Automate cancer-data download from figshare #42
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@gwaygenomics, based on whether #39 or this is merged first, one of us will have to do some extra work. |
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| # In[3]: | |||
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| # We're going to be building a 'TP53' classifier | |||
| GENE = 'TP53' | |||
| GENE = '7157' # TP53 | |||
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Is algorithms/scripts/SGDClassifier-master.py the nbconverted 2.TCGA-MLexample.ipynb? It is difficult to compare the diffs between 1.TCGA-MLexample.ipynb and 2.TCGA-MLexample.ipynb
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I had forgotten to delete scripts/1.TCGA-MLexample.py. I did a force push. Now see the diff for "scripts/1.TCGA-MLexample.py → scripts/2.TCGA-MLexample.py"
`1.download.ipynb` queries the figshare API to find the latest versions of the files and downloads them. Changes directory for storing downloaded data from `data` to `download`, following the convention of cognoma/cancer-data. Add `requests` library to environment. Add an execute script that executes notebooks in the root directory in order and exports them to scripts. In `algorithms`, notebooks were not updated besides `SGDClassifier-master.ipynb` which is the example notebook and template for new implementations.
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LGTM - excited about the progress! I will now remove the download logic in #39 |
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Okay will merge now. You will probably have to rebase your PR. |
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1.download.ipynbqueries the figshare API to find the latest versions of the files and downloads them.Changes directory for storing downloaded data from
datatodownload, following the convention ofcognoma/cancer-data.Add
requestslibrary to environment.Add an execute script that executes notebooks in the root directory in order and exports them to scripts.
In
algorithms, notebooks were not updated besidesSGDClassifier-master.ipynbwhich is the example notebook and template for new implementations.