From c235e5326a82fe03e36cdec956508b4b9dfdfce1 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@udo.edu>
Date: Thu, 22 Apr 2021 11:20:53 +0200
Subject: [PATCH 1/2] add cosmic database download wrapper

---
 bio/cosmic-db/environment.yaml |  8 ++++
 bio/cosmic-db/meta.yaml        |  9 +++++
 bio/cosmic-db/test/Snakefile   | 16 ++++++++
 bio/cosmic-db/wrapper.py       | 67 ++++++++++++++++++++++++++++++++++
 test.py                        |  8 ++++
 5 files changed, 108 insertions(+)
 create mode 100644 bio/cosmic-db/environment.yaml
 create mode 100644 bio/cosmic-db/meta.yaml
 create mode 100644 bio/cosmic-db/test/Snakefile
 create mode 100644 bio/cosmic-db/wrapper.py

diff --git a/bio/cosmic-db/environment.yaml b/bio/cosmic-db/environment.yaml
new file mode 100644
index 00000000000..be6a91a1f3b
--- /dev/null
+++ b/bio/cosmic-db/environment.yaml
@@ -0,0 +1,8 @@
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - curl =7
+  - python >=3.6.2
+  - requests =2.25
diff --git a/bio/cosmic-db/meta.yaml b/bio/cosmic-db/meta.yaml
new file mode 100644
index 00000000000..809a0fff19a
--- /dev/null
+++ b/bio/cosmic-db/meta.yaml
@@ -0,0 +1,9 @@
+name: cosmic-db
+description: |
+  Download cosmic databases from https://cancer.sanger.ac.uk/cosmic/download
+authors:
+  - Till Hartmann
+input:
+  - genome build, cosmic release version, dataset and file name
+output:
+  - database
diff --git a/bio/cosmic-db/test/Snakefile b/bio/cosmic-db/test/Snakefile
new file mode 100644
index 00000000000..10fbafd1b6a
--- /dev/null
+++ b/bio/cosmic-db/test/Snakefile
@@ -0,0 +1,16 @@
+envvars:
+    "COSMIC_EMAIL",
+    "COSMIC_PW"
+
+rule cosmic_download:
+    output:
+        "resources/{db}"
+    params:
+        build="GRCh38",
+        dataset="cosmic",
+        version="v92",
+        file=lambda wc: wc.db  # e.g. "CosmicHGNC.tsv.gz"
+    log:
+        "logs/cosmic-db/{db}.log"
+    wrapper:
+        "master/bio/cosmic-db"
diff --git a/bio/cosmic-db/wrapper.py b/bio/cosmic-db/wrapper.py
new file mode 100644
index 00000000000..999360ec10a
--- /dev/null
+++ b/bio/cosmic-db/wrapper.py
@@ -0,0 +1,67 @@
+"""Snakemake wrapper for trimming paired-end reads using cutadapt."""
+
+__author__ = "Till Hartmann"
+__copyright__ = "Copyright 2021, Till Hartmann"
+__email__ = "till.hartmann@udo.edu"
+__license__ = "MIT"
+
+import requests
+import os
+from typing import List
+from snakemake.shell import shell
+
+email = os.environ["COSMIC_EMAIL"]
+password = os.environ["COSMIC_PW"]
+assert email, "$COSMIC_EMAIL is not set"
+assert password, "$COSMIC_PW is not set"
+
+COSMIC_URL = "https://cancer.sanger.ac.uk/cosmic/file_download"
+
+
+def available_builds() -> List[str]:
+    builds = requests.get(COSMIC_URL).json()
+    return builds
+
+
+def available_datasets(build: str) -> List[str]:
+    datasets = requests.get(f"{COSMIC_URL}/{build}").json()
+    return [d.rpartition("/")[-1] for d in datasets]
+
+
+def available_versions(build: str, dataset: str) -> List[str]:
+    versions = requests.get(f"{COSMIC_URL}/{build}/{dataset}").json()
+    return [v.rpartition("/")[-1] for v in versions]
+
+
+def available_files(build: str, dataset: str, version: str) -> List[str]:
+    files = requests.get(f"{COSMIC_URL}/{build}/{dataset}/{version}").json()
+    return [f.rpartition("/")[-1] for f in files]
+
+
+def download_path(build: str, dataset: str, version: str, file: str) -> str:
+    return f"{COSMIC_URL}/{build}/{dataset}/{version}/{file}"
+
+
+build = snakemake.params.get("build", "")
+dataset = snakemake.params.get("dataset", "")
+version = snakemake.params.get("version", "")
+file = snakemake.params.get("file", "")
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
+builds = available_builds()
+assert build in builds, f"{build} is not available. Choose one of: {builds}."
+
+datasets = available_datasets(build)
+assert dataset in datasets, f"{dataset} is not available. Choose one of: {datasets}."
+
+versions = available_versions(build, dataset)
+assert version in versions, f"{version} is not available. Choose one of: {versions}."
+
+files = available_files(build, dataset, version)
+assert file in files, f"{file} is not available. Choose one of: {files}."
+
+download_url = requests.get(
+    download_path(build, dataset, version, file), auth=(email, password)
+).json()["url"].strip()
+
+shell('curl "{download_url}" -o {snakemake.output[0]} {log}')
diff --git a/test.py b/test.py
index 964479541c2..aeb4c3f0913 100644
--- a/test.py
+++ b/test.py
@@ -125,6 +125,14 @@ def run(wrapper, cmd, check_log=None):
             os.chdir(origdir)
 
 
+@skip_if_not_modified
+def test_download_cosmic_db():
+    run(
+        "bio/cosmic-db",
+        ["snakemake", "--cores", "1", "--use-conda", "resources/CosmicHGNC.tsv.gz"],
+    )
+
+
 @skip_if_not_modified
 def test_open_cravat_run():
     run(

From 4818014d61e06d6a73160df497141b6e0f642660 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@udo.edu>
Date: Thu, 22 Apr 2021 11:31:02 +0200
Subject: [PATCH 2/2] black reformat

---
 bio/cosmic-db/wrapper.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/bio/cosmic-db/wrapper.py b/bio/cosmic-db/wrapper.py
index 999360ec10a..e769ff551ee 100644
--- a/bio/cosmic-db/wrapper.py
+++ b/bio/cosmic-db/wrapper.py
@@ -60,8 +60,10 @@ def download_path(build: str, dataset: str, version: str, file: str) -> str:
 files = available_files(build, dataset, version)
 assert file in files, f"{file} is not available. Choose one of: {files}."
 
-download_url = requests.get(
-    download_path(build, dataset, version, file), auth=(email, password)
-).json()["url"].strip()
+download_url = (
+    requests.get(download_path(build, dataset, version, file), auth=(email, password))
+    .json()["url"]
+    .strip()
+)
 
 shell('curl "{download_url}" -o {snakemake.output[0]} {log}')