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Add dummy retro prov return to execute()
1 parent 8ec9cb7 commit 8004ad7

2 files changed

Lines changed: 53 additions & 78 deletions

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‎examples/noodles_fw.ipynb‎

Lines changed: 43 additions & 74 deletions
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@@ -2,15 +2,15 @@
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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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"id": "characteristic-renaissance",
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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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"id": "auburn-korea",
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"metadata": {},
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"source": [
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"## Define the steps of your workflow\n",
@@ -19,8 +19,8 @@
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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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"execution_count": 1,
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"id": "natural-hunger",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -29,8 +29,8 @@
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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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"execution_count": 2,
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"id": "rational-retro",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -42,8 +42,8 @@
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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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"execution_count": 3,
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"id": "forward-fundamentals",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -55,8 +55,8 @@
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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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"execution_count": 4,
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"id": "ahead-devices",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -68,8 +68,8 @@
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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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"execution_count": 5,
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"id": "metric-referral",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -82,7 +82,7 @@
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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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"id": "european-viking",
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"metadata": {},
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"source": [
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"## Define your workflow using @fairworkflow\n",
@@ -91,8 +91,8 @@
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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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"execution_count": 6,
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"id": "atmospheric-granny",
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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": "sustained-sweden",
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"id": "intimate-correction",
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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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"execution_count": 7,
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"id": "hazardous-nancy",
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"metadata": {},
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"outputs": [
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{
@@ -127,7 +127,7 @@
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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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"execution_count": 7,
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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": "code",
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"execution_count": 16,
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"id": "confirmed-hudson",
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"execution_count": 8,
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"id": "under-costa",
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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": "outside-glance",
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"id": "informal-cosmetic",
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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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"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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]
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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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"execution_count": 14,
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"id": "baking-perspective",
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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": 13,
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"execution_count": 14,
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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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"result, prov = fw.execute(num_threads=2)\n",
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"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": "precious-domain",
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"id": "attached-spirit",
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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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"cell_type": "code",
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"execution_count": null,
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"id": "concerned-massage",
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"id": "fifteen-floating",
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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": "raw",
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"id": "continent-editing",
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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": "capital-minority",
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"id": "governing-gauge",
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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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"id": "ultimate-setup",
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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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"id": "distant-distance",
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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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"id": "opening-duration",
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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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"id": "constitutional-stand",
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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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"id": "celtic-cookbook",
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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": "specific-humanitarian",
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"id": "phantom-cowboy",
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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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"id": "controlled-premium",
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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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"id": "artistic-quantity",
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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": "respiratory-netscape",
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"id": "magnetic-lesbian",
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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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"id": "alpine-ethnic",
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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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"id": "indoor-dating",
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"metadata": {},
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"outputs": [],
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"source": []

‎fairworkflows/fairworkflow.py‎

Lines changed: 10 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -350,10 +350,16 @@ def execute(self, num_threads=1):
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if not hasattr(self, 'noodles_promise'):
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raise ValueError('Cannot execute workflow as no noodles promise has been constructed.')
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import noodles
353-
if num_threads==1:
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return noodles.run_single(self.noodles_promise)
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elif num_threads>1:
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return noodles.run_parallel(self.noodles_promise, num_threads)
353+
result = noodles.run_parallel(self.noodles_promise, num_threads)
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retroprov = """Not implemented yet. The sort of info we have looks like
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2021-01-19 13:16:44,750 - job 217: mul(22, -3) -> -66
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2021-01-19 13:16:44,750 - job 218: weird(5, 3) -> 22
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2021-01-19 13:16:44,750 - job 219: add(1, 4) -> 5
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2021-01-19 13:16:44,750 - job 220: sub(1, 4) -> -3
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2021-01-19 13:16:44,755 - result mul(22, -3) -> -66]: -66
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2021-01-19 13:16:44,755 - -end-of-queue-"""
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return result, retroprov
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def draw(self, filepath):
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"""Visualize workflow.

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