From 2c69ca48ce1a9ab431afcc891bdad8c495c9768e Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 6 Apr 2020 14:11:41 -0400
Subject: Add service to automatically run a workflow on collections uploaded
 to a project.

---
 bh20seqanalyzer/main.py | 55 +++++++++++++++++++++++++++++++++++++++++++++++++
 bh20sequploader/main.py |  1 -
 setup.py                |  5 +++--
 3 files changed, 58 insertions(+), 3 deletions(-)
 create mode 100644 bh20seqanalyzer/main.py

diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
new file mode 100644
index 0000000..23e58e9
--- /dev/null
+++ b/bh20seqanalyzer/main.py
@@ -0,0 +1,55 @@
+import argparse
+import arvados
+import time
+import subprocess
+import tempfile
+import json
+
+def start_analysis(api, collection, analysis_project, workflow_uuid):
+    project = api.groups().create(body={
+        "group_class": "project",
+        "name": "Analysis of %s" % collection["name"],
+        "owner_uuid": analysis_project,
+    }, ensure_unique_name=True).execute()
+
+    with tempfile.NamedTemporaryFile() as tmp:
+        inputobj = json.dumps({
+            "sequence": {
+                "class": "File",
+                "location": "keep:%s/sequence.fasta" % collection["portable_data_hash"]
+            },
+            "metadata": {
+                "class": "File",
+                "location": "keep:%s/metadata.jsonld" % collection["portable_data_hash"]
+            }
+        }, indent=2)
+        tmp.write(inputobj.encode('utf-8'))
+        tmp.flush()
+        cmd = ["arvados-cwl-runner",
+               "--submit",
+               "--no-wait",
+               "--debug",
+               "--project-uuid=%s" % project["uuid"],
+               "arvwf:%s" % workflow_uuid,
+               tmp.name]
+        print("Running %s" % ' '.join(cmd))
+        comp = subprocess.run(cmd, capture_output=True)
+    if comp.returncode != 0:
+        print(comp.stderr.decode('utf-8'))
+    else:
+        api.collections().update(uuid=collection["uuid"], body={"owner_uuid": project['uuid']}).execute()
+
+def main():
+    parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project')
+    parser.add_argument('--uploader-project', type=str, default='lugli-j7d0g-n5clictpuvwk8aa', help='')
+    parser.add_argument('--analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='')
+    parser.add_argument('--workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='')
+    args = parser.parse_args()
+
+    api = arvados.api()
+
+    while True:
+        new_collections = api.collections().list(filters=[['owner_uuid', '=', args.uploader_project]]).execute()
+        for c in new_collections["items"]:
+            start_analysis(api, c, args.analysis_project, args.workflow_uuid)
+        time.sleep(10)
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 049a21c..9de51f4 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -10,7 +10,6 @@ import getpass
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
 UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
-WORKFLOW=''
 
 def main():
     parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis')
diff --git a/setup.py b/setup.py
index d5c71b2..9e73ff0 100644
--- a/setup.py
+++ b/setup.py
@@ -29,13 +29,14 @@ setup(
     author="Peter Amstutz",
     author_email="peter.amstutz@curii.com",
     license="Apache 2.0",
-    packages=["bh20sequploader"],
+    packages=["bh20sequploader", "bh20seqanalyzer"],
     install_requires=install_requires,
     setup_requires=[] + pytest_runner,
     tests_require=["pytest<5"],
     entry_points={
         "console_scripts": [
-            "bh20-seq-uploader=bh20sequploader.main:main"
+            "bh20-seq-uploader=bh20sequploader.main:main",
+            "bh20-seq-analyzer=bh20seqanalyzer.main:main"
         ]
     },
     zip_safe=True,
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