From 6fee3f0f33c2811cfce31916ac5424b5786178e1 Mon Sep 17 00:00:00 2001
From: pkupczyk <piotr.kupczyk@id.ethz.ch>
Date: Mon, 16 Oct 2017 16:29:43 +0200
Subject: [PATCH] SSDM-5738 pyBIS : Support for semantic annotations -
 documentation

---
 .../PyBis/pybis playground localhost.ipynb    | 122 +++++++++---------
 1 file changed, 62 insertions(+), 60 deletions(-)

diff --git a/src/python/PyBis/pybis playground localhost.ipynb b/src/python/PyBis/pybis playground localhost.ipynb
index b86d13688f7..751df34b170 100644
--- a/src/python/PyBis/pybis playground localhost.ipynb	
+++ b/src/python/PyBis/pybis playground localhost.ipynb	
@@ -17,9 +17,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -52,9 +50,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -85,9 +81,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -114,9 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -182,7 +174,6 @@
    "cell_type": "code",
    "execution_count": 8,
    "metadata": {
-    "collapsed": false,
     "scrolled": true
    },
    "outputs": [
@@ -290,9 +281,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -435,9 +424,7 @@
   {
    "cell_type": "code",
    "execution_count": 20,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -498,9 +485,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -683,9 +668,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "new_sample = o.new_sample(sample_name='my_wonderful_sample_name', space_name='VERMEUL', tags=['uno','due','tre'])"
@@ -694,9 +677,7 @@
   {
    "cell_type": "code",
    "execution_count": 17,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -716,9 +697,7 @@
   {
    "cell_type": "code",
    "execution_count": 19,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -738,9 +717,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -761,9 +738,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -1102,9 +1077,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -1175,9 +1148,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "ds1 = o.get_dataset('20160705105115020-196')"
@@ -1186,9 +1157,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -1220,9 +1189,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -1247,9 +1214,7 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -1270,9 +1235,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -1312,13 +1275,52 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {
     "collapsed": true
    },
+   "source": [
+    "## Semantic Annotation "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "# create semantic annotation for sample type\n",
+    "o.new_semantic_annotation(entityType = 'UNKNOWN')\n",
+    "\n",
+    "# create sementic annotation for property type\n",
+    "o.new_semantic_annotation(propertyType = 'DESCRIPTION')\n",
+    "\n",
+    "# create semantic annotation for sample property assignment\n",
+    "o.new_semantic_annotation(entityType = 'UNKNOWN', propertyType = 'DESCRIPTION')\n",
+    "\n",
+    "# create semantic annotation with additional fields\n",
+    "o.new_semantic_annotation(entityType = 'UNKNOWN', \n",
+    "                          predicateOntologyId = 'po_id', \n",
+    "                          predicateOntologyVersion = 'po_version', \n",
+    "                          predicateAccessionId = 'pa_id',\n",
+    "                          descriptorOntologyId = 'do_id',\n",
+    "                          descriptorOntologyVersion = 'do_version',\n",
+    "                          descriptorAccessionId = 'da_id')\n",
+    "\n",
+    "# get all semantic annotations\n",
+    "o.get_semantic_annotations()\n",
+    "\n",
+    "# get semantic annotation by perm id\n",
+    "sa = o.get_semantic_annotation(\"20171015135637955-30\")\n",
+    "\n",
+    "# update semantic annotation\n",
+    "sa.predicateOntologyId = 'new_po_id'\n",
+    "sa.descriptorOntologyId = 'new_do_id'\n",
+    "sa.save()\n",
+    "                          \n",
+    "# delete semantic annotation\n",
+    "sa.delete('reason')"
+   ]
   }
  ],
  "metadata": {
@@ -1337,9 +1339,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.1"
+   "version": "3.6.3"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }
-- 
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