Add post_json as some DCC objects are created with post requests.

[htsworkflow.git] / htsworkflow / submission / encoded.py

diff --git a/htsworkflow/submission/encoded.py b/htsworkflow/submission/encoded.py
index f113bebd36121d5e403754caeb236e61697fcb88..f056f8e198e989c230989031650562e4246c03c5 100644 (file)
--- a/htsworkflow/submission/encoded.py
+++ b/htsworkflow/submission/encoded.py
@@ -10,9 +10,8 @@ import logging
 import json
 import jsonschema
 import requests
-from requests.utils import urlparse, urlunparse
 import types
-from urlparse import urljoin
+from urlparse import urljoin, urlparse, urlunparse
 
 LOGGER = logging.getLogger(__name__)
 
@@ -21,13 +20,17 @@ ENCODED_CONTEXT = {
     # provide common defaults.
     None: {
         # terms in multiple encoded objects
+        'award': { '@type': '@id' },
+        'dataset': {'@type': '@id'},
         'description': 'rdf:description',
+        'documents': { '@type': '@id' },
         'experiment': {'@type': '@id'},
         'href': { '@type': '@id' },
         'lab': { '@type': '@id' },
         'library': {'@type': '@id' },
         'pi': { '@type': '@id' },
         'platform': { '@type': '@id' },
+        'replicates': { '@type': '@id' },
         'submitted_by': { '@type': '@id' },
         'url': { '@type': '@id' },
     },
@@ -40,9 +43,8 @@ ENCODED_CONTEXT = {
     },
     'experiment': {
         "assay_term_id": { "@type": "@id" },
-    },
-    'file': {
-        'dataset': {'@type': '@id'},
+        "files": { "@type": "@id" },
+        "original_files": { "@type": "@id"},
     },
     # I tried to use the JSON-LD mapping capabilities to convert the lab
     # contact information into a vcard record, but the encoded model
@@ -54,11 +56,7 @@ ENCODED_CONTEXT = {
     #    "state": "vcard:region",
     #    "country": "vcard:country"
     #},
-    'human_donor': {
-        'award': { '@type': '@id' },
-    },
     'library': {
-        'award': { '@type': '@id' },
         'nucleic_acid_term_id': { '@type': '@id' }
     }
 }
@@ -82,6 +80,7 @@ ENCODED_NAMESPACES = {
     # OBI: available from http://svn.code.sf.net/p/obi/code/releases/2012-07-01/merged/merged-obi-comments.owl
     'SO': 'http://purl.obolibrary.org/obo/SO_', # Sequence ontology
     # SO: available from http://www.berkeleybop.org/ontologies/so.owl
+    # NTR: New Term Request space for DCC to implement new ontology terms
 
 }
 
@@ -95,6 +94,7 @@ class ENCODED:
         self.username = None
         self.password = None
         self.contexts = contexts if contexts else ENCODED_CONTEXT
+        self.json_headers = {'Content-Type': 'application/json'}
         self.schemas = {}
 
     def get_auth(self):
@@ -189,9 +189,9 @@ class ENCODED:
         LOGGER.info('requesting url: {}'.format(url))
 
         # do the request
-        headers = {'content-type': 'application/json'}
+
         LOGGER.debug('username: %s, password: %s', self.username, self.password)
-        response = requests.get(url, auth=self.auth, headers=headers, params=kwargs)
+        response = requests.get(url, auth=self.auth, headers=self.json_headers, params=kwargs)
         if not response.status_code == requests.codes.ok:
             LOGGER.error("Error http status: {}".format(response.status_code))
             response.raise_for_status()
@@ -217,7 +217,7 @@ class ENCODED:
     def get_schema_url(self, obj):
         obj_type = self.get_object_type(obj)
         if obj_type:
-            return self.prepare_url(ENCODED_SCHEMA_ROOT + obj_type + '.json')
+            return self.prepare_url(ENCODED_SCHEMA_ROOT + obj_type + '.json') + '#'
 
     def _is_encoded_object(self, obj):
         '''Test to see if an object is a JSON-LD object
@@ -238,16 +238,26 @@ class ENCODED:
         """
         url = self.prepare_url(obj_id)
         payload = json.dumps(changes)
-        response = requests.patch(url, auth=self.auth, data=payload)
+        response = requests.patch(url, auth=self.auth, headers=self.json_headers, data=payload)
         if response.status_code != requests.codes.ok:
             LOGGER.error("Error http status: {}".format(response.status_code))
+            LOGGER.error("Response: %s", response.text)
             response.raise_for_status()
         return response.json()
 
     def put_json(self, obj_id, new_object):
         url = self.prepare_url(obj_id)
         payload = json.dumps(new_object)
-        response = requests.put(url, auth=self.auth, data=payload)
+        response = requests.put(url, auth=self.auth, headers=self.json_headers, data=payload)
+        if response.status_code != requests.codes.created:
+            LOGGER.error("Error http status: {}".format(response.status_code))
+            response.raise_for_status()
+        return response.json()
+
+    def post_json(self, collection_id, new_object):
+        url = self.prepare_url(collection_id)
+        payload = json.dumps(new_object)
+        response = requests.post(url, auth=self.auth, headers=self.json_headers, data=payload)
         if response.status_code != requests.codes.created:
             LOGGER.error("Error http status: {}".format(response.status_code))
             response.raise_for_status()
@@ -271,12 +281,34 @@ class ENCODED:
         # clean up potentially messy urls
         url = urlparse(request_url)._asdict()
         if not url['scheme']:
-            url['scheme'] = 'http'
+            url['scheme'] = 'https'
         if not url['netloc']:
             url['netloc'] = self.server
         url = urlunparse(url.values())
         return url
 
+    def search_jsonld(self, term, **kwargs):
+        '''Send search request to ENCODED
+        '''
+        url = self.prepare_url('/search/')
+        result = self.get_json(url, searchTerm=term, **kwargs)
+        self.convert_search_to_jsonld(result)
+        return result
+
+    def convert_search_to_jsonld(self, result):
+        '''Add the context to search result
+
+        Also remove hard to handle nested attributes
+          e.g. remove object.term when we have no id
+        '''
+        graph = result['@graph']
+        for i, obj in enumerate(graph):
+            # suppress nested attributes
+            graph[i] = {k: v for k, v in obj.items() if '.' not in k}
+
+        self.add_jsonld_context(result, self.prepare_url(result['@id']))
+        return result
+
     def validate(self, obj):
         obj_type = self.get_object_type(obj)
         schema_url = self.get_schema_url(obj)