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Update example notebook
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‎examples/noodles_fw.ipynb‎

Lines changed: 145 additions & 41 deletions
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"cells": [
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{
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"cell_type": "markdown",
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"id": "characteristic-renaissance",
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"id": "regulated-intermediate",
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"metadata": {},
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"source": [
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"# FairWorkflows execution demo"
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]
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},
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{
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"cell_type": "markdown",
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"id": "auburn-korea",
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"id": "handed-swedish",
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"metadata": {},
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"source": [
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"## Define the steps of your workflow\n",
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "natural-hunger",
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"id": "unusual-speed",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "rational-retro",
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"id": "least-confusion",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "forward-fundamentals",
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"id": "sized-desperate",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "ahead-devices",
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"id": "closed-fortune",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "metric-referral",
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"id": "growing-foster",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "european-viking",
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"id": "palestinian-poverty",
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"metadata": {},
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"source": [
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"## Define your workflow using @fairworkflow\n",
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "atmospheric-granny",
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"id": "retired-assignment",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "intimate-correction",
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"id": "protecting-street",
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"metadata": {},
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"source": [
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"## Create an instance of your workflow and display it"
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{
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"cell_type": "code",
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"execution_count": 7,
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"id": "hazardous-nancy",
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"id": "printable-storage",
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"metadata": {},
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"outputs": [
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{
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "under-costa",
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"id": "atomic-background",
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"metadata": {},
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"outputs": [
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{
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},
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{
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"cell_type": "markdown",
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"id": "informal-cosmetic",
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"id": "false-imagination",
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"metadata": {},
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"source": [
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"## Publish the (prospective) workflow\n",
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"You may publish the workflow, and its steps, as nanopublications in the usual manner:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"id": "statewide-search",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Published to http://purl.org/np/RANKki6Fh-QYTHJ39yhJNOEcQLZOJld1VZFEvaLeILgCA\n",
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"Published concept to http://purl.org/np/RANKki6Fh-QYTHJ39yhJNOEcQLZOJld1VZFEvaLeILgCA#step\n",
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"Published to http://purl.org/np/RAsljALsS_3aL57HIU-8tdyxYl3ESlSkQu3kCfWBxvZV0\n",
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"Published concept to http://purl.org/np/RAsljALsS_3aL57HIU-8tdyxYl3ESlSkQu3kCfWBxvZV0#step\n",
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"Published to http://purl.org/np/RAUod2ToGWqyvBbFqKRPB4ilwjx78fYR1l37ORKDXLsk4\n",
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"Published concept to http://purl.org/np/RAUod2ToGWqyvBbFqKRPB4ilwjx78fYR1l37ORKDXLsk4#step\n",
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"Published to http://purl.org/np/RAuKOFZgd1RehE5vOclqdvJo2zchDUUF33VIh8A_8DXtM\n",
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"Published concept to http://purl.org/np/RAuKOFZgd1RehE5vOclqdvJo2zchDUUF33VIh8A_8DXtM#step\n",
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"Published to http://purl.org/np/RAFHW530LVNe6DwMV4uvA5cDLItEuvEbHJhfczfW92nMg\n",
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"Published concept to http://purl.org/np/RAFHW530LVNe6DwMV4uvA5cDLItEuvEbHJhfczfW92nMg#plan\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"{'nanopub_uri': 'http://purl.org/np/RAFHW530LVNe6DwMV4uvA5cDLItEuvEbHJhfczfW92nMg',\n",
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" 'concept_uri': 'http://purl.org/np/RAFHW530LVNe6DwMV4uvA5cDLItEuvEbHJhfczfW92nMg#plan'}"
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]
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},
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"execution_count": 9,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"fw.publish_as_nanopub()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "fabulous-hydrogen",
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"metadata": {},
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"source": [
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"Be warned though - the above will keep publishing to the 'real' nanopub server network. For testing you may prefer to publish to the test servers as follows (note that this will refuse to publish a workflow you have already published :"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"id": "breeding-barrier",
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/robinrichardson/miniconda3/envs/fairworkflows/lib/python3.8/site-packages/fairworkflows/rdf_wrapper.py:213: UserWarning: Cannot publish() this Fair object. This rdf is already published (at http://purl.org/np/RAFHW530LVNe6DwMV4uvA5cDLItEuvEbHJhfczfW92nMg#plan) and has not been modified locally.\n",
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" warnings.warn(f'Cannot publish() this Fair object. '\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"{'nanopub_uri': None, 'concept_uri': None}"
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]
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},
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"execution_count": 10,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"fw.publish_as_nanopub(use_test_server=True)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "large-biography",
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"metadata": {},
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"source": [
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"You can then find your nanopublications by replacing the base of the URI with http://test-server.nanopubs.lod.labs.vu.nl/"
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]
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},
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{
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"cell_type": "markdown",
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"id": "balanced-filing",
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"metadata": {},
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"source": [
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"## Execute your workflow using .execute()\n",
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"Set num_threads greater than 1 if you wish to exploit parallelisation in your workflow. A separate RetroProv object is also returned that can (optionally) be published as a nanopublication. This is not yet implemented, pending one of the RDF tasks set out in the planning document."
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"Set num_threads greater than 1 if you wish to exploit parallelisation in your workflow. A separate RetroProv object is also returned that can (optionally) be published as a nanopublication."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"id": "baking-perspective",
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"execution_count": 11,
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"id": "scheduled-forest",
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"metadata": {},
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"outputs": [
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{
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"-66"
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]
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},
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"execution_count": 14,
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"execution_count": 11,
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "markdown",
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"id": "attached-spirit",
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"id": "pressing-hartford",
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"metadata": {},
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"source": [
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"## Get Plex RDF of workflow"
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" ## Retrospective prov\n",
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" The retrospective prov object is not yet implemented, pending one of the RDF tasks set out in the planning document. For now, you may see simply the provenance trace for this run. We wish to turn this into a (Plex) RDF nanopublication:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "fifteen-floating",
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"execution_count": 12,
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"id": "straight-watch",
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"2021-01-24 21:31:39,751 - job 13: add(1, 4)\n",
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"2021-01-24 21:31:39,751 - job 14: sub(1, 4)\n",
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"2021-01-24 21:31:39,753 - result 13 [add(1, 4)]: retrieved -> 5\n",
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"2021-01-24 21:31:39,753 - job 15: weird(5, 3)\n",
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"2021-01-24 21:31:39,754 - result 14 [sub(1, 4)]: retrieved -> -3\n",
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"2021-01-24 21:31:39,754 - result 15 [weird(5, 3)]: retrieved -> 22\n",
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"2021-01-24 21:31:39,755 - job 16: mul(22, -3)\n",
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"2021-01-24 21:31:39,755 - result 16 [mul(22, -3)]: retrieved -> -66\n",
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"2021-01-24 21:31:39,755 - -end-of-queue-\n",
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"\n"
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]
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}
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],
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"source": [
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"fw.get_workflow()"
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"print(prov)"
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]
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},
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{
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"cell_type": "raw",
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"id": "cooked-ridge",
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"metadata": {},
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "governing-gauge",
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"id": "iraqi-messaging",
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ultimate-setup",
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"id": "confident-emission",
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "distant-distance",
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"id": "exterior-duplicate",
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"metadata": {},
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"outputs": [],
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"source": []
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},
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"cell_type": "code",
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"execution_count": null,
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"id": "opening-duration",
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"id": "administrative-complex",
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"metadata": {},
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"outputs": [],
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"source": []
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},
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"cell_type": "code",
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"id": "constitutional-stand",
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"id": "killing-investing",
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"metadata": {},
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"source": []
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},
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{
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"cell_type": "code",
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"id": "celtic-cookbook",
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"id": "mathematical-departure",
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},
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"cell_type": "code",
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"id": "phantom-cowboy",
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"id": "caroline-lending",
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"metadata": {},
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"source": []
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},
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"cell_type": "code",
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"execution_count": null,
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"id": "controlled-premium",
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"id": "ultimate-monte",
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"metadata": {},
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},
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"cell_type": "code",
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"execution_count": null,
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"id": "artistic-quantity",
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"id": "greater-whole",
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"metadata": {},
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"outputs": [],
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"source": []
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{
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"id": "magnetic-lesbian",
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"id": "minimal-wagon",
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"metadata": {},
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"source": []
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{
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"cell_type": "code",
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"id": "alpine-ethnic",
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"id": "administrative-nation",
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"metadata": {},
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "indoor-dating",
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"id": "analyzed-belief",
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"metadata": {},
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"outputs": [],
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"source": []

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