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Merge pull request #4 from mart-r/separateFoldersForParts
Using different data folder for each part of tutorial
2 parents 1af1a5c + 18c41a4 commit 6be35a6

10 files changed

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-16402
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‎notebooks/introductory/Part_2_Dataset_Analysis_and_Preparation.html‎

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‎notebooks/introductory/Part_2_Dataset_Analysis_and_Preparation.ipynb‎

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},
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"outputs": [],
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"source": [
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"DATA_DIR = \"./data/\""
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"DATA_DIR = \"./data_p2/\"\n",
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"! DATA_DIR=\"./data_p2/\""
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]
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},
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{
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"outputs": [],
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"source": [
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"# Load files if in google colab, otherwise skip this step\n",
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"! wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/noteevents.csv -P ./data/\n",
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"! wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/patients.csv -P ./data/"
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"! wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/noteevents.csv -P $DATA_DIR\n",
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"! wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/patients.csv -P $DATA_DIR"
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]
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{

‎notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb‎

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},
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"outputs": [],
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"source": [
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"DATA_DIR = \"./data/\""
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"DATA_DIR = \"./data_p3.1/\"\n",
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"! DATA_DIR=\"./data_p3.1/\""
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]
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},
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{
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],
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"source": [
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"# Load files if in google colab, otherwise skip this step\n",
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"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/cdb_simple.csv -P ./data/\n",
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"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/cdb_advanced.csv -P ./data/\n",
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"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/vocab_data.txt -P ./data/"
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"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/cdb_simple.csv -P $DATA_DIR\n",
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"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/cdb_advanced.csv -P $DATA_DIR\n",
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"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/vocab_data.txt -P $DATA_DIR"
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]
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},
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{

‎notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.ipynb‎

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},
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"outputs": [],
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"source": [
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"DATA_DIR = \"./data/\"\n",
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"DATA_DIR = \"./data_p3.2/\"\n",
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"! DATA_DIR=\"./data_p3.2/\"\n",
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"model_pack_path = DATA_DIR + \"medmen_wstatus_2021_oct.zip\""
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]
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},
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],
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"# Download the models and required data\n",
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"!wget https://medcat.rosalind.kcl.ac.uk/media/medmen_wstatus_2021_oct.zip -P ./data/\n",
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"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/pt_notes.csv -P ./data/"
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"!wget -N https://medcat.rosalind.kcl.ac.uk/media/medmen_wstatus_2021_oct.zip -P $DATA_DIR\n",
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"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/pt_notes.csv -P $DATA_DIR"
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]
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{

‎notebooks/introductory/Part_4_1_ByteLevelBPETokenizer_and_Embeddings.html‎

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<div class="prompt input_prompt">In&nbsp;[2]:</div>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">DATA_DIR</span> <span class="o">=</span> <span class="s2">&quot;./data/&quot;</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">DATA_DIR</span> <span class="o">=</span> <span class="s2">&quot;./data_p4.1/&quot;</span>
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<span class="o">!</span> <span class="nv">DATA_DIR</span><span class="o">=</span><span class="s2">&quot;./data_p4.1/&quot;</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="o">!</span>mkdir ./data
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<span class="o">!</span>mkdir ./models
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<span class="o">!</span>wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/noteevents.csv -P ./data/
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<div class=" highlight hl-ipython3"><pre><span></span><span class="o">!</span>mkdir ./models
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<span class="o">!</span>wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/noteevents.csv -P <span class="nv">$DATA_DIR</span>
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‎notebooks/introductory/Part_4_1_ByteLevelBPETokenizer_and_Embeddings.ipynb‎

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"outputs": [],
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"DATA_DIR = \"./data/\""
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"DATA_DIR = \"./data_p4.1/\"\n",
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"! DATA_DIR=\"./data_p4.1/\""
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}
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"source": [
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"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/noteevents.csv -P ./data/"
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"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/noteevents.csv -P $DATA_DIR"
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{

‎notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.html‎

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<div class="prompt input_prompt">In&nbsp;[2]:</div>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">DATA_DIR</span> <span class="o">=</span> <span class="s2">&quot;./data/&quot;</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">DATA_DIR</span> <span class="o">=</span> <span class="s2">&quot;./data_p4.2/&quot;</span>
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<span class="o">!</span> <span class="nv">DATA_DIR</span><span class="o">=</span><span class="s2">&quot;./data_p4.2/&quot;</span>
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<span class="n">vocab_path</span> <span class="o">=</span> <span class="n">DATA_DIR</span> <span class="o">+</span> <span class="s2">&quot;vocab.dat&quot;</span>
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<span class="n">cdb_path</span> <span class="o">=</span> <span class="n">DATA_DIR</span> <span class="o">+</span> <span class="s2">&quot;cdb-medmen-v1_2.dat&quot;</span>
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<div class="inner_cell">
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<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Download the models and required data</span>
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<span class="o">!</span>wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/MedCAT_Export.json -P ./data/
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<span class="o">!</span>wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/MedCAT_Export.json -P <span class="nv">$DATA_DIR</span>
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<span class="c1"># You can also use the models created in Part 4.1 of the Tutorial</span>
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<span class="o">!</span>wget https://medcat.rosalind.kcl.ac.uk/media/mc_status.zip -P ./data/
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<span class="o">!</span>wget -N https://medcat.rosalind.kcl.ac.uk/media/mc_status.zip -P <span class="nv">$DATA_DIR</span>
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<span class="c1"># Get MedCAT models components (Alternatively you can use a previously created MedCAT model packs)</span>
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<span class="o">!</span>wget https://medcat.rosalind.kcl.ac.uk/media/vocab.dat -P ./data/
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<span class="o">!</span>wget https://medcat.rosalind.kcl.ac.uk/media/cdb-medmen-v1_2.dat -P ./data/
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<span class="o">!</span>wget -N https://medcat.rosalind.kcl.ac.uk/media/vocab.dat -P <span class="nv">$DATA_DIR</span>
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<span class="o">!</span>wget -N https://medcat.rosalind.kcl.ac.uk/media/cdb-medmen-v1_2.dat -P <span class="nv">$DATA_DIR</span>
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‎notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.ipynb‎

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"# Download the models and required data\n",
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{

‎notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.ipynb‎

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},
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"outputs": [],
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"source": [
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"DATA_DIR = \"./data/\"\n",
329+
"DATA_DIR = \"./data_p4.3/\"\n",
330+
"! DATA_DIR=\"./data_p4.3/\"\n",
330331
"MODEL_DIR = \"./models/\"\n",
332+
"! MODEL_DIR=\"./models/\"\n",
331333
"model_pack_path = MODEL_DIR + \"medmen_wstatus_2021_oct.zip\""
332334
]
333335
},
@@ -384,11 +386,11 @@
384386
],
385387
"source": [
386388
"# Download the models and required data\n",
387-
"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/pt_notes.csv -P ./data/\n",
388-
"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/MedCAT_Export.json -P ./data/\n",
389+
"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/pt_notes.csv -P $DATA_DIR\n",
390+
"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/MedCAT_Export.json -P $DATA_DIR\n",
389391
"\n",
390392
"# Download the medcat modelpack\n",
391-
"!wget https://medcat.rosalind.kcl.ac.uk/media/medmen_wstatus_2021_oct.zip -P ./models/\n"
393+
"!wget -N https://medcat.rosalind.kcl.ac.uk/media/medmen_wstatus_2021_oct.zip -P $MODEL_DIR\n"
392394
]
393395
},
394396
{
@@ -496,7 +498,7 @@
496498
}
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],
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"source": [
499-
"!wget https://raw.githubusercontent.com/CogStack/MedCAT/master/tutorial/data/pt_notes.csv -P ./data/"
501+
"!wget -N https://raw.githubusercontent.com/CogStack/MedCAT/master/tutorial/data/pt_notes.csv -P $DATA_DIR"
500502
]
501503
},
502504
{

‎notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.ipynb‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -320,7 +320,8 @@
320320
},
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"outputs": [],
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"source": [
323-
"DATA_DIR = \"./data/\"\n",
323+
"DATA_DIR = \"./data_p5/\"\n",
324+
"! DATA_DIR=\"./data_p5/\"\n",
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"model_pack_path = DATA_DIR + \"medmen_wstatus_2021_oct.zip\""
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]
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},
@@ -397,11 +398,11 @@
397398
],
398399
"source": [
399400
"# Download the models and required data\n",
400-
"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/pt_notes.csv -P ./data/\n",
401-
"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/MedCAT_Export.json -P ./data/\n",
402-
"!wget https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/cui_location.json -P ./data/\n",
401+
"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/pt_notes.csv -P $DATA_DIR\n",
402+
"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/MedCAT_Export.json -P $DATA_DIR\n",
403+
"!wget -N https://raw.githubusercontent.com/CogStack/MedCATtutorials/main/notebooks/introductory/data/cui_location.json -P $DATA_DIR\n",
403404
"\n",
404-
"!wget https://medcat.rosalind.kcl.ac.uk/media/medmen_wstatus_2021_oct.zip -P ./data/"
405+
"!wget -N https://medcat.rosalind.kcl.ac.uk/media/medmen_wstatus_2021_oct.zip -P $DATA_DIR"
405406
]
406407
},
407408
{

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