |
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| 233 | def wrap( self, value ): |
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| 234 | """ |
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| 235 | Turns a stored value into its usable form. |
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| 236 | """ |
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| 237 | return self.param.wrap( value ) |
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| 238 | def unwrap( self, value ): |
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| 239 | """ |
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| 240 | Turns an incoming value into its storable form. |
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| 241 | """ |
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| 242 | return self.param.unwrap( value ) |
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| 243 | |
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| 244 | MetadataElement = Statement( MetadataElementSpec ) |
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| 245 | |
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| 246 | """ |
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| 247 | MetadataParameter sub-classes. |
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| 248 | """ |
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| 249 | |
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| 250 | class SelectParameter( MetadataParameter ): |
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| 251 | def __init__( self, spec ): |
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| 252 | MetadataParameter.__init__( self, spec ) |
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| 253 | self.values = self.spec.get( "values" ) |
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| 254 | self.multiple = string_as_bool( self.spec.get( "multiple" ) ) |
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| 255 | |
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| 256 | def to_string( self, value ): |
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| 257 | if value in [ None, [] ]: |
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| 258 | return str( self.spec.no_value ) |
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| 259 | if not isinstance( value, list ): |
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| 260 | value = [value] |
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| 261 | return ",".join( map( str, value ) ) |
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| 262 | |
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| 263 | def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): |
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| 264 | field = form_builder.SelectField( self.spec.name, multiple=self.multiple, display=self.spec.get("display") ) |
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| 265 | if self.values: |
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| 266 | value_list = self.values |
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| 267 | elif values: |
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| 268 | value_list = values |
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| 269 | elif value: |
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| 270 | value_list = [ ( v, v ) for v in listify( value )] |
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| 271 | else: |
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| 272 | value_list = [] |
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| 273 | for val, label in value_list: |
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| 274 | try: |
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| 275 | if ( self.multiple and val in value ) or ( not self.multiple and val == value ): |
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| 276 | field.add_option( label, val, selected=True ) |
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| 277 | else: |
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| 278 | field.add_option( label, val, selected=False ) |
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| 279 | except TypeError: |
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| 280 | field.add_option( val, label, selected=False ) |
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| 281 | return field |
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| 282 | |
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| 283 | def get_html( self, value, context={}, other_values={}, values=None, **kwd ): |
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| 284 | if self.spec.get("readonly"): |
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| 285 | if value in [ None, [] ]: |
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| 286 | return str( self.spec.no_value ) |
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| 287 | return ", ".join( map( str, value ) ) |
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| 288 | return MetadataParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) |
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| 289 | |
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| 290 | def wrap( self, value ): |
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| 291 | value = self.marshal( value ) #do we really need this (wasteful)? - yes because we are not sure that all existing selects have been stored previously as lists. Also this will handle the case where defaults/no_values are specified and are single non-list values. |
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| 292 | if self.multiple: |
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| 293 | return value |
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| 294 | elif value: |
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| 295 | return value[0] #single select, only return the first value |
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| 296 | return None |
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| 297 | |
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| 298 | @classmethod |
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| 299 | def marshal( cls, value ): |
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| 300 | # Store select as list, even if single item |
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| 301 | if value is None: return [] |
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| 302 | if not isinstance( value, list ): return [value] |
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| 303 | return value |
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| 304 | |
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| 305 | class DBKeyParameter( SelectParameter ): |
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| 306 | def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd): |
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| 307 | try: |
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| 308 | values = kwd['trans'].db_builds |
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| 309 | except KeyError: |
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| 310 | pass |
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| 311 | return super(DBKeyParameter, self).get_html_field( value, context, other_values, values, **kwd) |
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| 312 | def get_html( self, value=None, context={}, other_values={}, values=None, **kwd): |
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| 313 | try: |
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| 314 | values = kwd['trans'].db_builds |
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| 315 | except KeyError: |
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| 316 | pass |
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| 317 | return super(DBKeyParameter, self).get_html( value, context, other_values, values, **kwd) |
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| 318 | |
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| 319 | class RangeParameter( SelectParameter ): |
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| 320 | def __init__( self, spec ): |
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| 321 | SelectParameter.__init__( self, spec ) |
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| 322 | # The spec must be set with min and max values |
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| 323 | self.min = spec.get( "min" ) or 1 |
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| 324 | self.max = spec.get( "max" ) or 1 |
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| 325 | self.step = self.spec.get( "step" ) or 1 |
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| 326 | |
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| 327 | def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): |
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| 328 | if values is None: |
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| 329 | values = zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step )) |
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| 330 | return SelectParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) |
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| 331 | |
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| 332 | def get_html( self, value, context={}, other_values={}, values=None, **kwd ): |
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| 333 | if values is None: |
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| 334 | values = zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step )) |
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| 335 | return SelectParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) |
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| 336 | |
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| 337 | @classmethod |
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| 338 | def marshal( cls, value ): |
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| 339 | value = SelectParameter.marshal( value ) |
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| 340 | values = [ int(x) for x in value ] |
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| 341 | return values |
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| 342 | |
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| 343 | class ColumnParameter( RangeParameter ): |
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| 344 | |
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| 345 | def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): |
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| 346 | if values is None and context: |
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| 347 | column_range = range( 1, context.columns+1, 1 ) |
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| 348 | values = zip( column_range, column_range ) |
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| 349 | return RangeParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) |
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| 350 | |
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| 351 | def get_html( self, value, context={}, other_values={}, values=None, **kwd ): |
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| 352 | if values is None and context: |
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| 353 | column_range = range( 1, context.columns+1, 1 ) |
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| 354 | values = zip( column_range, column_range ) |
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| 355 | return RangeParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) |
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| 356 | |
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| 357 | class ColumnTypesParameter( MetadataParameter ): |
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| 358 | |
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| 359 | def to_string( self, value ): |
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| 360 | return ",".join( map( str, value ) ) |
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| 361 | |
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| 362 | class PythonObjectParameter( MetadataParameter ): |
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| 363 | |
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| 364 | def to_string( self, value ): |
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| 365 | if not value: |
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| 366 | return self.spec._to_string( self.spec.no_value ) |
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| 367 | return self.spec._to_string( value ) |
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| 368 | |
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| 369 | def get_html_field( self, value=None, context={}, other_values={}, **kwd ): |
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| 370 | return form_builder.TextField( self.spec.name, value=self._to_string( value ) ) |
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| 371 | |
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| 372 | def get_html( self, value=None, context={}, other_values={}, **kwd ): |
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| 373 | return str( self ) |
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| 374 | |
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| 375 | @classmethod |
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| 376 | def marshal( cls, value ): |
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| 377 | return value |
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| 378 | |
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| 379 | class FileParameter( MetadataParameter ): |
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| 380 | |
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| 381 | def to_string( self, value ): |
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| 382 | if not value: |
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| 383 | return str( self.spec.no_value ) |
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| 384 | return value.file_name |
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| 385 | |
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| 386 | def get_html_field( self, value=None, context={}, other_values={}, **kwd ): |
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| 387 | return form_builder.TextField( self.spec.name, value=str( value.id ) ) |
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| 388 | |
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| 389 | def get_html( self, value=None, context={}, other_values={}, **kwd ): |
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| 390 | return "<div>No display available for Metadata Files</div>" |
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| 391 | |
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| 392 | def wrap( self, value ): |
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| 393 | if value is None: |
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| 394 | return None |
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| 395 | if isinstance( value, galaxy.model.MetadataFile ) or isinstance( value, MetadataTempFile ): |
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| 396 | return value |
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| 397 | if DATABASE_CONNECTION_AVAILABLE: |
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| 398 | try: |
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| 399 | # FIXME: this query requires a monkey patch in assignmapper.py since |
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| 400 | # MetadataParameters do not have a handle to the sqlalchemy session |
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| 401 | return galaxy.model.MetadataFile.get( value ) |
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| 402 | except: |
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| 403 | #value was not a valid id |
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| 404 | return None |
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| 405 | else: |
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| 406 | mf = galaxy.model.MetadataFile() |
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| 407 | mf.id = value #we assume this is a valid id, since we cannot check it |
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| 408 | return mf |
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| 409 | def make_copy( self, value, target_context, source_context ): |
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| 410 | value = self.wrap( value ) |
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| 411 | if value: |
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| 412 | new_value = galaxy.model.MetadataFile( dataset = target_context.parent, name = self.spec.name ) |
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| 413 | object_session( target_context.parent ).add( new_value ) |
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| 414 | object_session( target_context.parent ).flush() |
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| 415 | shutil.copy( value.file_name, new_value.file_name ) |
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| 416 | return self.unwrap( new_value ) |
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| 417 | return None |
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| 418 | |
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| 419 | @classmethod |
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| 420 | def marshal( cls, value ): |
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| 421 | if isinstance( value, galaxy.model.MetadataFile ): |
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| 422 | value = value.id |
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| 423 | return value |
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| 424 | |
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| 425 | def from_external_value( self, value, parent ): |
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| 426 | """ |
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| 427 | Turns a value read from a external dict into its value to be pushed directly into the metadata dict. |
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| 428 | """ |
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| 429 | if MetadataTempFile.is_JSONified_value( value ): |
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| 430 | value = MetadataTempFile.from_JSON( value ) |
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| 431 | if isinstance( value, MetadataTempFile ): |
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| 432 | mf = parent.metadata.get( self.spec.name, None) |
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| 433 | if mf is None: |
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| 434 | mf = self.new_file( dataset = parent, **value.kwds ) |
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| 435 | shutil.move( value.file_name, mf.file_name ) |
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| 436 | value = mf.id |
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| 437 | return value |
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| 438 | def to_external_value( self, value ): |
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| 439 | """ |
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| 440 | Turns a value read from a metadata into its value to be pushed directly into the external dict. |
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| 441 | """ |
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| 442 | if isinstance( value, galaxy.model.MetadataFile ): |
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| 443 | value = value.id |
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| 444 | elif isinstance( value, MetadataTempFile ): |
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| 445 | value = MetadataTempFile.to_JSON( value ) |
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| 446 | return value |
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| 447 | |
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| 448 | def new_file( self, dataset = None, **kwds ): |
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| 449 | if DATABASE_CONNECTION_AVAILABLE: |
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| 450 | mf = galaxy.model.MetadataFile( name = self.spec.name, dataset = dataset, **kwds ) |
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| 451 | object_session( dataset ).add( mf ) |
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| 452 | object_session( dataset ).flush() #flush to assign id |
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| 453 | return mf |
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| 454 | else: |
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| 455 | #we need to make a tmp file that is accessable to the head node, |
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| 456 | #we will be copying its contents into the MetadataFile objects filename after restoring from JSON |
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| 457 | #we do not include 'dataset' in the kwds passed, as from_JSON_value() will handle this for us |
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| 458 | return MetadataTempFile( **kwds ) |
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| 459 | |
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| 460 | #This class is used when a database file connection is not available |
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| 461 | class MetadataTempFile( object ): |
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| 462 | tmp_dir = 'database/tmp' #this should be overwritten as necessary in calling scripts |
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| 463 | def __init__( self, **kwds ): |
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| 464 | self.kwds = kwds |
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| 465 | self._filename = None |
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| 466 | @property |
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| 467 | def file_name( self ): |
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| 468 | if self._filename is None: |
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| 469 | #we need to create a tmp file, accessable across all nodes/heads, save the name, and return it |
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| 470 | self._filename = relpath( tempfile.NamedTemporaryFile( dir = self.tmp_dir, prefix = "metadata_temp_file_" ).name ) |
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| 471 | open( self._filename, 'wb+' ) #create an empty file, so it can't be reused using tempfile |
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| 472 | return self._filename |
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| 473 | def to_JSON( self ): |
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| 474 | return { '__class__':self.__class__.__name__, 'filename':self.file_name, 'kwds':self.kwds } |
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| 475 | @classmethod |
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| 476 | def from_JSON( cls, json_dict ): |
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| 477 | #need to ensure our keywords are not unicode |
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| 478 | rval = cls( **stringify_dictionary_keys( json_dict['kwds'] ) ) |
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| 479 | rval._filename = json_dict['filename'] |
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| 480 | return rval |
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| 481 | @classmethod |
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| 482 | def is_JSONified_value( cls, value ): |
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| 483 | return ( isinstance( value, dict ) and value.get( '__class__', None ) == cls.__name__ ) |
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| 484 | @classmethod |
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| 485 | def cleanup_from_JSON_dict_filename( cls, filename ): |
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| 486 | try: |
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| 487 | for key, value in simplejson.load( open( filename ) ).items(): |
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| 488 | if cls.is_JSONified_value( value ): |
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| 489 | value = cls.from_JSON( value ) |
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| 490 | if isinstance( value, cls ) and os.path.exists( value.file_name ): |
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| 491 | log.debug( 'Cleaning up abandoned MetadataTempFile file: %s' % value.file_name ) |
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| 492 | os.unlink( value.file_name ) |
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| 493 | except Exception, e: |
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| 494 | log.debug( 'Failed to cleanup MetadataTempFile temp files from %s: %s' % ( filename, e ) ) |
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| 495 | |
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| 496 | #Class with methods allowing set_meta() to be called externally to the Galaxy head |
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| 497 | class JobExternalOutputMetadataWrapper( object ): |
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| 498 | #this class allows access to external metadata filenames for all outputs associated with a job |
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| 499 | #We will use JSON as the medium of exchange of information, except for the DatasetInstance object which will use pickle (in the future this could be JSONified as well) |
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| 500 | def __init__( self, job ): |
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| 501 | self.job_id = job.id |
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| 502 | def get_output_filenames_by_dataset( self, dataset, sa_session ): |
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| 503 | if isinstance( dataset, galaxy.model.HistoryDatasetAssociation ): |
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| 504 | return sa_session.query( galaxy.model.JobExternalOutputMetadata ) \ |
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| 505 | .filter_by( job_id = self.job_id, history_dataset_association_id = dataset.id ) \ |
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| 506 | .first() #there should only be one or None |
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| 507 | elif isinstance( dataset, galaxy.model.LibraryDatasetDatasetAssociation ): |
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| 508 | return sa_session.query( galaxy.model.JobExternalOutputMetadata ) \ |
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| 509 | .filter_by( job_id = self.job_id, library_dataset_dataset_association_id = dataset.id ) \ |
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| 510 | .first() #there should only be one or None |
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| 511 | return None |
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| 512 | def get_dataset_metadata_key( self, dataset ): |
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| 513 | # Set meta can be called on library items and history items, |
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| 514 | # need to make different keys for them, since ids can overlap |
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| 515 | return "%s_%d" % ( dataset.__class__.__name__, dataset.id ) |
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| 516 | def setup_external_metadata( self, datasets, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, |
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| 517 | output_fnames=None, config_root=None, datatypes_config=None, job_metadata=None, kwds={} ): |
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| 518 | #fill in metadata_files_dict and return the command with args required to set metadata |
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| 519 | def __metadata_files_list_to_cmd_line( metadata_files ): |
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| 520 | def __get_filename_override(): |
---|
| 521 | if output_fnames: |
---|
| 522 | for dataset_path in output_fnames: |
---|
| 523 | if dataset_path.false_path and dataset_path.real_path == metadata_files.dataset.file_name: |
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| 524 | return dataset_path.false_path |
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| 525 | return "" |
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| 526 | return "%s,%s,%s,%s,%s,%s" % ( metadata_files.filename_in, metadata_files.filename_kwds, metadata_files.filename_out, metadata_files.filename_results_code, __get_filename_override(), metadata_files.filename_override_metadata ) |
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| 527 | if not isinstance( datasets, list ): |
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| 528 | datasets = [ datasets ] |
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| 529 | if exec_dir is None: |
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| 530 | exec_dir = os.path.abspath( os.getcwd() ) |
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| 531 | if tmp_dir is None: |
---|
| 532 | tmp_dir = MetadataTempFile.tmp_dir |
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| 533 | if dataset_files_path is None: |
---|
| 534 | dataset_files_path = galaxy.model.Dataset.file_path |
---|
| 535 | if config_root is None: |
---|
| 536 | config_root = os.path.abspath( os.getcwd() ) |
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| 537 | if datatypes_config is None: |
---|
| 538 | datatypes_config = 'datatypes_conf.xml' |
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| 539 | metadata_files_list = [] |
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| 540 | for dataset in datasets: |
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| 541 | key = self.get_dataset_metadata_key( dataset ) |
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| 542 | #future note: |
---|
| 543 | #wonkiness in job execution causes build command line to be called more than once |
---|
| 544 | #when setting metadata externally, via 'auto-detect' button in edit attributes, etc., |
---|
| 545 | #we don't want to overwrite (losing the ability to cleanup) our existing dataset keys and files, |
---|
| 546 | #so we will only populate the dictionary once |
---|
| 547 | metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session ) |
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| 548 | if not metadata_files: |
---|
| 549 | metadata_files = galaxy.model.JobExternalOutputMetadata( dataset = dataset) |
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| 550 | metadata_files.job_id = self.job_id |
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| 551 | #we are using tempfile to create unique filenames, tempfile always returns an absolute path |
---|
| 552 | #we will use pathnames relative to the galaxy root, to accommodate instances where the galaxy root |
---|
| 553 | #is located differently, i.e. on a cluster node with a different filesystem structure |
---|
| 554 | |
---|
| 555 | #file to store existing dataset |
---|
| 556 | metadata_files.filename_in = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_in_%s_" % key ).name ) |
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| 557 | |
---|
| 558 | #FIXME: HACK |
---|
| 559 | #sqlalchemy introduced 'expire_on_commit' flag for sessionmaker at version 0.5x |
---|
| 560 | #This may be causing the dataset attribute of the dataset_association object to no-longer be loaded into memory when needed for pickling. |
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| 561 | #For now, we'll simply 'touch' dataset_association.dataset to force it back into memory. |
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| 562 | dataset.dataset #force dataset_association.dataset to be loaded before pickling |
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| 563 | #A better fix could be setting 'expire_on_commit=False' on the session, or modifying where commits occur, or ? |
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| 564 | |
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| 565 | cPickle.dump( dataset, open( metadata_files.filename_in, 'wb+' ) ) |
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| 566 | #file to store metadata results of set_meta() |
---|
| 567 | metadata_files.filename_out = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_out_%s_" % key ).name ) |
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| 568 | open( metadata_files.filename_out, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) |
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| 569 | #file to store a 'return code' indicating the results of the set_meta() call |
---|
| 570 | #results code is like (True/False - if setting metadata was successful/failed , exception or string of reason of success/failure ) |
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| 571 | metadata_files.filename_results_code = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_results_%s_" % key ).name ) |
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| 572 | simplejson.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) |
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| 573 | #file to store kwds passed to set_meta() |
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| 574 | metadata_files.filename_kwds = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name ) |
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| 575 | simplejson.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True ) |
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| 576 | #existing metadata file parameters need to be overridden with cluster-writable file locations |
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| 577 | metadata_files.filename_override_metadata = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_override_%s_" % key ).name ) |
---|
| 578 | open( metadata_files.filename_override_metadata, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) |
---|
| 579 | override_metadata = [] |
---|
| 580 | for meta_key, spec_value in dataset.metadata.spec.iteritems(): |
---|
| 581 | if isinstance( spec_value.param, FileParameter ) and dataset.metadata.get( meta_key, None ) is not None: |
---|
| 582 | metadata_temp = MetadataTempFile() |
---|
| 583 | shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name ) |
---|
| 584 | override_metadata.append( ( meta_key, metadata_temp.to_JSON() ) ) |
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| 585 | simplejson.dump( override_metadata, open( metadata_files.filename_override_metadata, 'wb+' ) ) |
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| 586 | #add to session and flush |
---|
| 587 | sa_session.add( metadata_files ) |
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| 588 | sa_session.flush() |
---|
| 589 | metadata_files_list.append( metadata_files ) |
---|
| 590 | #return command required to build |
---|
| 591 | return "%s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, config_root, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) |
---|
| 592 | |
---|
| 593 | def external_metadata_set_successfully( self, dataset, sa_session ): |
---|
| 594 | metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session ) |
---|
| 595 | if not metadata_files: |
---|
| 596 | return False # this file doesn't exist |
---|
| 597 | rval, rstring = simplejson.load( open( metadata_files.filename_results_code ) ) |
---|
| 598 | if not rval: |
---|
| 599 | log.debug( 'setting metadata externally failed for %s %s: %s' % ( dataset.__class__.__name__, dataset.id, rstring ) ) |
---|
| 600 | return rval |
---|
| 601 | |
---|
| 602 | def cleanup_external_metadata( self, sa_session ): |
---|
| 603 | log.debug( 'Cleaning up external metadata files' ) |
---|
| 604 | for metadata_files in sa_session.query( galaxy.model.Job ).get( self.job_id ).external_output_metadata: |
---|
| 605 | #we need to confirm that any MetadataTempFile files were removed, if not we need to remove them |
---|
| 606 | #can occur if the job was stopped before completion, but a MetadataTempFile is used in the set_meta |
---|
| 607 | MetadataTempFile.cleanup_from_JSON_dict_filename( metadata_files.filename_out ) |
---|
| 608 | dataset_key = self.get_dataset_metadata_key( metadata_files.dataset ) |
---|
| 609 | for key, fname in [ ( 'filename_in', metadata_files.filename_in ), ( 'filename_out', metadata_files.filename_out ), ( 'filename_results_code', metadata_files.filename_results_code ), ( 'filename_kwds', metadata_files.filename_kwds ), ( 'filename_override_metadata', metadata_files.filename_override_metadata ) ]: |
---|
| 610 | try: |
---|
| 611 | os.remove( fname ) |
---|
| 612 | except Exception, e: |
---|
| 613 | log.debug( 'Failed to cleanup external metadata file (%s) for %s: %s' % ( key, dataset_key, e ) ) |
---|
| 614 | def set_job_runner_external_pid( self, pid, sa_session ): |
---|
| 615 | for metadata_files in sa_session.query( galaxy.model.Job ).get( self.job_id ).external_output_metadata: |
---|
| 616 | metadata_files.job_runner_external_pid = pid |
---|
| 617 | sa_session.add( metadata_files ) |
---|
| 618 | sa_session.flush() |
---|