🎨 Simplify use case

Signed-off-by: zethson <[email protected]>
laminlabs · Sep 26, 2024 · faa11a7 · faa11a7
1 parent 713f779
commit faa11a7
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Showing 3 changed files with 10 additions and 59 deletions.
diff --git a/docs/mcmicro.ipynb b/docs/mcmicro.ipynb
@@ -54,54 +54,6 @@
     "import lamindb as ln"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "27c76922",
-   "metadata": {},
-   "source": [
-    "## Run mcmicro/exemplar pipeline"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "2d7fa65b",
-   "metadata": {},
-   "source": [
-    "Register the `exemplar-001` data as input of the mcmicro pipeline by running the script below:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6cd3e0a0",
-   "metadata": {
-    "tags": [
-     "hide-input",
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "from IPython.display import display, Code\n",
-    "\n",
-    "with open('mcmicro_exemplar.py', 'r') as file:\n",
-    "    display(Code(file.read(), language='python'))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "cc5c9e59",
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "!python mcmicro_exemplar.py exemplar-001"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "ecb68cf2-1188-4f8b-a2ab-01c60d5779b8",
@@ -123,6 +75,8 @@
    },
    "outputs": [],
    "source": [
+    "from IPython.display import display, Code\n",
+    "\n",
     "with open('mcmicro.py', 'r') as file:\n",
     "    display(Code(file.read(), language='python'))"
    ]
@@ -239,7 +193,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.11.7"
   },
   "nbproject": {
    "id": "8124Vtle6ZrO",

diff --git a/docs/mcmicro.py b/docs/mcmicro.py
@@ -1,5 +1,3 @@
-# mcmicro.py
-
 """This script runs the MCMICRO pipeline and tracks input/output data in LaminDB.
 
 Usage: python mcmicro.py exemplar-001
@@ -25,10 +23,10 @@
 run = ln.context.run
 
 # get the input data from LaminDB
-mcmicro_input = ln.Artifact.filter(description=args.input).one()
+mcmicro_input = ln.Artifact.using("laminlabs/lamindata").get(uid="iTLHluoQczqH6ZypgDxA")
 input_dir = mcmicro_input.cache()
 
-# execute the nextflow pipeline to download example data
+# execute the nextflow pipeline
 report = f"{args.input}-mcmicro-execution_report.html"
 subprocess.run(
     [
@@ -71,4 +69,4 @@
 output = ln.Artifact.from_dir(f"{input_dir}/registration")
 ln.save(output)
 
-ln.finish()
+ln.context.finish()
diff --git a/docs/mcmicro_exemplar.py b/docs/mcmicro_exemplar.py
@@ -1,15 +1,14 @@
-# mcmicro_exemplar.py
-
 """This script downloads the MCMICRO exemplar data and registers it in LaminDB.
 
-Usage: python mcmicro_exemplar.py exemplar-001
+The here registered data is used for the Nextflow use case.
+Note that the Nextflow use case simulates the concatenation of two subsequent pipelines where
+this script executes the first pipeline and the Nextflow use case the second pipeline.
 """
 
 import lamindb as ln
 import subprocess
 import argparse
 
-
 # get args from command line
 parser = argparse.ArgumentParser()
 parser.add_argument("name", type=str, help="Name of the example data.")
@@ -64,4 +63,4 @@
 exemplar_dir = ln.Artifact(args.name, description=args.name)
 exemplar_dir.save()
 
-ln.finish()
+ln.context.finish()