source: ndgCommon/trunk/ndg/common/src/models/Atom.py @ 5472

Subversion URL: http://proj.badc.rl.ac.uk/svn/ndg/ndgCommon/trunk/ndg/common/src/models/Atom.py@5472
Revision 5472, 54.0 KB checked in by cbyrom, 10 years ago (diff)

Cope with different versions of Atoms - these may have their content
namespaces slightly differently specified.

Line 
1'''
2 Class representing data in  atom format - allowing moles data to be stored and accessed in a web feed compatible way
3 
4 @author: C Byrom, Tessella Jun 2008
5'''
6import sys, logging, re, datetime
7from xml.sax.saxutils import escape, unescape
8from xml.etree import cElementTree as ET
9import csml.parser as CsmlParser
10import ndg.common.src.clients.xmldb.eXist.dbconstants as dc
11from ndg.common.src.lib.ETxmlView import et2text
12import ndg.common.src.lib.utilities as utilities
13from ndg.common.src.models.vocabtermdata import VocabTermData as VTD
14from ndg.common.src.models import MolesEntity as ME
15from ndg.common.src.models import Deployment as Deployment
16from ndg.common.src.models import AtomState
17from ndg.common.src.models.ndgObject import ndgObject
18
19class AtomError(Exception):
20    """
21    Exception handling for Atom class.
22    """
23    def __init__(self, msg):
24        logging.error(msg)
25        Exception.__init__(self, msg)
26
27
28class Person(object):
29    '''
30    Class representing atom author type data - with name, uri and role attributes
31    @keyword personType: Type of person to create - specified using the Person.._Type
32    values.  Default is AUTHOR_TYPE.
33    @keyword namespace: a two value array of format, ['short_namespace_name', 'full_namespace_name']
34    - e.g. ['moles', 'http://ndg.nerc.ac.uk/schema/moles2beta']
35    '''
36    AUTHOR_TYPE = 0
37    CONTRIBUTOR_TYPE = 1
38    RESPONSIBLE_PARTY_TYPE = 2
39    ELEMENT_NAMES = ["author", "contributor", "responsibleParty"]
40   
41    def __init__(self, personType = AUTHOR_TYPE, namespace = None):
42        self.type = personType
43        if namespace:
44            self.ns_shortname = namespace[0]
45            self.ns_fullname = namespace[1]
46        else:
47            self.ns_shortname = ""
48            self.ns_fullname = ndgObject.ATOM_NS
49           
50        self.name = ""
51        self.uri = ""
52        self.role = ""
53       
54        # NB, the atom format specifies slightly different data contents
55        self.uriTagName = "email"
56        # NB, responsible party data is always stored in the moles section
57        if self.type == self.RESPONSIBLE_PARTY_TYPE:
58            self.ns_shortname = 'moles'
59            self.ns_fullname = ndgObject.MOLES_NS
60            self.uriTagName = "uri"
61
62    def __str__(self):
63        if self.name or self.uri or self.role:
64            return self.name + " | " + self.uri + " | " + self.role
65        return ""
66
67
68    def hasValue(self):
69        if self.name or self.uri or self.role:
70            return True
71        return False
72   
73    def fromString(self, personString):
74        (self.name, self.uri, self.role) = utilities.getTripleData(personString)
75       
76    def fromETElement(self, personTag):
77        self.name = unescape(personTag.findtext('{%s}name' %self.ns_fullname) or "")
78        self.role = unescape(personTag.findtext('{%s}role' %self.ns_fullname) or "")
79        self.uri = unescape(personTag.findtext('{%s}%s' %(self.ns_fullname, self.uriTagName)) or "")
80        logging.debug("Added name: '%s', role: '%s', %s: '%s'" \
81                      %(self.name, self.role, self.uriTagName, self.uri))
82
83    def toXML(self):
84        prefix = ""
85        if self.ns_shortname:
86            prefix = self.ns_shortname + ':'
87
88        author = ET.Element(prefix + self.ELEMENT_NAMES[self.type])
89
90        if self.name:
91            name = ET.SubElement(author, prefix + "name")
92            name.text = escape(self.name)
93       
94        if self.uri:
95            uri = ET.SubElement(author, prefix + self.uriTagName)
96            uri.text = escape(self.uri)
97       
98        if self.role:
99            role = ET.SubElement(author, prefix + "role")
100            role.text = escape(self.role)
101
102        return author
103   
104    def __cmp__(self, person1):
105        '''
106        Override comparison to allow proper object comparison when checking
107        if Person objects are in an array already - i.e. if person in personArray...
108        '''
109        if not person1:
110            return -1
111       
112        if self is person1:
113            return 0
114        elif self.uri == person1.uri and self.name == person1.name and \
115                self.role == person1.role and self.type == person1.type:
116            return 0
117        return 1
118
119
120class Link(object):
121    '''
122    Class representing an atom link - with href, title and rel attributes
123    '''
124
125    def __init__(self):
126        self.href = ""
127        self.title = ""
128        self.rel = ""
129
130    def fromString(self, linkString):
131        (self.href, self.title, self.rel) = utilities.getTripleData(linkString, doEscape=False)
132        # ensure no funny characters are included on data ingest
133        self.title = utilities.escapeSpecialCharacters(self.title)
134       
135    def fromETElement(self, linkTag):
136        # remove any url quoting when reading in from XML - to avoid need for
137        # correction on display
138        self.href = unescape(linkTag.attrib.get('href') or "")
139        self.rel = unescape(linkTag.attrib.get('rel') or "")
140        self.title = unescape(linkTag.attrib.get('title') or "")
141
142    def toXML(self):
143        # ensure the xml element doesn't contain things like '&' - which will
144        # cause problems when running xqueries
145        link = ET.Element("link")
146        link.attrib["href"] = escape(self.href)
147        link.attrib["title"] = escape(self.title)
148        link.attrib["rel"] = escape(self.rel)
149        return link
150
151    def hasValue(self):
152        # NB, just a rel on its own is meaningless - so ignore
153        if self.href or self.title:
154            return True
155        return False
156   
157    def __str__(self):
158        if self.href or self.title or self.rel:
159            return self.href + " | " + self.title + " | " + self.rel
160        return ""
161   
162    def isChildAtom(self):
163        '''
164        Determines whether the link refers to another atom - e.g. a link to
165        a data granule
166        @return True, if so; False otherwise
167        '''
168        if self.rel.endswith(VTD.GRANULE_TERM) or \
169            self.rel.endswith(VTD.DEPLOYMENT_TERM) or \
170            self.rel.endswith(VTD.ACTIVITY_TERM) or \
171            self.rel.endswith(VTD.DPT_TERM) or \
172            self.rel.endswith(VTD.OBS_TERM):
173            return True
174       
175        return False
176   
177    def __cmp__(self, link1):
178        '''
179        Override comparison to allow proper object comparison when checking
180        if Link objects are in an array already - i.e. if link in linkArray...
181        '''
182        if not link1:
183            return -1
184       
185        if self is link1:
186            return 0
187        elif self.href == link1.href and self.title == link1.title and \
188                self.rel == link1.rel:
189            return 0
190        return 1
191
192
193class Category(object):
194    '''
195    Class representing an atom category - with term, scheme and label attributes
196    '''
197    def __init__(self):
198        self.term = ""
199        self.scheme = ""
200        self.label = ""
201
202    def fromString(self, linkString, escapeSpecialCharacters=True):
203        '''
204        Create Category from triple string of format, 'label | scheme | term'
205        @param linkString: triple string to create category with
206        @keyword escapeSpecialCharacters: if set to True, special characters in
207        triple string are escaped (default)
208        '''
209        (self.label, self.scheme, self.term) = utilities.getTripleData(linkString, \
210            doEscape=escapeSpecialCharacters)
211
212        # also replace any double quotes with single apostrophes - since this data
213        # is stored as an attribute - i.e. already surrounded by double quotes
214        self.label = self.label.replace("\"", "'")
215        self.scheme = self.scheme.replace("\"", "'")
216        self.term = self.term.replace("\"", "'")
217       
218       
219    def fromETElement(self, linkTag):
220        self.term = unescape(linkTag.attrib.get('term') or "")
221        self.label = unescape(linkTag.attrib.get('label') or "")
222        self.scheme = unescape(linkTag.attrib.get('scheme') or "")
223
224    def toXML(self):
225        link = ET.Element("category")
226        link.attrib["term"] = escape(self.term)
227        link.attrib["scheme"] = escape(self.scheme)
228        link.attrib["label"] = escape(self.label)
229        return link
230   
231    def hasValue(self):
232        if self.scheme or self.label or self.term:
233            return True
234        return False
235
236
237class Atom(object):
238
239    # labels for use with the atom categories
240    ATOM_TYPE = "ATOM_TYPE"
241    ATOM_SUBTYPE = "ATOM_SUBTYPE"
242
243    # labels for use with the templates to set/extract specific inputs
244    ONLINE_REF_LABEL = "online_ref"
245    PARAMETER_LABEL = "parameter"
246    ATOM_REF_LABEL = "atom_ref"
247    DELIMITER = "---"
248    REMOVE_LABEL = "remove"
249   
250    # format to use for t1-t2 date range
251    YEAR_FORMAT = '%Y-%m-%d'
252
253    # subtype name, when not defined
254    SUB_TYPE_NOT_DEFINED_NAME = "Not currently defined"
255
256    def __init__(self, atomType = None, vocabTermData = None, ndgObject = None, \
257                 xmlString = None, state = AtomState.WORKING_STATE, **inputs):
258        '''
259        Constructor - initialise the atom variables
260        @keyword atomType: type of atom to set up
261        @keyword vocabTermData: instance of VocabTermData object to use with atom
262        @keywork ndgObject: instance of ndgObject to use with atom
263        @keyword xmlString: XML representation of atom - will be parsed to populate
264        the atom data
265        @keyword state:  AtomState object representing the state of the atom
266        @param inputs: a dict with vals to set directly against the object fields
267        '''
268        logging.info("Initialising atom")
269        if atomType:
270            logging.info(" - of type '%s'" %atomType)
271        self.atomTypeID = atomType
272
273        # some data have further subtypes specified
274        self.subtypeID = None # this should be the termID
275        self.subtype = None # and this should be the fully formed vocab URL
276       
277        self.ndgObject = ndgObject
278
279        self.atomName = None
280        self.files = []
281        self.author = Person()
282        self.contributors = []
283        self.atomAuthors = []
284        self.parameters = []
285        self.spatialData = []
286        self.temporalData = []
287        self.relatedLinks = []
288        self.summary = ""
289        self.content = []
290        # NB, this deployments data duplicates other atom data - and is only used for a
291        # convenient way to collect the info (by lookupAssociatedData()) for use in templates
292        self.deployments = []
293        # ditto for the following field
294        self.dataEntities = []
295           
296        self.csmlFile = None
297        self.cdmlFile = None
298        # general variable to use for setting the atom content - NB, if a csmlFile is specified
299        # (either directly or via a cdmlFile specification), this will be the content by default
300        # for this purpose
301        self.contentFile = None     
302        self.title = None
303        self.datasetID = None        # NB, the dataset id ends up in the atomName - <path><datasetID>.atom
304        self.atomID = None
305   
306        # boundary box info - to replace spatial/temporalData?
307        self.minX = None
308        self.minY = None
309        self.maxX = None
310        self.maxY = None
311        self.t1 = None
312        self.t2 = None
313
314        self.ME = ME.MolesEntity(**inputs)
315       
316        # date when the atom was first ingested
317        self.publishedDate = None
318
319        # last update date
320        self.updatedDate = None
321
322        # assume atom in working state by default - this is used to define what collection
323        # in eXist the atom is stored in
324        self.state = state
325       
326        # additional, non standard atom data can be included in the molesExtra element
327        if vocabTermData:
328            self.VTD = vocabTermData
329        else:
330            self.VTD = VTD()
331       
332        if xmlString:
333            self.fromString(xmlString)
334
335        # retain old title, in case it has changed - NB, this will be done by applying
336        # the inputs dict - and might require other atoms to be updated
337        self.oldTitle = self.title
338           
339        # if inputs passed in as dict, add these now
340        if inputs:
341            logging.info("Adding info to atom from input dict")
342            logging.debug(inputs)
343           
344            # avoid the initial case being caught - i.e. when there is no title at all
345            if inputs.has_key('title'):
346                newTitle = inputs.get('title')
347                if not self.title:
348                    self.oldTitle = newTitle
349                   
350            self.__dict__.update(inputs)
351            self.ME.__dict__.update(inputs)
352           
353            # NB, this doesn't trigger the Content Property, so do this
354            # explicitly, if need be
355            if inputs.has_key('Content'):
356                self.Content = inputs.get('Content')
357            if inputs.has_key('author'):
358                name = inputs.get('author')
359                author = Person()
360                author.fromString(name)
361                self.author = author
362
363        if self.atomTypeID:
364            self.atomTypeName = self.VTD.TERM_DATA[self.atomTypeID].title
365
366        self.deploymentsURL = ""
367        self.dataEntitiesURL = ""
368
369        logging.info("Atom initialised")
370
371
372    def addOnlineReferences(self, links):
373        '''
374        Add online reference data associated with the atom
375        - NB, care needs to be taken here since this data is stored in the atom
376        link elements and these are also used for the various atom associations
377        @param links: a Link or array of Links to add to the relatedLinks attribute
378        '''
379        logging.debug("Adding online references")
380        if not links:
381            return
382       
383        if type(links) is not list:
384            links = [links]
385       
386        # firstly clear out any online refs data from the existing related links
387        newLinks = []
388        for link in self.relatedLinks:
389            if link.isChildAtom():
390                newLinks.append(link)
391       
392        newLinks.extend(links)
393        self.relatedLinks = newLinks
394        logging.debug("Online references added")
395
396
397    def addUniqueRelatedLinks(self, links):
398        '''
399        Add links to relatedLinks array - if they are not already included
400        @param links: a Link or array of Links to add to the relatedLinks attribute
401        '''
402        self.addUniqueLinks(self.relatedLinks, links)
403       
404
405    def removeRelatedLinks(self, linksToDelete):
406        '''
407        Remove any links in the input list from the atom's related links list
408        @param linksToDelete: array of Link objects to remove from atom
409        '''
410        logging.debug("Removing related links from atom")
411        if not linksToDelete:
412            return
413       
414        if type(linksToDelete) is not list:
415            linksToDelete = [linksToDelete]
416       
417        updatedLinks = []
418        for link in self.relatedLinks:
419            if type(link) is not Link:
420                logging.warning("Link is not of 'Link' object type (type='%s') - skipping" %type(link))
421                continue
422            if link in linksToDelete:
423                logging.debug("- found link to remove")
424            else:
425                updatedLinks.append(link)
426
427        self.relatedLinks = updatedLinks
428        logging.debug("Links removed")
429
430    def getPublicationStatePath(self):
431        '''
432        Determine the correct publication state collection for the atom
433        @return collectionPath: collection path for the publication state of the atom
434        '''
435        logging.debug("Getting collection path for atom publication state")
436        collectionPath = dc.ATOM_COLLECTION_PATH + self.state.collectionPath
437        logging.debug("Returning publication state collection, '%s'" %collectionPath)
438        return collectionPath
439       
440
441    def getDefaultEntityCollectionPath(self):
442        '''
443        Determine the correct collection for the entity type of the atom
444        @return entityPath: collection path for the data type of the atom
445        '''
446        logging.debug("Getting collection path for atom entity type")
447        collectionPath = self.getPublicationStatePath()
448       
449        if self.atomTypeID == VTD.DE_TERM:
450            collectionPath += dc.DE_COLLECTION_PATH
451        elif self.atomTypeID == VTD.GRANULE_TERM:
452            collectionPath += dc.GRANULE_COLLECTION_PATH
453        elif self.atomTypeID == VTD.ACTIVITY_TERM and \
454            self.subtypeID == VTD.DEPLOYMENT_TERM:
455            collectionPath += dc.DEPLOYMENTS_COLLECTION_PATH
456        else:
457            collectionPath += dc.DEPLOYMENT_COLLECTION_PATH
458       
459        logging.debug("Returning entity collection, '%s'" %collectionPath)
460        return collectionPath
461       
462
463    def getDefaultCollectionPath(self):
464        '''
465        Determine the correct collection to use for the atom in eXist
466        '''
467        logging.debug("Getting default collection path for atom")
468        collectionPath = self.getDefaultEntityCollectionPath()
469        if not self.ME.providerID:
470            raise AtomError("Error: cannot determine atom collection path because " + \
471                            "the provider ID is not defined")
472           
473        collectionPath += self.ME.providerID + "/"
474        logging.debug("Returning collection, '%s'" %collectionPath)
475        return collectionPath
476
477
478    def __addAtomTypeDataXML(self, root):
479        '''
480        Add the atom type, and subtype data, if available, to atom categories
481        - and lookup and add the appropriate vocab term data
482        '''
483        if self.atomTypeID:
484            logging.info("Adding atom type info to XML output")
485            category = Category()
486            category.label = self.atomTypeID
487            # look up the appropriate vocab term data
488            category.scheme = self.VTD.getTermCurrentVocabURL(self.atomTypeID)
489            category.term = self.ATOM_TYPE
490            root.append(category.toXML())
491
492        if self.subtypeID:
493            logging.info("Adding atom subtype info to XML output")
494            # NB subtypes not all defined, so leave this out for the moment
495            category.label = self.subtypeID
496            # look up the appropriate vocab term data
497            category.scheme = self.VTD.getTermCurrentVocabURL(self.subtypeID)
498            category.term = self.ATOM_SUBTYPE
499            root.append(category.toXML())
500
501
502    def addMolesEntityData(self, abbreviation, provider_id, object_creation_time):
503        '''
504        Add data to include in the moles entity element
505        '''
506        logging.debug('Adding moles entity information')
507        self.ME.abbreviation = abbreviation
508        self.ME.providerID = provider_id
509        self.ME.createdDate = utilities.getISO8601Date(object_creation_time)
510        logging.debug('Moles entity information added')
511
512
513    def addAuthors(self, authors):
514        '''
515        Add author data appropriately to the atom
516        NB, these will overwrite any existing authors of the same type
517        @param authors: list of Person objects with the author data
518        '''
519        logging.debug('Adding authors data to Atom')
520        isFirstAuthor = {}
521        authorArray = None
522        for author in authors:
523            # NB, we're only allowed one atom author
524            if author.type == Person.AUTHOR_TYPE:
525                self.author = author
526                   
527                if isFirstAuthor.has_key(author.type):
528                    raise AtomError("Error: an atom can only have one author specified")
529                isFirstAuthor[author.type] = 1
530                continue
531            elif author.type == Person.CONTRIBUTOR_TYPE:
532                authorArray = self.contributors
533            elif author.type == Person.RESPONSIBLE_PARTY_TYPE:
534                authorArray = self.ME.responsibleParties
535               
536            # check if this is the first addition - if so, clear out the
537            # array in advance
538            if not isFirstAuthor.has_key(author.type):
539                logging.debug("Clearing out author array")
540                # NB, need to be careful to clear the array, not create a ref
541                # to a new array
542                del authorArray[:]
543                isFirstAuthor[author.type] = 1
544
545            if author.hasValue() and author not in authorArray:
546                logging.debug("Adding author (type:'%s', name:'%s', uri:'%s', role:'%s')" \
547                              %(author.type, author.name, author.uri, author.role))
548                authorArray.append(author)
549
550        logging.debug('Finished adding authors data')
551
552
553    def _isNewParameter(self, param):
554        '''
555        Check if a parameter is already specified in the atom, return False if
556        so, otherwise return True
557        '''
558        for p in self.parameters:
559            if p.term == param.term and \
560                p.scheme == param.scheme and \
561                p.label == param.label:
562                return False
563        return True
564
565
566    def addRelatedLinks(self, linkVals):
567        '''
568        Add related links in string format - converting to Link objects
569        NB, only add the link if it is unique
570       
571        @param linkVals: string of format, 'uri | title | vocabServerURL'
572        '''
573        link = self.objectify(linkVals, 'relatedLinks')
574        if link not in self.relatedLinks:
575            self.relatedLinks.append(link)
576
577
578    def addParameters(self, params):
579        '''
580        Add a parameter to list - ensuring it is unique and has been formatted and tidied appropriately
581        @params param: parameter, as string array, to add to atom parameters collection
582        '''
583        # avoid strings being parsed character by character
584        if type(params) is str:
585            params = [params]
586           
587        for param in params:
588            # firstly tidy parameter
589            param = utilities.tidyUpParameters(param)
590            category = Category()
591            # NB, data already tidied up here, so set keyword to avoid this happening again
592            category.fromString(param, escapeSpecialCharacters=False)
593
594            # now check for uniqueness
595            if self._isNewParameter(category):
596                logging.debug("Adding new parameter: %s" %param)
597                self.parameters.append(category)
598   
599   
600    def _linksToXML(self, root):
601        '''
602        Add required links to the input element
603        @param root: element to add links to - NB, should be the root element of the atom
604        '''
605        selfLink = ET.SubElement(root, "link")
606        selfLink.attrib["href"] = self.atomBrowseURL
607        selfLink.attrib["rel"] = "self"
608       
609        for relatedLink in self.relatedLinks:
610            if relatedLink.hasValue():
611                root.append(relatedLink.toXML())
612   
613    def toXML(self):
614        '''
615        Convert the atom into XML representation and return this
616        @return: xml version of atom
617        '''
618        logging.info("Creating formatted XML version of Atom")
619        root = ET.Element("entry")
620        root.attrib["xmlns"] = ndgObject.ATOM_NS
621        root.attrib["xmlns:moles"] = ndgObject.MOLES_NS
622        root.attrib["xmlns:georss"] = ndgObject.GEOSS_NS
623        root.attrib["xmlns:gml"] = ndgObject.GML_NS
624        id = ET.SubElement(root, "id")
625        id.text = self.atomID
626        title = ET.SubElement(root, "title")
627        title.text = escape(self.title or "")
628        self._linksToXML(root)
629
630        if self.author and self.author.hasValue():
631            root.append(self.author.toXML())
632           
633        for contributor in self.contributors:
634            root.append(contributor.toXML())
635
636        # add parameters data
637        for param in self.parameters:
638            if param.hasValue():
639                root.append(param.toXML())
640
641        # add the type and subtype data
642        self.__addAtomTypeDataXML(root)
643                   
644        summary = ET.SubElement(root, "summary")
645        summary.text = escape(self.summary)
646                   
647        # add link to content, if required - NB, can only have one content element in atom
648        # - and this is mandatory
649        content = ET.SubElement(root, "content")
650        contentFile = self.contentFile or self.csmlFile or self.cdmlFile
651        if contentFile:
652            content.attrib["type"] = "application/xml"
653            content.attrib["src"] = contentFile
654        else:
655            content.attrib["type"] = "xhtml"
656            div = ET.SubElement(content, 'xhtml:div')
657            div.attrib["xmlns:xhtml"] = ndgObject.XHTML_NS
658           
659            div.text = self.Content
660       
661        # if there's a published date already defined, assume we're doing an update now
662        # NB, update element is mandatory
663        currentDate = datetime.datetime.today().strftime("%Y-%m-%dT%H:%M:%SZ")
664        if not self.publishedDate:
665            self.publishedDate = currentDate
666
667        updated = ET.SubElement(root, "updated")
668        if not self.updatedDate:
669            self.updatedDate = currentDate
670        updated.text = self.updatedDate
671
672        published = ET.SubElement(root, "published")
673        published.text = self.publishedDate
674
675        # add the moles entity section, if it is required
676        if self.ME:
677            root.append(self.ME.toXML())
678
679        # add temporal range data, if available
680        temporalRange = ET.SubElement(root, "moles:temporalRange")
681        if self.t1:
682            temporalRange.text = escape(self.t1)
683            if self.t2:
684                temporalRange.text += "/" + escape(self.t2)
685
686        # add spatial range data, if available
687        self._addSpatialData(root)
688
689        tree = ET.ElementTree(root)
690        logging.info("XML version of Atom created")
691        return tree
692
693
694    def __getContent(self):
695        logging.debug("Getting content data")
696        contentString = ""
697        # NB, there must be content specified in an atom
698        if not self.content:
699            return "Metadata document"
700       
701        for content_line in self.content:
702            contentString += content_line + "\n"
703
704        return contentString
705
706    def __setContent(self, content):
707        logging.debug("Adding content data")
708        self.content = []
709        if not content:
710            return
711       
712        for content_line in content.split('\n'):
713            self.content.append(content_line)
714           
715    Content = property(fset=__setContent, fget=__getContent, doc="Atom content")
716
717           
718    def fromString(self, xmlString):
719        '''
720        Initialise Atom object using an xmlString
721        @param xmlString: representation of atom as an XML string
722        '''
723        logging.info("Ingesting data from XML string")
724        logging.debug("Create elementtree instance with XML string")
725        tree = ET.fromstring(xmlString)
726        title = tree.findtext('{%s}title' %ndgObject.ATOM_NS)
727        if title:
728            logging.debug("Adding title data")
729            self.title = unescape(title)
730
731        summary = tree.findtext('{%s}summary' %ndgObject.ATOM_NS)
732        if summary:
733            self.summary = unescape(summary)
734
735        authorElement = tree.find('{%s}author' %ndgObject.ATOM_NS)
736        if authorElement:
737            logging.debug("Adding author data")
738            author = Person()
739            author.fromETElement(authorElement)
740            self.author = author
741
742        contributorElements = tree.findall('{%s}contributor' %ndgObject.ATOM_NS)
743        for contributorElement in contributorElements:
744            logging.debug("Adding contributor data")
745            contributor = Person(personType = Person.CONTRIBUTOR_TYPE)
746            contributor.fromETElement(contributorElement)
747            self.contributors.append(contributor)
748
749        molesElement = tree.find('{%s}entity' %ndgObject.MOLES_NS)
750        if molesElement:
751            self.ME.fromET(molesElement)
752               
753        atomID = tree.findtext('{%s}id' %ndgObject.ATOM_NS)
754        self.__parseAtomID(atomID)
755       
756        self._parseCategoryData(tree.findall('{%s}category' %ndgObject.ATOM_NS))
757
758        self._parseLinksData(tree.findall('{%s}link' %ndgObject.ATOM_NS))
759           
760        contentTag = tree.find('{%s}content' %ndgObject.ATOM_NS)
761        if contentTag != None:
762            logging.debug("Found content tag - checking for CSML/CDML file data")
763            file = contentTag.attrib.get('src')
764            if file:
765                # NB, the path will reveal more reliably whether we're dealing with CSML and CDML files
766                if file.upper().find('CSML') > -1:
767                    logging.debug("Adding CSML file data")
768                    self.csmlFile = file
769                elif file.upper().find('CDML') > -1:
770                    logging.debug("Adding CDML file data")
771                    self.cdmlFile = file
772                self.contentFile = file
773            else:
774                logging.debug("No file data - adding contents of element instead")
775                # the div ns is sometimes handled differently - cope with both
776                # options
777                divEl = contentTag.find('{%s}div'%ndgObject.XHTML_NS)
778                if not divEl:
779                    divEl = contentTag.find('{%s}div'%ndgObject.ATOM_NS)
780                   
781                if divEl:
782                    div = divEl.text
783                   
784                    # NB, this can contain xhtml, so check for children
785                    for child in divEl.getchildren():
786                        div += ET.tostring(child)
787   
788                    # NB, Elementtree tends to revert the namespace of the xhtml
789                    # elements to the parent Atom NS - so switch this back
790                    div = div.replace(ndgObject.ATOM_NS, ndgObject.XHTML_NS)
791                    self.Content = div
792       
793        range = tree.findtext('{%s}temporalRange' %ndgObject.MOLES_NS)
794        if range:
795            logging.debug("Adding temporal range data")
796            timeData = range.split('/')
797            self.t1 = unescape(timeData[0])
798            if len(timeData) > 1:
799                self.t2 = unescape(timeData[1])
800       
801        where = tree.find('{%s}where' %ndgObject.GEOSS_NS)
802        if where:
803            # NB, this parser won't mind if we're dealing with Envelope or EnvelopeWithTimePeriod
804            minBBox = where.findall('.//{%s}lowerCorner' %ndgObject.GML_NS)
805            if minBBox:
806                logging.debug("Adding min spatial range data")
807                minBBox = minBBox[0]
808                spatialData = minBBox.text.split()
809                self.minX = unescape(spatialData[0])
810                if len(spatialData) > 1:
811                    self.minY = unescape(spatialData[1])
812           
813            maxBBox = where.findall('.//{%s}upperCorner' %ndgObject.GML_NS)
814            if maxBBox:
815                maxBBox = maxBBox[0]
816                logging.debug("Adding max spatial range data")
817                spatialData = maxBBox.text.split()
818                self.maxX = unescape(spatialData[0])
819                if len(spatialData) > 1:
820                    self.maxY = unescape(spatialData[1])
821               
822        publishedDate = tree.findtext('{%s}published' %ndgObject.ATOM_NS)
823        if publishedDate:
824            logging.debug("Adding published date")
825            self.publishedDate = publishedDate
826               
827        updatedDate = tree.findtext('{%s}updated' %ndgObject.ATOM_NS)
828        if updatedDate:
829            logging.debug("Adding updated date")
830            self.updatedDate = updatedDate
831           
832        logging.info("Completed data ingest")
833   
834   
835    def _parseCategoryData(self, categories):
836        logging.debug("Adding category/parameters data")
837        for category in categories:
838            cat = Category()
839            cat.fromETElement(category)
840           
841            if cat.term == self.ATOM_TYPE:
842                logging.debug("Found atom type data")
843                self.atomTypeID = cat.label
844                self.atomTypeName = self.VTD.TERM_DATA[cat.label].title
845                continue
846            elif cat.term == self.ATOM_SUBTYPE:
847                logging.debug("Found atom subtype data")
848                self.subtypeID = cat.label
849                self.subtype = cat.scheme
850                continue
851
852            self.parameters.append(cat)
853
854
855    def __parseAtomID(self, atomID):
856        '''
857        Given an atom ID, extract the useful bits of info and set these on
858        the relevant atom attributes
859        @param atomID: an atom ID in the 'tag' format
860        '''
861        logging.debug("Extracting atom info from ID, '%s'" %atomID)
862        self.atomID = atomID
863        self.datasetID = atomID.split("__ATOM__")[-1]
864        self._generateAtomName(self.datasetID)
865        logging.debug("- all info extracted")
866   
867
868    def setDatasetID(self, datasetID):
869        '''
870        Set the dataset ID for the atom - and generate an appropriate atom name using this
871        @param datasetID: ID to set for the atom
872        '''
873        self.datasetID = datasetID
874        self._generateAtomName(datasetID) 
875        self.atomID = self.createAtomID(datasetID)
876
877
878    def createAtomID(self, datasetID):
879        '''
880        Create a unique ID, conforming to atom standards, for atom
881        NB, see http://diveintomark.org/archives/2004/05/28/howto-atom-id
882        @param datasetID: ID of atom's dataset
883        @return: unique ID
884        '''
885        logging.info("Creating unique ID for atom")
886        if not self.atomBrowseURL:
887            self._generateAtomName(datasetID)
888        urlBit = self.atomBrowseURL.split('://')[1]
889        urlBit = urlBit.replace('#', '')
890        urlBits = urlBit.split('/')
891        host = urlBits[0].split(':')[0] # avoid the port colon - as this breaks the ID format
892        dateBit = datetime.datetime.today().strftime("%Y-%m-%d")
893       
894        id = "tag:" + host + "," + dateBit + ":/" + "/".join(urlBits[1:])
895        logging.info("- unique ID created for atom")
896        logging.debug(" - '%s'" %id)
897        return id
898       
899       
900    def _generateAtomName(self, datasetID):
901        '''
902        Generate a consistent name for the atom - with full eXist doc path
903        @param datasetID: ID of atom's dataset
904        '''
905        self.atomName = datasetID + ".atom"
906        if not self.ME.providerID:
907            raise ValueError("Provider ID has not been specified for atom - please add this and retry")
908        self.ndgURI = self.ME.providerID + "__ATOM__" + datasetID
909        self.atomBrowseURL = VTD.BROWSE_ROOT_URL + self.ndgURI
910
911
912    def _parseLinksData(self, links):
913        '''
914        Extract links and atom data from array of link elements in the XML representation of the atom
915        @param links: an array of <link> elements
916        '''
917        # firstly, get all data to start with, so we can properly process it afterwards
918        linkData = {}
919        logging.debug("Getting link data")
920        for linkTag in links:
921            link = Link()
922            link.fromETElement(linkTag)
923
924            if not linkData.has_key(link.rel):
925                linkData[link.rel] = []
926           
927            linkData[link.rel].append(link)
928
929        # there should be one self referencing link - which will provide info on the atom itself
930        if not linkData.has_key('self'):
931            errorMessage = "Atom does not have self referencing link - " + \
932                "cannot ascertain datasetID without this - please fix"
933            logging.error(errorMessage)
934            raise ValueError(errorMessage)
935       
936        # this is the link describing the atom itself
937        self.atomBrowseURL = linkData['self'][0].href
938       
939        self.datasetID = self.atomBrowseURL.split("__ATOM__")[-1]
940        self.atomName = self.datasetID + ".atom"
941        # NB, only split on the stem, since the browse host may not be
942        # the same as that defined in VTD
943        self.ndgURI = self.atomBrowseURL.split(VTD.BROWSE_STEM_URL)[-1]
944       
945        # now remove this value and the associated moles doc link
946        del linkData['self']
947        molesDoc = self.atomBrowseURL.replace('ATOM', 'NDG-B1')
948        if linkData.has_key('related'):
949            relatedLinks = []
950            for link in linkData['related']:
951                if link.href != molesDoc:
952                    relatedLinks.append(link)
953           
954            linkData['related'] = relatedLinks
955               
956        # now add the remaining links to the atom
957        for key in linkData:
958            for link in linkData[key]:
959                logging.debug("Adding link data")
960                self.relatedLinks.append(link)
961       
962
963    def _addSpatialData(self, element):
964        '''
965        Add spatial coverage element to an input element
966        @param element: element to add coverage data to
967        '''
968        logging.info("Adding spatial data to Atom")
969        if not self.minX:
970            logging.info("No spatial data specified")
971            return
972        bbox = ET.SubElement(element, "georss:where")
973        envelope = ET.SubElement(bbox, "gml:Envelope")
974        lc = ET.SubElement(envelope, "gml:lowerCorner")
975        lc.text = escape(str(self.minX) + " " + str(self.minY))
976        uc = ET.SubElement(envelope, "gml:upperCorner")
977        uc.text = escape(str(self.maxX) + " " + str(self.maxY))
978
979       
980    def setAttribute(self, attributeName, attributeValue, escapeSpecials = True):
981        '''
982        Set the value of an atom attribute - and do some basic tidying up of the string content
983        - to escape any XML unfriendly characters
984        @param attributeName: name of the attribute whose value to set
985        @param attributeValue: value to set the attribute to 
986        @keyword escapeSpecials: if true, escape any special characters in the attribute
987        content.  Default = True
988        '''
989        logging.debug("Setting attribute, %s, to %s" %(attributeName, attributeValue))
990        origValue = attributeValue
991       
992        # escape any special characters if a value has been specified
993        # NB, need to cope with both single values and arrays
994        isList = True
995        if attributeValue:
996            if not isinstance(attributeValue, list):
997                attributeValue = [attributeValue]
998                isList = False
999               
1000            newVals = []
1001            for val in attributeValue:
1002                data = val
1003                if escapeSpecials:
1004                    utilities.escapeSpecialCharacters(val)
1005                newVals.append(self.objectify(data, attributeName))
1006            attributeValue = newVals
1007
1008        # handle the special case of authors; only one author is allowed per atom
1009        # - the others should be treated as contributors
1010        if attributeName == "authors":
1011            setattr(self, "author", attributeValue[0])
1012            if len(attributeValue) > 1:
1013                setattr(self, "contributors", attributeValue[1:])
1014        elif attributeName == "atomAuthors":
1015            self.ME.responsibleParties.extend(attributeValue)
1016        elif attributeName == "files":
1017            self.addUniqueRelatedLinks(attributeValue)
1018        else:
1019            if not isList:
1020                attributeValue = attributeValue[0]
1021            setattr(self, attributeName, attributeValue)
1022
1023
1024    def objectify(self, objectVals, attributeName):
1025        '''
1026        Some inputs are specified as strings but need to be converted into
1027        objects - do this here
1028        @param objectVals: a '|' delimited string of values
1029        @param attributeName: name of attribute the values belong to
1030        '''
1031        obj = None
1032        if type(objectVals) != str:
1033            return objectVals
1034       
1035        if attributeName == "relatedLinks":
1036            obj = Link()
1037        elif attributeName == "atomAuthors":
1038            obj = Person(personType = Person.RESPONSIBLE_PARTY_TYPE)
1039        elif attributeName == "authors":
1040            # NB, ensure there is only one author tag - extra authors are contributors
1041            authorType = Person.AUTHOR_TYPE
1042            if self.author and self.author.hasValue():
1043                authorType= Person.CONTRIBUTOR_TYPE
1044            obj = Person(personType = authorType)
1045        elif attributeName == 'files':
1046            obj = Link()
1047            objectVals = '%s|%s|%s' \
1048                %(self.VTD.getTermCurrentVocabURL(VTD.METADATA_SOURCE_TERM), objectVals, VTD.METADATA_SOURCE_TERM)
1049
1050        if obj:
1051            obj.fromString(objectVals)
1052            # NB, need to set it now, just in case we don't set it before coming back
1053            if attributeName == "authors" and (not self.author or not self.author.hasValue()):
1054                self.author = obj
1055            return obj
1056       
1057        return objectVals
1058
1059
1060    def toPrettyXML(self):
1061        '''
1062        Returns nicely formatted XML as string
1063        '''
1064        atomXML = self.toXML()
1065
1066        # create the string
1067        logging.debug("Converting the elementtree object into a string")
1068        prettyXML = et2text(atomXML.getroot())
1069
1070        # add XML version tag
1071        prettyXML = "<?xml version=\"1.0\" encoding=\"utf-8\" ?>\n" + prettyXML
1072        logging.info("Created formatted version of XML object")
1073        return prettyXML
1074
1075
1076    def getLinksOfType(self, termID):
1077        '''
1078        Returns links in the atom related links attribute which match the specified
1079        term ID
1080        @param termID: the termID to look for in the related links - NB, this is
1081        matched to the end of the link.rel value
1082        @return links: array of Link objects with matching term type
1083        '''
1084        logging.debug("Getting atom links of type, '%s'" %termID)
1085        matchingLinks = []
1086        for link in self.relatedLinks:
1087            # firstly, handle special case where we only want the online ref type links
1088            # returned
1089            if termID == self.ONLINE_REF_LABEL:
1090                if not link.isChildAtom():
1091                    logging.debug("- found link with matching term type")
1092                    matchingLinks.append(link)
1093               
1094            elif link and link.rel and link.rel.lower().endswith(termID.lower()):
1095                logging.debug("- found link with matching term type")
1096                matchingLinks.append(link)
1097               
1098        logging.debug("Returning matched links")
1099        return matchingLinks
1100       
1101       
1102    def getLogos(self):
1103        '''
1104        Return related links that are logos
1105        @return: array of Links containing the logos for the atom
1106        '''
1107        logos = []
1108        for link in self.relatedLinks:
1109            if link.rel.lower().endswith(VTD.LOGO_TERM.lower()):
1110                logos.append(link)
1111               
1112        return logos
1113   
1114   
1115    def isGranule(self):
1116        if self.atomTypeID == VTD.GRANULE_TERM:
1117            return True
1118        return False
1119   
1120   
1121    def isDE(self):
1122        if self.atomTypeID == VTD.DE_TERM:
1123            return True
1124        return False
1125   
1126    def isDeployment(self):
1127        if self.subtypeID and self.subtypeID == VTD.DEPLOYMENT_TERM:
1128            return True
1129        return False
1130   
1131    def isDeployable(self):
1132        if (self.atomTypeID == VTD.ACTIVITY_TERM and self.subtypeID != VTD.DEPLOYMENT_TERM) or \
1133            self.atomTypeID == VTD.DPT_TERM or \
1134            self.atomTypeID == VTD.OBS_TERM:
1135            return True
1136        return False
1137   
1138    def isPublished(self):
1139        '''
1140        Check state of atom doc - if published or Published return True,
1141        otherwise return False
1142        '''
1143        return self.state.isPublishedState()
1144       
1145       
1146    def addCSMLData(self, csmlName, csmlContent, aggregateCoverage=False, useCSMLID=False):
1147        '''
1148        Parse CSML data and add extracted info to the atom
1149        @param csmlName: name of the csml file
1150        @param csmlContent: content of the csml file - NB, if this is set to None and the
1151        file, csmlName, is available locally, CsmlParser.Dataset will read in the file
1152        directly
1153        @keyword aggregateCoverage: if set to True, only coverage data that extends the
1154        atom coverage data will be added
1155        @keyword useCSMLID: if True, use the CSML doc ID as the dataset ID - NB,
1156        this should only be True if creating a new atom - e.g. from a granulite
1157        @return csmlDoc: the CsmlParser.Dataset object with the csml data in
1158        '''
1159        logging.info("Creating CSML data model")
1160        self.csmlFile = csmlName
1161        self.contentFile = csmlName
1162        content = csmlContent or csmlName
1163   
1164        csmlDoc = CsmlParser.Dataset(file=content)
1165       
1166        logging.info("Extracting info from CSML file")
1167        logging.debug("Got dataset ID: %s" %csmlDoc.id)
1168        if useCSMLID:
1169            logging.debug(" - using this ID for the atom")
1170            self.setDatasetID(VTD.GRANULE_TERM + '_' + csmlDoc.id)
1171       
1172        title = csmlDoc.name.CONTENT
1173        logging.debug("Got dataset name (title): '%s'" %title)
1174        # NB, if a title is specified (and not as the default value), it automatically is used in
1175        # place of anything in the granulite file
1176        if title and title != "NAME OF DATASET GOES HERE":
1177            logging.info("Title, '%s', extracted from CSML file" %title)
1178            if self.title:
1179                logging.info("- NB, this will override the title specified in the granulite file ('%s')" \
1180                             %self.title)
1181            self.title = title
1182               
1183        bbox1 = csmlDoc.getBoundingBox()
1184        bbox2 = csmlDoc.getCSMLBoundingBox()
1185
1186        time = None
1187        if bbox2:
1188            time = bbox2.getTimeLimits()
1189   
1190        # now check for other parameters to add to granule
1191        # Firstly, extract the bounding envelope
1192        if bbox1:
1193            w, e = utilities.normaliseLongitude(bbox1[0],bbox1[2])
1194            n, s = (bbox1[3], bbox1[1])
1195   
1196            if not aggregateCoverage or (not self.maxY or float(n) > float(self.maxY)):
1197                self.maxY = n
1198               
1199            if not aggregateCoverage or (not self.minY or float(s) < float(self.minY)):
1200                self.minY = s
1201           
1202            if not aggregateCoverage or (not self.minX or float(w) < float(self.minX)):
1203                self.minX = w
1204   
1205            if not aggregateCoverage or (not self.maxX or float(e) > float(self.maxX)):
1206                self.maxX = e
1207           
1208            logging.debug("Got bounding box data from file: (%s, %s) , (%s, %s)" \
1209                          %(w, s, e, n))
1210           
1211            logging.debug("Updated atom bounding box data: (%s, %s) , (%s, %s)" \
1212                          %(self.minX, self.minY, self.maxX, self.maxY))
1213        else:
1214            logging.debug("No valid bounding box data found")
1215   
1216        if time:
1217            t1 = utilities.formatDateYYYYMMDD(time[0])
1218            if not aggregateCoverage or \
1219                (not self.t1 or datetime.datetime.strptime(t1, YEAR_FORMAT) < \
1220                    datetime.datetime.strptime(self.t1, YEAR_FORMAT)):
1221                self.t1 = t1
1222   
1223            t2 = time[1]
1224            if t2 and t2 != 'None':
1225                t2 = utilities.formatDateYYYYMMDD(t2)
1226                if not aggregateCoverage or \
1227                    (not self.t2 or datetime.datetime.strptime(t2, YEAR_FORMAT) > \
1228                        datetime.datetime.strptime(self.t2, YEAR_FORMAT)):
1229                    self.t2 = t2
1230           
1231            logging.debug("Got time range: %s -> %s" %(self.t1, self.t2))
1232        else:
1233            logging.debug("No valid time range data found")
1234   
1235        #create parameter summaries:
1236        #set up list to hold the parameters data
1237        parameters = []
1238        for feature in csmlDoc.featureCollection.featureMembers:
1239            if hasattr(feature.parameter, 'href'):
1240                paramTriple = ""
1241                if hasattr(feature, 'description'):
1242                    paramTriple = feature.description.CONTENT
1243                    paramTriple += " | " + feature.parameter.href
1244                   
1245                    term = ""
1246                    if hasattr(feature, 'name'):
1247                        term = feature.name.CONTENT
1248   
1249                    paramTriple += " | " + term
1250                   
1251                    logging.debug("Got parameter info: %s" %paramTriple)
1252                    parameters.append(paramTriple)
1253       
1254        # update the atom with the extracted parameters
1255        logging.info("Adding CSML parameters to granule atom")
1256        self.addParameters(parameters)
1257        logging.info("Finished adding CSML data")
1258        return csmlDoc
1259
1260
1261    def lookupAssociatedData(self, type, searchClient, lookupIndirectReferences=False):
1262        '''
1263        Check through the atom links and retrieve any associated data of the
1264        specified type
1265        @param type: type of associated data to lookup - currently VTD.DEPLOYMENT_TERM
1266        or VTD.DE_TERM
1267        @param searchClient: Client implementing the AbstractSearchXMLDBClient class
1268        @keyword lookupIndirectReferences: if True, the atom ID is used to search
1269        defined deployments to find those which reference it, otherwise only
1270        deployments data featured in the atom related links are processed
1271        '''
1272        logging.info("Looking up %s info" %type)
1273        self.allActivities = []
1274        self.allObs = []
1275        self.allDpts = []
1276
1277        if type != VTD.DE_TERM and type != VTD.DEPLOYMENT_TERM:
1278            raise ValueError('Unrecognised associated data type: %s' %type)
1279       
1280        # avoid duplicating lookup effort
1281        if (type == VTD.DEPLOYMENT_TERM and self.deployments) or \
1282            (type == VTD.DE_TERM and self.dataEntities):
1283            logging.info("- this info has already been looked up - returning")
1284            return
1285
1286        # firstly, collect all the references to the info required
1287        if lookupIndirectReferences:
1288            logging.info("Looking up indirect references")
1289           
1290            # if we're looking up DE data for deployments data, need to have the
1291            # deployments info looked up first
1292            if type == VTD.DE_TERM and self.isDeployable() and not self.deployments:
1293                self.lookupAssociatedData(VTD.DEPLOYMENT_TERM, searchClient, 
1294                                          lookupIndirectReferences = lookupIndirectReferences)
1295           
1296            logging.info("Looking up references to this atom from other %s" %type)
1297           
1298            # NB, if we're looking up deployments info, we only look up references
1299            # to this atom - if we're looking up DEs, we need to look up references
1300            # to the deployments referenced by this atom
1301            urls = [self.atomBrowseURL]
1302           
1303            if type == VTD.DE_TERM and self.isDeployable():
1304                urls = []
1305                for dep in self.deployments:
1306                    urls.append(dep.browseURL)
1307                   
1308            links = []
1309            for url in urls:
1310                doc = searchClient.getNDGDoc(type, ndgObject.ASSOCIATED_ATOM_DOC_TYPE, url,
1311                                             targetCollection = dc.ATOM_COLLECTION_PATH)
1312                # now need to turn this results set into actual atoms
1313                tree = ET.fromstring(doc)
1314                for atom in tree:
1315                    logging.debug("- found reference in %s" %type)
1316                    links.append(ET.tostring(atom))
1317                   
1318            logging.info("Finished looking up indirect references")
1319        else:
1320            links = self.getLinksOfType(self.VTD.DEPLOYMENT_TERM)
1321
1322        # now retrieve the references and extract the required data
1323        logging.info("Retrieving info from %s references" %type)
1324        if type == VTD.DEPLOYMENT_TERM:
1325            logging.info("Extracting links data to deployment entitites")
1326            self.deployments = []
1327            for link in links:
1328                if lookupIndirectReferences:
1329                    deploymentAtom = link
1330                else:
1331                    localID = link.href.split("__ATOM__")[-1]
1332                    deploymentAtom = searchClient.getNDGDoc('', 
1333                                                            'ATOM', localID, 
1334                                                            targetCollection = dc.ATOM_COLLECTION_PATH)
1335   
1336                deployment = Deployment.Deployment(Atom(xmlString=str(deploymentAtom)))
1337                self.deployments.append(deployment)
1338               
1339                self.addUniqueLinks(self.allActivities, deployment.activities)
1340                self.addUniqueLinks(self.allObs, deployment.obs)
1341                self.addUniqueLinks(self.allDpts, deployment.dpts)
1342        else:
1343            # for DE data, just store the title + link in a Link object
1344            self.dataEntities = []
1345            logging.info("Extracting links data to data entitites")
1346            for data in links:
1347                atom = Atom(xmlString=str(data))
1348                link = Link()
1349                link.title = atom.title
1350                link.href = atom.atomBrowseURL
1351                link.rel = atom.datasetID
1352               
1353                # NB, different deployments may be used by the same DE - so
1354                # avoid duplication
1355                self.addUniqueLinks(self.dataEntities, link)
1356           
1357        logging.info("Finished looking up %s info" %type)
1358
1359
1360    def addUniqueLinks(self, dataArray, links):
1361        '''
1362        Add links to specified array - if they are not already included
1363        @param dataArray: a list, potentially arlready containing links
1364        @param links: a Link or array of Links to add to the dataArray
1365        '''
1366        logging.debug("Adding new links")
1367        if not links:
1368            return
1369       
1370        if type(links) is not list:
1371            links = [links]
1372       
1373        for link in links:
1374            if type(link) is not Link:
1375                logging.warning("Link is not of 'Link' object type (type='%s') - skipping" %type(link))
1376                continue
1377            if link not in dataArray:
1378                logging.debug("- adding unique link")
1379                dataArray.append(link)
1380        logging.debug("Finished adding links")
1381
1382       
1383    def getFullPath(self):
1384        '''
1385        Return full path to atom in eXist, if it exists, or None, otherwise
1386        @return fullPath: string - collection + filename of atom in eXist
1387        '''
1388        # NB, name assigned when atom created in eXist - so if not defined, not
1389        # in eXist
1390        logging.debug("Getting full path to atom")
1391        if self.atomName:
1392            logging.debug("Return full path to atom in eXist")
1393            return self.getDefaultCollectionPath() + self.atomName
1394        logging.debug("Atom doesn't currently exist in eXist - return 'None'")
1395        return None
1396   
1397   
1398    def getSubTypePrettyName(self):
1399        '''
1400        Return the subtype of the atom in a human readable form
1401        @return: sub type of atom as a verbose string
1402        '''
1403        logging.debug("Getting human readable version of atom subtype")
1404        subType = self.SUB_TYPE_NOT_DEFINED_NAME
1405        if self.subtypeID:
1406           subType = self.VTD.tidySubTypeTitle(self.subtypeID)
1407           
1408        logging.debug("- returning subtype: '%s'" %subType)
1409        return subType
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