source: ndgCommon/trunk/ndg/common/src/models/Atom.py @ 5215

Subversion URL: http://proj.badc.rl.ac.uk/svn/ndg/ndgCommon/trunk/ndg/common/src/models/Atom.py@5215
Revision 5215, 53.5 KB checked in by cbyrom, 11 years ago (diff)

Remove Summary property and just use the simpler 'summary' single
string field.

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)
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, 'div')
657            div.attrib["xmlns:xhtml"] = ndgObject.XHTML_NS
658            div.text = self.Content
659       
660        # if there's a published date already defined, assume we're doing an update now
661        # NB, update element is mandatory
662        currentDate = datetime.datetime.today().strftime("%Y-%m-%dT%H:%M:%SZ")
663        if not self.publishedDate:
664            self.publishedDate = currentDate
665
666        updated = ET.SubElement(root, "updated")
667        if not self.updatedDate:
668            self.updatedDate = currentDate
669        updated.text = self.updatedDate
670
671        published = ET.SubElement(root, "published")
672        published.text = self.publishedDate
673
674        # add the moles entity section, if it is required
675        if self.ME:
676            root.append(self.ME.toXML())
677
678        # add temporal range data, if available
679        temporalRange = ET.SubElement(root, "moles:temporalRange")
680        if self.t1:
681            temporalRange.text = escape(self.t1)
682            if self.t2:
683                temporalRange.text += "/" + escape(self.t2)
684
685        # add spatial range data, if available
686        self._addSpatialData(root)
687
688        tree = ET.ElementTree(root)
689        logging.info("XML version of Atom created")
690        return tree
691
692
693    def __getContent(self):
694        logging.debug("Getting content data")
695        contentString = ""
696        # NB, there must be content specified in an atom
697        if not self.content:
698            return "Metadata document"
699       
700        for content_line in self.content:
701            contentString += content_line + "\n"
702
703        return contentString
704
705    def __setContent(self, content):
706        logging.debug("Adding content data")
707        self.content = []
708        if not content:
709            return
710       
711        for content_line in content.split('\n'):
712            self.content.append(content_line)
713           
714    Content = property(fset=__setContent, fget=__getContent, doc="Atom content")
715
716           
717    def fromString(self, xmlString):
718        '''
719        Initialise Atom object using an xmlString
720        @param xmlString: representation of atom as an XML string
721        '''
722        logging.info("Ingesting data from XML string")
723        logging.debug("Create elementtree instance with XML string")
724        tree = ET.fromstring(xmlString)
725        title = tree.findtext('{%s}title' %ndgObject.ATOM_NS)
726        if title:
727            logging.debug("Adding title data")
728            self.title = unescape(title)
729
730        summary = tree.findtext('{%s}summary' %ndgObject.ATOM_NS)
731        if summary:
732            self.summary = unescape(summary)
733
734        authorElement = tree.find('{%s}author' %ndgObject.ATOM_NS)
735        if authorElement:
736            logging.debug("Adding author data")
737            author = Person()
738            author.fromETElement(authorElement)
739            self.author = author
740
741        contributorElements = tree.findall('{%s}contributor' %ndgObject.ATOM_NS)
742        for contributorElement in contributorElements:
743            logging.debug("Adding contributor data")
744            contributor = Person(personType = Person.CONTRIBUTOR_TYPE)
745            contributor.fromETElement(contributorElement)
746            self.contributors.append(contributor)
747
748        molesElement = tree.find('{%s}entity' %ndgObject.MOLES_NS)
749        if molesElement:
750            self.ME.fromET(molesElement)
751               
752        atomID = tree.findtext('{%s}id' %ndgObject.ATOM_NS)
753        self.__parseAtomID(atomID)
754       
755        self._parseCategoryData(tree.findall('{%s}category' %ndgObject.ATOM_NS))
756
757        self._parseLinksData(tree.findall('{%s}link' %ndgObject.ATOM_NS))
758           
759        contentTag = tree.find('{%s}content' %ndgObject.ATOM_NS)
760        if contentTag != None:
761            logging.debug("Found content tag - checking for CSML/CDML file data")
762            file = contentTag.attrib.get('src')
763            if file:
764                # NB, the path will reveal more reliably whether we're dealing with CSML and CDML files
765                if file.upper().find('CSML') > -1:
766                    logging.debug("Adding CSML file data")
767                    self.csmlFile = file
768                elif file.upper().find('CDML') > -1:
769                    logging.debug("Adding CDML file data")
770                    self.cdmlFile = file
771                self.contentFile = file
772            else:
773                logging.debug("No file data - adding contents of element instead")
774                divEl = contentTag.find('{%s}div'%ndgObject.ATOM_NS)#XHTML_NS)
775                div = divEl.text
776               
777                # NB, this can contain xhtml, so check for children
778                for child in divEl.getchildren():
779                    div += ET.tostring(child)
780                   
781                self.Content = div
782       
783        range = tree.findtext('{%s}temporalRange' %ndgObject.MOLES_NS)
784        if range:
785            logging.debug("Adding temporal range data")
786            timeData = range.split('/')
787            self.t1 = unescape(timeData[0])
788            if len(timeData) > 1:
789                self.t2 = unescape(timeData[1])
790       
791        where = tree.find('{%s}where' %ndgObject.GEOSS_NS)
792        if where:
793            # NB, this parser won't mind if we're dealing with Envelope or EnvelopeWithTimePeriod
794            minBBox = where.findall('.//{%s}lowerCorner' %ndgObject.GML_NS)
795            if minBBox:
796                logging.debug("Adding min spatial range data")
797                minBBox = minBBox[0]
798                spatialData = minBBox.text.split()
799                self.minX = unescape(spatialData[0])
800                if len(spatialData) > 1:
801                    self.minY = unescape(spatialData[1])
802           
803            maxBBox = where.findall('.//{%s}upperCorner' %ndgObject.GML_NS)
804            if maxBBox:
805                maxBBox = maxBBox[0]
806                logging.debug("Adding max spatial range data")
807                spatialData = maxBBox.text.split()
808                self.maxX = unescape(spatialData[0])
809                if len(spatialData) > 1:
810                    self.maxY = unescape(spatialData[1])
811               
812        publishedDate = tree.findtext('{%s}published' %ndgObject.ATOM_NS)
813        if publishedDate:
814            logging.debug("Adding published date")
815            self.publishedDate = publishedDate
816               
817        updatedDate = tree.findtext('{%s}updated' %ndgObject.ATOM_NS)
818        if updatedDate:
819            logging.debug("Adding updated date")
820            self.updatedDate = updatedDate
821           
822        logging.info("Completed data ingest")
823   
824   
825    def _parseCategoryData(self, categories):
826        logging.debug("Adding category/parameters data")
827        for category in categories:
828            cat = Category()
829            cat.fromETElement(category)
830           
831            if cat.term == self.ATOM_TYPE:
832                logging.debug("Found atom type data")
833                self.atomTypeID = cat.label
834                self.atomTypeName = self.VTD.TERM_DATA[cat.label].title
835                continue
836            elif cat.term == self.ATOM_SUBTYPE:
837                logging.debug("Found atom subtype data")
838                self.subtypeID = cat.label
839                self.subtype = cat.scheme
840                continue
841
842            self.parameters.append(cat)
843
844
845    def __parseAtomID(self, atomID):
846        '''
847        Given an atom ID, extract the useful bits of info and set these on
848        the relevant atom attributes
849        @param atomID: an atom ID in the 'tag' format
850        '''
851        logging.debug("Extracting atom info from ID, '%s'" %atomID)
852        self.atomID = atomID
853        self.datasetID = atomID.split("__ATOM__")[-1]
854        self._generateAtomName(self.datasetID)
855        logging.debug("- all info extracted")
856   
857
858    def setDatasetID(self, datasetID):
859        '''
860        Set the dataset ID for the atom - and generate an appropriate atom name using this
861        @param datasetID: ID to set for the atom
862        '''
863        self.datasetID = datasetID
864        self._generateAtomName(datasetID) 
865        self.atomID = self.createAtomID(datasetID)
866
867
868    def createAtomID(self, datasetID):
869        '''
870        Create a unique ID, conforming to atom standards, for atom
871        NB, see http://diveintomark.org/archives/2004/05/28/howto-atom-id
872        @param datasetID: ID of atom's dataset
873        @return: unique ID
874        '''
875        logging.info("Creating unique ID for atom")
876        if not self.atomBrowseURL:
877            self._generateAtomName(datasetID)
878        urlBit = self.atomBrowseURL.split('://')[1]
879        urlBit = urlBit.replace('#', '')
880        urlBits = urlBit.split('/')
881        host = urlBits[0].split(':')[0] # avoid the port colon - as this breaks the ID format
882        dateBit = datetime.datetime.today().strftime("%Y-%m-%d")
883       
884        id = "tag:" + host + "," + dateBit + ":/" + "/".join(urlBits[1:])
885        logging.info("- unique ID created for atom")
886        logging.debug(" - '%s'" %id)
887        return id
888       
889       
890    def _generateAtomName(self, datasetID):
891        '''
892        Generate a consistent name for the atom - with full eXist doc path
893        @param datasetID: ID of atom's dataset
894        '''
895        self.atomName = datasetID + ".atom"
896        if not self.ME.providerID:
897            raise ValueError("Provider ID has not been specified for atom - please add this and retry")
898        self.ndgURI = self.ME.providerID + "__ATOM__" + datasetID
899        self.atomBrowseURL = VTD.BROWSE_ROOT_URL + self.ndgURI
900
901
902    def _parseLinksData(self, links):
903        '''
904        Extract links and atom data from array of link elements in the XML representation of the atom
905        @param links: an array of <link> elements
906        '''
907        # firstly, get all data to start with, so we can properly process it afterwards
908        linkData = {}
909        logging.debug("Getting link data")
910        for linkTag in links:
911            link = Link()
912            link.fromETElement(linkTag)
913
914            if not linkData.has_key(link.rel):
915                linkData[link.rel] = []
916           
917            linkData[link.rel].append(link)
918
919        # there should be one self referencing link - which will provide info on the atom itself
920        if not linkData.has_key('self'):
921            errorMessage = "Atom does not have self referencing link - " + \
922                "cannot ascertain datasetID without this - please fix"
923            logging.error(errorMessage)
924            raise ValueError(errorMessage)
925       
926        # this is the link describing the atom itself
927        self.atomBrowseURL = linkData['self'][0].href
928       
929        self.datasetID = self.atomBrowseURL.split("__ATOM__")[-1]
930        self.atomName = self.datasetID + ".atom"
931        # NB, only split on the stem, since the browse host may not be
932        # the same as that defined in VTD
933        self.ndgURI = self.atomBrowseURL.split(VTD.BROWSE_STEM_URL)[-1]
934       
935        # now remove this value and the associated moles doc link
936        del linkData['self']
937        molesDoc = self.atomBrowseURL.replace('ATOM', 'NDG-B1')
938        if linkData.has_key('related'):
939            relatedLinks = []
940            for link in linkData['related']:
941                if link.href != molesDoc:
942                    relatedLinks.append(link)
943           
944            linkData['related'] = relatedLinks
945               
946        # now add the remaining links to the atom
947        for key in linkData:
948            for link in linkData[key]:
949                logging.debug("Adding link data")
950                self.relatedLinks.append(link)
951       
952
953    def _addSpatialData(self, element):
954        '''
955        Add spatial coverage element to an input element
956        @param element: element to add coverage data to
957        '''
958        logging.info("Adding spatial data to Atom")
959        if not self.minX:
960            logging.info("No spatial data specified")
961            return
962        bbox = ET.SubElement(element, "georss:where")
963        envelope = ET.SubElement(bbox, "gml:Envelope")
964        lc = ET.SubElement(envelope, "gml:lowerCorner")
965        lc.text = escape(str(self.minX) + " " + str(self.minY))
966        uc = ET.SubElement(envelope, "gml:upperCorner")
967        uc.text = escape(str(self.maxX) + " " + str(self.maxY))
968
969       
970    def setAttribute(self, attributeName, attributeValue, escapeSpecials = True):
971        '''
972        Set the value of an atom attribute - and do some basic tidying up of the string content
973        - to escape any XML unfriendly characters
974        @param attributeName: name of the attribute whose value to set
975        @param attributeValue: value to set the attribute to 
976        @keyword escapeSpecials: if true, escape any special characters in the attribute
977        content.  Default = True
978        '''
979        logging.debug("Setting attribute, %s, to %s" %(attributeName, attributeValue))
980        origValue = attributeValue
981       
982        # escape any special characters if a value has been specified
983        # NB, need to cope with both single values and arrays
984        isList = True
985        if attributeValue:
986            if not isinstance(attributeValue, list):
987                attributeValue = [attributeValue]
988                isList = False
989               
990            newVals = []
991            for val in attributeValue:
992                data = val
993                if escapeSpecials:
994                    utilities.escapeSpecialCharacters(val)
995                newVals.append(self.objectify(data, attributeName))
996            attributeValue = newVals
997
998        # handle the special case of authors; only one author is allowed per atom
999        # - the others should be treated as contributors
1000        if attributeName == "authors":
1001            setattr(self, "author", attributeValue[0])
1002            if len(attributeValue) > 1:
1003                setattr(self, "contributors", attributeValue[1:])
1004        elif attributeName == "atomAuthors":
1005            self.ME.responsibleParties.extend(attributeValue)
1006        elif attributeName == "files":
1007            self.addUniqueRelatedLinks(attributeValue)
1008        else:
1009            if not isList:
1010                attributeValue = attributeValue[0]
1011            setattr(self, attributeName, attributeValue)
1012
1013
1014    def objectify(self, objectVals, attributeName):
1015        '''
1016        Some inputs are specified as strings but need to be converted into
1017        objects - do this here
1018        @param objectVals: a '|' delimited string of values
1019        @param attributeName: name of attribute the values belong to
1020        '''
1021        obj = None
1022        if type(objectVals) != str:
1023            return objectVals
1024       
1025        if attributeName == "relatedLinks":
1026            obj = Link()
1027        elif attributeName == "atomAuthors":
1028            obj = Person(personType = Person.RESPONSIBLE_PARTY_TYPE)
1029        elif attributeName == "authors":
1030            # NB, ensure there is only one author tag - extra authors are contributors
1031            authorType = Person.AUTHOR_TYPE
1032            if self.author and self.author.hasValue():
1033                authorType= Person.CONTRIBUTOR_TYPE
1034            obj = Person(personType = authorType)
1035        elif attributeName == 'files':
1036            obj = Link()
1037            objectVals = '%s|%s|%s' \
1038                %(self.VTD.getTermCurrentVocabURL(VTD.METADATA_SOURCE_TERM), objectVals, VTD.METADATA_SOURCE_TERM)
1039
1040        if obj:
1041            obj.fromString(objectVals)
1042            # NB, need to set it now, just in case we don't set it before coming back
1043            if attributeName == "authors" and (not self.author or not self.author.hasValue()):
1044                self.author = obj
1045            return obj
1046       
1047        return objectVals
1048
1049
1050    def toPrettyXML(self):
1051        '''
1052        Returns nicely formatted XML as string
1053        '''
1054        atomXML = self.toXML()
1055
1056        # create the string
1057        logging.debug("Converting the elementtree object into a string")
1058        prettyXML = et2text(atomXML.getroot())
1059
1060        # add XML version tag
1061        prettyXML = "<?xml version=\"1.0\" encoding=\"utf-8\" ?>\n" + prettyXML
1062        logging.info("Created formatted version of XML object")
1063        return prettyXML
1064
1065
1066    def getLinksOfType(self, termID):
1067        '''
1068        Returns links in the atom related links attribute which match the specified
1069        term ID
1070        @param termID: the termID to look for in the related links - NB, this is
1071        matched to the end of the link.rel value
1072        @return links: array of Link objects with matching term type
1073        '''
1074        logging.debug("Getting atom links of type, '%s'" %termID)
1075        matchingLinks = []
1076        for link in self.relatedLinks:
1077            # firstly, handle special case where we only want the online ref type links
1078            # returned
1079            if termID == self.ONLINE_REF_LABEL:
1080                if not link.isChildAtom():
1081                    logging.debug("- found link with matching term type")
1082                    matchingLinks.append(link)
1083               
1084            elif link and link.rel and link.rel.lower().endswith(termID.lower()):
1085                logging.debug("- found link with matching term type")
1086                matchingLinks.append(link)
1087               
1088        logging.debug("Returning matched links")
1089        return matchingLinks
1090       
1091       
1092    def getLogos(self):
1093        '''
1094        Return related links that are logos
1095        @return: array of Links containing the logos for the atom
1096        '''
1097        logos = []
1098        for link in self.relatedLinks:
1099            if link.rel.lower().endswith(VTD.LOGO_TERM.lower()):
1100                logos.append(link)
1101               
1102        return logos
1103   
1104   
1105    def isGranule(self):
1106        if self.atomTypeID == VTD.GRANULE_TERM:
1107            return True
1108        return False
1109   
1110   
1111    def isDE(self):
1112        if self.atomTypeID == VTD.DE_TERM:
1113            return True
1114        return False
1115   
1116    def isDeployment(self):
1117        if self.subtypeID and self.subtypeID == VTD.DEPLOYMENT_TERM:
1118            return True
1119        return False
1120   
1121    def isDeployable(self):
1122        if (self.atomTypeID == VTD.ACTIVITY_TERM and self.subtypeID != VTD.DEPLOYMENT_TERM) or \
1123            self.atomTypeID == VTD.DPT_TERM or \
1124            self.atomTypeID == VTD.OBS_TERM:
1125            return True
1126        return False
1127   
1128    def isPublished(self):
1129        '''
1130        Check state of atom doc - if published or Published return True,
1131        otherwise return False
1132        '''
1133        return self.state.isPublishedState()
1134       
1135       
1136    def addCSMLData(self, csmlName, csmlContent, aggregateCoverage=False, useCSMLID=False):
1137        '''
1138        Parse CSML data and add extracted info to the atom
1139        @param csmlName: name of the csml file
1140        @param csmlContent: content of the csml file - NB, if this is set to None and the
1141        file, csmlName, is available locally, CsmlParser.Dataset will read in the file
1142        directly
1143        @keyword aggregateCoverage: if set to True, only coverage data that extends the
1144        atom coverage data will be added
1145        @keyword useCSMLID: if True, use the CSML doc ID as the dataset ID - NB,
1146        this should only be True if creating a new atom - e.g. from a granulite
1147        @return csmlDoc: the CsmlParser.Dataset object with the csml data in
1148        '''
1149        logging.info("Creating CSML data model")
1150        self.csmlFile = csmlName
1151        self.contentFile = csmlName
1152        content = csmlContent or csmlName
1153   
1154        csmlDoc = CsmlParser.Dataset(file=content)
1155       
1156        logging.info("Extracting info from CSML file")
1157        logging.debug("Got dataset ID: %s" %csmlDoc.id)
1158        if useCSMLID:
1159            logging.debug(" - using this ID for the atom")
1160            self.setDatasetID(VTD.GRANULE_TERM + '_' + csmlDoc.id)
1161       
1162        title = csmlDoc.name.CONTENT
1163        logging.debug("Got dataset name (title): '%s'" %title)
1164        # NB, if a title is specified (and not as the default value), it automatically is used in
1165        # place of anything in the granulite file
1166        if title and title != "NAME OF DATASET GOES HERE":
1167            logging.info("Title, '%s', extracted from CSML file" %title)
1168            if self.title:
1169                logging.info("- NB, this will override the title specified in the granulite file ('%s')" \
1170                             %self.title)
1171            self.title = title
1172               
1173        bbox1 = csmlDoc.getBoundingBox()
1174        bbox2 = csmlDoc.getCSMLBoundingBox()
1175
1176        time = None
1177        if bbox2:
1178            time = bbox2.getTimeLimits()
1179   
1180        # now check for other parameters to add to granule
1181        # Firstly, extract the bounding envelope
1182        if bbox1:
1183            w, e = utilities.normaliseLongitude(bbox1[0],bbox1[2])
1184            n, s = (bbox1[3], bbox1[1])
1185   
1186            if not aggregateCoverage or (not self.maxY or float(n) > float(self.maxY)):
1187                self.maxY = n
1188               
1189            if not aggregateCoverage or (not self.minY or float(s) < float(self.minY)):
1190                self.minY = s
1191           
1192            if not aggregateCoverage or (not self.minX or float(w) < float(self.minX)):
1193                self.minX = w
1194   
1195            if not aggregateCoverage or (not self.maxX or float(e) > float(self.maxX)):
1196                self.maxX = e
1197           
1198            logging.debug("Got bounding box data from file: (%s, %s) , (%s, %s)" \
1199                          %(w, s, e, n))
1200           
1201            logging.debug("Updated atom bounding box data: (%s, %s) , (%s, %s)" \
1202                          %(self.minX, self.minY, self.maxX, self.maxY))
1203        else:
1204            logging.debug("No valid bounding box data found")
1205   
1206        if time:
1207            t1 = utilities.formatDateYYYYMMDD(time[0])
1208            if not aggregateCoverage or \
1209                (not self.t1 or datetime.datetime.strptime(t1, YEAR_FORMAT) < \
1210                    datetime.datetime.strptime(self.t1, YEAR_FORMAT)):
1211                self.t1 = t1
1212   
1213            t2 = time[1]
1214            if t2 and t2 != 'None':
1215                t2 = utilities.formatDateYYYYMMDD(t2)
1216                if not aggregateCoverage or \
1217                    (not self.t2 or datetime.datetime.strptime(t2, YEAR_FORMAT) > \
1218                        datetime.datetime.strptime(self.t2, YEAR_FORMAT)):
1219                    self.t2 = t2
1220           
1221            logging.debug("Got time range: %s -> %s" %(self.t1, self.t2))
1222        else:
1223            logging.debug("No valid time range data found")
1224   
1225        #create parameter summaries:
1226        #set up list to hold the parameters data
1227        parameters = []
1228        for feature in csmlDoc.featureCollection.featureMembers:
1229            if hasattr(feature.parameter, 'href'):
1230                paramTriple = ""
1231                if hasattr(feature, 'description'):
1232                    paramTriple = feature.description.CONTENT
1233                    paramTriple += " | " + feature.parameter.href
1234                   
1235                    term = ""
1236                    if hasattr(feature, 'name'):
1237                        term = feature.name.CONTENT
1238   
1239                    paramTriple += " | " + term
1240                   
1241                    logging.debug("Got parameter info: %s" %paramTriple)
1242                    parameters.append(paramTriple)
1243       
1244        # update the atom with the extracted parameters
1245        logging.info("Adding CSML parameters to granule atom")
1246        self.addParameters(parameters)
1247        logging.info("Finished adding CSML data")
1248        return csmlDoc
1249
1250
1251    def lookupAssociatedData(self, type, searchClient, lookupIndirectReferences=False):
1252        '''
1253        Check through the atom links and retrieve any associated data of the
1254        specified type
1255        @param type: type of associated data to lookup - currently VTD.DEPLOYMENT_TERM
1256        or VTD.DE_TERM
1257        @param searchClient: Client implementing the AbstractSearchXMLDBClient class
1258        @keyword lookupIndirectReferences: if True, the atom ID is used to search
1259        defined deployments to find those which reference it, otherwise only
1260        deployments data featured in the atom related links are processed
1261        '''
1262        logging.info("Looking up %s info" %type)
1263        self.allActivities = []
1264        self.allObs = []
1265        self.allDpts = []
1266
1267        if type != VTD.DE_TERM and type != VTD.DEPLOYMENT_TERM:
1268            raise ValueError('Unrecognised associated data type: %s' %type)
1269       
1270        # avoid duplicating lookup effort
1271        if (type == VTD.DEPLOYMENT_TERM and self.deployments) or \
1272            (type == VTD.DE_TERM and self.dataEntities):
1273            logging.info("- this info has already been looked up - returning")
1274            return
1275
1276        # firstly, collect all the references to the info required
1277        if lookupIndirectReferences:
1278            logging.info("Looking up indirect references")
1279           
1280            # if we're looking up DE data for deployments data, need to have the
1281            # deployments info looked up first
1282            if type == VTD.DE_TERM and self.isDeployable() and not self.deployments:
1283                self.lookupAssociatedData(VTD.DEPLOYMENT_TERM, searchClient, 
1284                                          lookupIndirectReferences = lookupIndirectReferences)
1285           
1286            logging.info("Looking up references to this atom from other %s" %type)
1287           
1288            # NB, if we're looking up deployments info, we only look up references
1289            # to this atom - if we're looking up DEs, we need to look up references
1290            # to the deployments referenced by this atom
1291            urls = [self.atomBrowseURL]
1292           
1293            if type == VTD.DE_TERM and self.isDeployable():
1294                urls = []
1295                for dep in self.deployments:
1296                    urls.append(dep.browseURL)
1297                   
1298            links = []
1299            for url in urls:
1300                doc = searchClient.getNDGDoc(type, ndgObject.ASSOCIATED_ATOM_DOC_TYPE, url,
1301                                             targetCollection = dc.ATOM_COLLECTION_PATH)
1302                # now need to turn this results set into actual atoms
1303                tree = ET.fromstring(doc)
1304                for atom in tree:
1305                    logging.debug("- found reference in %s" %type)
1306                    links.append(ET.tostring(atom))
1307                   
1308            logging.info("Finished looking up indirect references")
1309        else:
1310            links = self.getLinksOfType(self.VTD.DEPLOYMENT_TERM)
1311
1312        # now retrieve the references and extract the required data
1313        logging.info("Retrieving info from %s references" %type)
1314        if type == VTD.DEPLOYMENT_TERM:
1315            logging.info("Extracting links data to deployment entitites")
1316            self.deployments = []
1317            for link in links:
1318                if lookupIndirectReferences:
1319                    deploymentAtom = link
1320                else:
1321                    localID = link.href.split("__ATOM__")[-1]
1322                    deploymentAtom = searchClient.getNDGDoc('', 
1323                                                            'ATOM', localID, 
1324                                                            targetCollection = dc.ATOM_COLLECTION_PATH)
1325   
1326                deployment = Deployment.Deployment(Atom(xmlString=str(deploymentAtom)))
1327                self.deployments.append(deployment)
1328               
1329                self.addUniqueLinks(self.allActivities, deployment.activities)
1330                self.addUniqueLinks(self.allObs, deployment.obs)
1331                self.addUniqueLinks(self.allDpts, deployment.dpts)
1332        else:
1333            # for DE data, just store the title + link in a Link object
1334            self.dataEntities = []
1335            logging.info("Extracting links data to data entitites")
1336            for data in links:
1337                atom = Atom(xmlString=str(data))
1338                link = Link()
1339                link.title = atom.title
1340                link.href = atom.atomBrowseURL
1341                link.rel = atom.datasetID
1342               
1343                # NB, different deployments may be used by the same DE - so
1344                # avoid duplication
1345                self.addUniqueLinks(self.dataEntities, link)
1346           
1347        logging.info("Finished looking up %s info" %type)
1348
1349
1350    def addUniqueLinks(self, dataArray, links):
1351        '''
1352        Add links to specified array - if they are not already included
1353        @param dataArray: a list, potentially arlready containing links
1354        @param links: a Link or array of Links to add to the dataArray
1355        '''
1356        logging.debug("Adding new links")
1357        if not links:
1358            return
1359       
1360        if type(links) is not list:
1361            links = [links]
1362       
1363        for link in links:
1364            if type(link) is not Link:
1365                logging.warning("Link is not of 'Link' object type (type='%s') - skipping" %type(link))
1366                continue
1367            if link not in dataArray:
1368                logging.debug("- adding unique link")
1369                dataArray.append(link)
1370        logging.debug("Finished adding links")
1371
1372       
1373    def getFullPath(self):
1374        '''
1375        Return full path to atom in eXist, if it exists, or None, otherwise
1376        @return fullPath: string - collection + filename of atom in eXist
1377        '''
1378        # NB, name assigned when atom created in eXist - so if not defined, not
1379        # in eXist
1380        logging.debug("Getting full path to atom")
1381        if self.atomName:
1382            logging.debug("Return full path to atom in eXist")
1383            return self.getDefaultCollectionPath() + self.atomName
1384        logging.debug("Atom doesn't currently exist in eXist - return 'None'")
1385        return None
1386   
1387   
1388    def getSubTypePrettyName(self):
1389        '''
1390        Return the subtype of the atom in a human readable form
1391        @return: sub type of atom as a verbose string
1392        '''
1393        logging.debug("Getting human readable version of atom subtype")
1394        subType = self.SUB_TYPE_NOT_DEFINED_NAME
1395        if self.subtypeID:
1396           subType = self.VTD.tidySubTypeTitle(self.subtypeID)
1397           
1398        logging.debug("- returning subtype: '%s'" %subType)
1399        return subType
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