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Merge pull request #144 from fair-workflows/issue139_implement_noodles_execution
Issue139 implement noodles execution
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‎examples/noodles_fw.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "designed-spoke",
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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": "secure-render",
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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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"Each step should be its own function. Mark the function as such with the @fairstep decorator."
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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": "spiritual-order",
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"metadata": {},
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"outputs": [],
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"source": [
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"from fairworkflows import is_fairworkflow, is_fairstep"
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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": "wired-bibliography",
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"metadata": {},
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"outputs": [],
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"source": [
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"@is_fairstep(label='Addition')\n",
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"def add(a:float, b:float) -> float:\n",
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" \"\"\"Adding up numbers!\"\"\"\n",
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" return a + b"
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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": 11,
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"id": "brilliant-thumb",
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"metadata": {},
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"outputs": [],
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"source": [
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"@is_fairstep(label='Subtraction')\n",
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"def sub(a: float, b: float) -> float:\n",
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" \"\"\"Subtracting numbers.\"\"\"\n",
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" return a - b"
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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": 12,
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"id": "interested-margin",
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"metadata": {},
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"outputs": [],
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"source": [
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"@is_fairstep(label='Multiplication')\n",
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"def mul(a: float, b: float) -> float:\n",
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" \"\"\"Multiplying numbers.\"\"\"\n",
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" return a * b"
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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": 13,
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"id": "closing-vatican",
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"metadata": {},
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"outputs": [],
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"source": [
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"@is_fairstep(label='A strange step with little use')\n",
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"def weird(a: float, b:float) -> float:\n",
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" \"\"\"A weird function\"\"\"\n",
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" return a * 2 + b * 4\n",
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" "
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]
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},
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{
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"cell_type": "markdown",
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"id": "centered-nowhere",
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"metadata": {},
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"source": [
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"## Define your workflow using @fairworkflow\n",
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"Now write a function which describes your workflow. Mark this function with the @fairworkflow decorator."
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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": "paperback-recycling",
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"metadata": {},
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"outputs": [],
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"source": [
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"@is_fairworkflow(label='My Workflow')\n",
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"def my_workflow(in1, in2, in3):\n",
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" \"\"\"\n",
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" A simple addition, subtraction, multiplication workflow\n",
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" \"\"\"\n",
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" t1 = add(in1, in2)\n",
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" t2 = sub(in1, in2)\n",
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" t3 = mul(weird(t1, in3), t2)\n",
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" return t3"
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]
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},
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{
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"cell_type": "markdown",
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"id": "sustained-sweden",
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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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},
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{
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"cell_type": "code",
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"execution_count": 15,
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"id": "noted-aviation",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"fairworkflows.fairworkflow.FairWorkflow"
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]
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},
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"execution_count": 15,
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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 = my_workflow(1, 4, 3)\n",
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"type(fw)"
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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": 16,
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"id": "confirmed-hudson",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/markdown": [
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"| workflow |\n",
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"| --- |\n",
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"| ![workflow workflow](control-workflow.svg) |"
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],
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"text/plain": [
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"<IPython.core.display.Markdown object>"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"fw.display()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "outside-glance",
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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."
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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": 13,
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"id": "front-abuse",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"-66"
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]
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},
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"execution_count": 13,
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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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"answer = fw.execute(num_threads=2)\n",
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"answer"
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]
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},
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{
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"cell_type": "markdown",
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"id": "compound-shepherd",
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"metadata": {},
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"source": [
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"## Get retrospective provenance of run\n",
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"This is not in RDF format yet, but we have all the information needed."
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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": 12,
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"id": "comprehensive-finland",
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"metadata": {},
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"outputs": [
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{
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"ename": "AttributeError",
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"evalue": "'FairWorkflow' object has no attribute 'prov'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m<ipython-input-12-fa58d0e49b7b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mfw\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprov\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
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"\u001b[0;31mAttributeError\u001b[0m: 'FairWorkflow' object has no attribute 'prov'"
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]
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}
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],
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"source": [
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"fw.prov()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "precious-domain",
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"metadata": {},
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"source": [
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"## Get Plex RDF of workflow"
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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": "concerned-massage",
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"metadata": {},
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"outputs": [],
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"source": [
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"fw.get_workflow()"
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]
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},
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{
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"cell_type": "raw",
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"id": "continent-editing",
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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": "capital-minority",
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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": "smoking-lebanon",
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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": "controversial-control",
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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": "alternate-template",
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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": "ecological-divorce",
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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": "liberal-queen",
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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": "specific-humanitarian",
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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": "thick-budapest",
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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": "italic-color",
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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": "respiratory-netscape",
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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": "marked-shark",
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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": "material-robertson",
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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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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎fairworkflows/__init__.py‎

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from ._version import __version__
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from .fairstep import FairStep, FairVariable, mark_as_fairstep
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from .fairworkflow import FairWorkflow
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from .fairstep import FairStep, FairVariable, mark_as_fairstep, is_fairstep
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from .fairworkflow import FairWorkflow, is_fairworkflow

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