fix egs in occurrences.get and related methods in docstrings

and in demos jupyter notebook fix #39
gbif · Oct 19, 2016 · 0c9a7ac · 0c9a7ac
1 parent f5f14f6
commit 0c9a7ac
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Showing 32 changed files with 253 additions and 188 deletions.
diff --git a/.gitignore b/.gitignore
@@ -22,3 +22,7 @@
 
 # pycharm project info
 .idea/
+
+# ipython notebook files
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
diff --git a/Changelog.rst b/Changelog.rst
@@ -1,6 +1,16 @@
 Changelog
 =========
 
+0.2.0 (2016-10-18)
+--------------------
+- Download methods much improved (#16) (#27) thanks @jlegind @stijnvanhoey @peterdesmet !
+- MULTIPOLYGON now supported in `geometry` parameter (#35)
+- xxx (#xx)
+- xxx (#xx)
+- xxx (#xx)
+- xxx (#xx)
+- xxx (#xx)
+
 0.1.5.4 (2016-10-01)
 --------------------
 - Added many new `occurrence.search` parameters, including `repatriated`, `kingdomKey`, `phylumKey`, `classKey`, `orderKey`, `familyKey`, `genusKey`, `subgenusKey`, `establishmentMeans`, `facet`, `facetMincount`, `facetMultiselect`, and support for facet paging via	`**kwargs` (#30) (#34)
@@ -13,7 +23,7 @@ Changelog
 - Changed default `limit` value to 300 for `occurrences.search` method
 - `tox` now included, via @xrotwang (#20)
 - Added more registry methods (#11)
-- Started occurrence download methods (#16
+- Started occurrence download methods (#16)
 - Added more names methods (#18)
 - All requests now send user-agent headers with `requests` and `pygbif` versions (#13)
 - Bug fix for `occurrences.download_get` (#23)

diff --git a/demos/pygbif-intro.ipynb b/demos/pygbif-intro.ipynb
@@ -17,66 +17,59 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 1,
    "metadata": {
     "collapsed": false
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "{u'colCoveragePct': 79,\n",
-       " u'colMatchingCount': 24335,\n",
+       "{u'colCoveragePct': 76,\n",
+       " u'colMatchingCount': 22483,\n",
        " u'countByConstituent': {},\n",
-       " u'countByIssue': {u'BACKBONE_MATCH_FUZZY': 573,\n",
-       "  u'BACKBONE_MATCH_NONE': 1306,\n",
-       "  u'VERNACULAR_NAME_INVALID': 7777},\n",
-       " u'countByKingdom': {u'ANIMALIA': 30,\n",
-       "  u'FUNGI': 3,\n",
-       "  u'INCERTAE_SEDIS': 26,\n",
-       "  u'PLANTAE': 10997,\n",
-       "  u'PROTOZOA': 1},\n",
-       " u'countByOrigin': {u'DENORMED_CLASSIFICATION': 2010,\n",
-       "  u'PROPARTE': 11,\n",
-       "  u'SOURCE': 28775},\n",
+       " u'countByIssue': {u'BACKBONE_MATCH_NONE': 1338,\n",
+       "  u'VERNACULAR_NAME_INVALID': 7852},\n",
+       " u'countByKingdom': {u'PLANTAE': 8949},\n",
+       " u'countByOrigin': {u'PROPARTE': 10, u'SOURCE': 29260},\n",
        " u'countByRank': {u'CLASS': 1,\n",
        "  u'FAMILY': 172,\n",
-       "  u'GENUS': 3255,\n",
+       "  u'GENUS': 1251,\n",
        "  u'ORDER': 55,\n",
-       "  u'SECTION': 323,\n",
+       "  u'SECTION': 326,\n",
        "  u'SERIES': 40,\n",
-       "  u'SPECIES': 6046,\n",
+       "  u'SPECIES': 6071,\n",
        "  u'SUBCLASS': 6,\n",
        "  u'SUBFAMILY': 150,\n",
-       "  u'SUBGENUS': 99,\n",
+       "  u'SUBGENUS': 101,\n",
        "  u'SUBSECTION': 56,\n",
-       "  u'SUBSPECIES': 742,\n",
+       "  u'SUBSPECIES': 737,\n",
        "  u'SUBTRIBE': 61,\n",
        "  u'SUPERORDER': 12,\n",
        "  u'TRIBE': 328,\n",
-       "  u'VARIETY': 863},\n",
-       " u'countExtRecordsByExtension': {u'DESCRIPTION': 10176,\n",
-       "  u'DISTRIBUTION': 29037,\n",
+       "  u'VARIETY': 871},\n",
+       " u'countExtRecordsByExtension': {u'DESCRIPTION': 10213,\n",
+       "  u'DISTRIBUTION': 29143,\n",
        "  u'IDENTIFIER': 0,\n",
        "  u'MULTIMEDIA': 0,\n",
        "  u'REFERENCE': 0,\n",
        "  u'SPECIES_PROFILE': 0,\n",
        "  u'TYPES_AND_SPECIMEN': 0,\n",
-       "  u'VERNACULAR_NAME': 32143},\n",
-       " u'countNamesByLanguage': {u'ENGLISH': 20864, u'FRENCH': 11279},\n",
-       " u'created': u'2015-08-19T16:44:57.166+0000',\n",
+       "  u'VERNACULAR_NAME': 32290},\n",
+       " u'countNamesByLanguage': {u'ENGLISH': 20989, u'FRENCH': 11301},\n",
+       " u'created': u'2016-07-27T20:34:07.015+0000',\n",
        " u'datasetKey': u'3f8a1297-3259-4700-91fc-acc4170b27ce',\n",
-       " u'distinctNamesCount': 30776,\n",
-       " u'downloaded': u'2015-08-19T16:04:50.099+0000',\n",
-       " u'key': 1481,\n",
+       " u'distinctNamesCount': 29254,\n",
+       " u'downloaded': u'2016-07-27T20:34:07.013+0000',\n",
+       " u'key': 55067,\n",
        " u'nubCoveragePct': 95,\n",
-       " u'nubMatchingCount': 29490,\n",
+       " u'nubMatchingCount': 27932,\n",
        " u'otherCount': {},\n",
-       " u'synonymsCount': 18587,\n",
-       " u'usagesCount': 30796}"
+       " u'synonymsCount': 19032,\n",
+       " u'usagesCount': 29270}"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 1,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -95,7 +88,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 2,
    "metadata": {
     "collapsed": false
    },
@@ -121,8 +114,11 @@
        "   u'phylum': u'Chordata',\n",
        "   u'phylumKey': 44,\n",
        "   u'rank': u'SPECIES',\n",
+       "   u'scientificName': u'Puma concolor (Linnaeus, 1771)',\n",
        "   u'species': u'Puma concolor',\n",
-       "   u'speciesKey': 2435099}],\n",
+       "   u'speciesKey': 2435099,\n",
+       "   u'status': u'ACCEPTED',\n",
+       "   u'synonym': False}],\n",
        " 'hierarchy': [{u'1': u'Animalia',\n",
        "   u'2435098': u'Puma',\n",
        "   u'359': u'Mammalia',\n",
@@ -131,7 +127,7 @@
        "   u'9703': u'Felidae'}]}"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -157,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 3,
    "metadata": {
     "collapsed": false
    },
@@ -177,7 +173,7 @@
        " u'Basidiomycota']"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -197,55 +193,88 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 5,
    "metadata": {
     "collapsed": false
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "{u'basisOfRecord': u'OBSERVATION',\n",
-       " u'catalogNumber': u'70875196',\n",
-       " u'collectionCode': u'7472',\n",
-       " u'continent': u'EUROPE',\n",
-       " u'country': u'United Kingdom',\n",
-       " u'countryCode': u'GB',\n",
-       " u'datasetKey': u'26a49731-9457-45b2-9105-1b96063deb26',\n",
-       " u'day': 30,\n",
-       " u'decimalLatitude': 52.51021,\n",
-       " u'decimalLongitude': -1.0193,\n",
-       " u'eventDate': u'2006-06-29T22:00:00.000+0000',\n",
+       "{u'basisOfRecord': u'PRESERVED_SPECIMEN',\n",
+       " u'bibliographicCitation': u'http://www.tropicos.org/Specimen/100889255',\n",
+       " u'catalogNumber': u'100889255',\n",
+       " u'class': u'Magnoliopsida',\n",
+       " u'classKey': 220,\n",
+       " u'collectionCode': u'MO',\n",
+       " u'collectionID': u'http://biocol.org/urn:lsid:biocol.org:col:15859',\n",
+       " u'continent': u'NORTH_AMERICA',\n",
+       " u'country': u'Panama',\n",
+       " u'countryCode': u'PA',\n",
+       " u'county': u'La Pintada',\n",
+       " u'crawlId': 18,\n",
+       " u'datasetKey': u'7bd65a7a-f762-11e1-a439-00145eb45e9a',\n",
+       " u'datasetName': u'Tropicos',\n",
+       " u'day': 11,\n",
+       " u'decimalLatitude': 8.68,\n",
+       " u'decimalLongitude': -80.60056,\n",
+       " u'elevation': 753.0,\n",
+       " u'eventDate': u'2016-01-11T00:00:00.000+0000',\n",
        " u'extensions': {},\n",
        " u'facts': [],\n",
-       " u'gbifID': u'252408386',\n",
+       " u'family': u'Juglandaceae',\n",
+       " u'familyKey': 2499,\n",
+       " u'fieldNumber': u'9',\n",
+       " u'gbifID': u'1258202889',\n",
+       " u'genericName': u'Alfaroa',\n",
+       " u'genus': u'Alfaroa',\n",
+       " u'genusKey': 7310533,\n",
        " u'geodeticDatum': u'WGS84',\n",
-       " u'identifiedBy': u'DA Lott',\n",
+       " u'identifier': u'urn:catalog:MO:Tropicos:100889255',\n",
        " u'identifiers': [],\n",
-       " u'institutionCode': u'Leicestershire and Rutland Environmental Records Centre',\n",
-       " u'issues': [u'COORDINATE_ROUNDED',\n",
-       "  u'GEODETIC_DATUM_ASSUMED_WGS84',\n",
-       "  u'TAXON_MATCH_NONE'],\n",
-       " u'key': 252408386,\n",
-       " u'lastCrawled': u'2013-09-07T07:08:17.000+0000',\n",
-       " u'lastInterpreted': u'2014-06-05T03:33:35.082+0000',\n",
-       " u'locality': u'Saddington Reservoir, Saddington Reservoir',\n",
-       " u'month': 6,\n",
+       " u'individualCount': 3,\n",
+       " u'institutionCode': u'MO',\n",
+       " u'issues': [u'COORDINATE_ROUNDED', u'GEODETIC_DATUM_ASSUMED_WGS84'],\n",
+       " u'key': 1258202889,\n",
+       " u'kingdom': u'Plantae',\n",
+       " u'kingdomKey': 6,\n",
+       " u'lastCrawled': u'2016-06-06T11:13:54.020+0000',\n",
+       " u'lastInterpreted': u'2016-08-04T03:07:30.466+0000',\n",
+       " u'lastParsed': u'2016-03-21T14:33:34.346+0000',\n",
+       " u'license': u'http://creativecommons.org/licenses/by/4.0/legalcode',\n",
+       " u'locality': u'Corregimiento del Harino. Parque Nacional General de Divisi\\xf3n Omar Torrijos Herrera (PNGDOTH) el Cop\\xe9, camino hacia La Rica, aproximadamente a 1.5 Km. al NO de la caba\\xf1a de visitantes del parque. Parcela Los corazones 1 (PP-Corazones-1).',\n",
+       " u'month': 1,\n",
+       " u'nomenclaturalCode': u'ICNafp',\n",
+       " u'nomenclaturalStatus': u'No opinion',\n",
+       " u'occurrenceID': u'urn:catalog:MO:Tropicos:100889255',\n",
+       " u'order': u'Fagales',\n",
+       " u'orderKey': 1354,\n",
+       " u'ownerInstitutionCode': u'MOBOT',\n",
+       " u'phylum': u'Tracheophyta',\n",
+       " u'phylumKey': 7707728,\n",
        " u'protocol': u'DWC_ARCHIVE',\n",
-       " u'publishingCountry': u'GB',\n",
-       " u'publishingOrgKey': u'07f617d0-c688-11d8-bf62-b8a03c50a862',\n",
-       " u'recordedBy': u'DA Lott',\n",
+       " u'publishingCountry': u'US',\n",
+       " u'publishingOrgKey': u'90fd6680-349f-11d8-aa2d-b8a03c50a862',\n",
+       " u'recordNumber': u'Flores Jim\\xe9nez 3724',\n",
+       " u'recordedBy': u'Rodolfo Flores|M. Madrid|Y. Pe\\xf1a|L. De Gracia V.|R. Berenguer|J. Rodr\\xedguez|J. Vargas|A. Gonzalez C.|C. L\\xf3pez V.|R. Vergara E.|H. Moreno',\n",
        " u'relations': [],\n",
-       " u'year': 2006}"
+       " u'rightsHolder': u'Missouri Botanical Garden',\n",
+       " u'scientificName': u'Alfaroa Standl.',\n",
+       " u'stateProvince': u'Cocl\\xe9',\n",
+       " u'taxonID': u'40009683',\n",
+       " u'taxonKey': 7310533,\n",
+       " u'taxonRank': u'GENUS',\n",
+       " u'type': u'PhysicalObject',\n",
+       " u'year': 2016}"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "occurrences.get(key = 252408386)"
+    "occurrences.get(key = 1258202889)"
    ]
   },
   {
@@ -257,36 +286,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 6,
    "metadata": {
     "collapsed": false
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "500283031"
+       "546341356"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "occurrences.count(isGeoreferenced = True)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    ""
-   ]
   }
  ],
  "metadata": {
@@ -298,7 +316,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2.0
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -310,4 +328,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}
diff --git a/docs/_build/doctrees/changelog_link.doctree b/docs/_build/doctrees/changelog_link.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/occurrences.doctree b/docs/_build/doctrees/occurrences.doctree
diff --git a/docs/_build/doctrees/species.doctree b/docs/_build/doctrees/species.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b90a377759b3467f2798c54589bc46ad
+config: 2a689e895ead89eed271b97632cf41a7
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview: module code &mdash; pygbif 0.1.5.4 documentation</title>
+  <title>Overview: module code &mdash; pygbif 0.1.6.0 documentation</title>
 
 
 
@@ -30,7 +30,7 @@
 
 
 
-    <link rel="top" title="pygbif 0.1.5.4 documentation" href="../index.html"/> 
+    <link rel="top" title="pygbif 0.1.6.0 documentation" href="../index.html"/> 
 
 
   <script src="../_static/js/modernizr.min.js"></script>
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.1.5.4
+                0.1.6.0
               </div>
 
 
@@ -170,7 +170,7 @@ <h1>All modules for which code is available</h1>
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'../',
-            VERSION:'0.1.5.4',
+            VERSION:'0.1.6.0',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true