Merge pull request #16 from materials-data-facility/mdfcc-dev

Tutorial updates, function reorg

Author: jgaff

.travis.yml

@@ -9,7 +9,7 @@ install:
 env:
 - TEST_ENV=travis
 script:
-- flake8 . && travis_wait 50 py.test
+- flake8 . && travis_wait 50 py.test --nbval-lax
 before_install:
 - openssl aes-256-cbc -K $encrypted_99dd1c7c40fb_key -iv $encrypted_99dd1c7c40fb_iv
   -in travis.tar.enc -out travis.tar -d

README.md

@@ -24,4 +24,4 @@ Documentation is available on [Read the Docs](https://mdf-connect-client.readthe
 
 
 # Support
-This work was performed under financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the [Center for Hierarchical Material Design (CHiMaD)](http://chimad.northwestern.edu). This work was also supported by the National Science Foundation as part of the [Midwest Big Data Hub](http://midwestbigdatahub.org) under NSF Award Number: 1636950 "BD Spokes: SPOKE: MIDWEST: Collaborative: Integrative Materials Design (IMaD): Leverage, Innovate, and Disseminate".
+This work was performed under financial assistance award 70NANB14H012 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the [Center for Hierarchical Material Design (CHiMaD)](http://chimad.northwestern.edu). This work was performed under the following financial assistance award 70NANB19H005 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD). This work was also supported by the National Science Foundation as part of the [Midwest Big Data Hub](http://midwestbigdatahub.org) under NSF Award Number: 1636950 "BD Spokes: SPOKE: MIDWEST: Collaborative: Integrative Materials Design (IMaD): Leverage, Innovate, and Disseminate".

docs/tutorials/Basic_MDF_Connect_Submission_Example.ipynb

@@ -51,7 +51,7 @@
     "# The DC block only requires a title and author.\n",
     "mdfcc.create_dc_block(title=\"Simple Test Dataset\", authors=\"A. Person\")\n",
     "# The data field requires one data location.\n",
-    "mdfcc.add_data(\"https://app.globus.org/file-manager?origin_id=e38ee745-6d04-11e5-ba46-22000b92c6ec&origin_path=%2Fcitrine_mdf_demo%2Falloy.pbe%2FAgAl%2F\")"
+    "mdfcc.add_data_source(\"https://app.globus.org/file-manager?origin_id=e38ee745-6d04-11e5-ba46-22000b92c6ec&origin_path=%2Fcitrine_mdf_demo%2Falloy.pbe%2FAgAl%2F\")"
    ]
   },
   {
@@ -61,9 +61,10 @@
    "outputs": [],
    "source": [
     "# Next, we'll add some optional settings.\n",
-    "# The 'globus_publish' service will get us a permanent publication and a DOI.\n",
-    "mdfcc.add_service(\"globus_publish\")\n",
+    "# The 'mdf_publish' service will get us a publication and a DOI.\n",
+    "mdfcc.add_service(\"mdf_publish\")\n",
     "# Since this is just an example and not a real submission, we'll set the 'test' flag to True.\n",
+    "# The DOI we will get with a test submission is a sandbox DOI, which is not permanent.\n",
     "mdfcc.set_test(True)"
    ]
   },
@@ -75,17 +76,18 @@
     {
      "data": {
       "text/plain": [
-       "{'data': ['https://app.globus.org/file-manager?origin_id=e38ee745-6d04-11e5-ba46-22000b92c6ec&origin_path=%2Fcitrine_mdf_demo%2Falloy.pbe%2FAgAl%2F'],\n",
+       "{'data_sources': ['https://app.globus.org/file-manager?origin_id=e38ee745-6d04-11e5-ba46-22000b92c6ec&origin_path=%2Fcitrine_mdf_demo%2Falloy.pbe%2FAgAl%2F'],\n",
        " 'dc': {'creators': [{'creatorName': 'Person, A.',\n",
        "    'familyName': 'Person',\n",
        "    'givenName': 'A.'}],\n",
-       "  'publicationYear': '2018',\n",
+       "  'publicationYear': '2019',\n",
        "  'publisher': 'Materials Data Facility',\n",
        "  'resourceType': {'resourceType': 'Dataset',\n",
        "   'resourceTypeGeneral': 'Dataset'},\n",
        "  'titles': [{'title': 'Simple Test Dataset'}]},\n",
-       " 'services': {'globus_publish': True},\n",
-       " 'test': True}"
+       " 'services': {'mdf_publish': True},\n",
+       " 'test': True,\n",
+       " 'update': False}"
       ]
      },
      "execution_count": 5,
@@ -113,7 +115,10 @@
     {
      "data": {
       "text/plain": [
-       "{'error': None, 'source_id': '_test_simple_test_dataset_v1-1', 'success': True}"
+       "{'error': None,\n",
+       " 'source_id': '_test_person_simple_v1.1',\n",
+       " 'status_code': 202,\n",
+       " 'success': True}"
       ]
      },
      "execution_count": 6,
@@ -122,6 +127,8 @@
     }
    ],
    "source": [
+    "# NBVAL_SKIP\n",
+    "\n",
     "# Let's submit the dataset.\n",
     "mdfcc.submit_dataset()"
    ]
@@ -136,27 +143,29 @@
      "output_type": "stream",
      "text": [
       "\n",
-      "Status of TEST convert submission _test_simple_test_dataset_v1-1 (Simple Test Dataset)\n",
-      "Submitted by Jonathon Gaff at 2018-11-29T19:21:13.861237Z\n",
+      "Status of TEST submission _test_person_simple_v1.1 (Simple Test Dataset)\n",
+      "Submitted by Jonathon Gaff at 2019-08-07T16:11:58.505899Z\n",
       "\n",
-      "Conversion initialization has not started yet.\n",
-      "Conversion data download has not started yet.\n",
+      "Submission initialization was successful.\n",
+      "Connect data download is in progress.\n",
+      "Primary data transfer has not started yet.\n",
       "Data conversion has not started yet.\n",
-      "Ingestion preparation has not started yet.\n",
-      "Ingestion initialization has not started yet.\n",
-      "Ingestion data download has not started yet.\n",
-      "Integration data download has not started yet.\n",
-      "Globus Search ingestion has not started yet.\n",
-      "Globus Publish publication has not started yet.\n",
+      "Dataset curation has not started yet.\n",
+      "MDF Search ingestion has not started yet.\n",
+      "Data transfer to secondary destinations has not started yet.\n",
+      "MDF Publish publication has not started yet.\n",
       "Citrine upload has not started yet.\n",
       "Materials Resource Registration has not started yet.\n",
       "Post-processing cleanup has not started yet.\n",
       "\n",
-      "This submission is active.\n"
+      "This submission is active.\n",
+      "\n"
      ]
     }
    ],
    "source": [
+    "# NBVAL_SKIP\n",
+    "\n",
     "# Now we can check the status of our submission.\n",
     "mdfcc.check_status()"
    ]