From afbc3ec99f638a2f8df96a8e952b5b9616dc99a8 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 7 Apr 2020 13:31:49 -0400
Subject: Now moves collections into 'validated sequences' project

Improve logging for seq service

Fix uploader bug

Runs workflow with all validated sequences.
---
 bh20sequploader/main.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'bh20sequploader/main.py')

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 17ad492..d3ebc0c 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -49,4 +49,5 @@ def main():
                  (properties['upload_user'], properties['upload_ip']),
                  properties=properties, ensure_unique_name=True)
 
-main()
+if __name__ == "__main__":
+    main()
-- 
cgit v1.2.3


From 07bc4c65535437b8e9e0744f08da8cea541d0116 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 7 Apr 2020 15:28:42 -0400
Subject: Add metadata validation with schema-salad

---
 bh20seqanalyzer/main.py            | 11 ++++++++---
 bh20sequploader/bh20seq-schema.yml | 36 ++++++++++++++++++++++++++++++++++++
 bh20sequploader/main.py            |  7 +++++--
 bh20sequploader/qc_metadata.py     | 26 +++++++++++++++++---------
 example/dummyschema.yaml           | 16 ----------------
 setup.py                           |  3 ++-
 6 files changed, 68 insertions(+), 31 deletions(-)
 create mode 100644 bh20sequploader/bh20seq-schema.yml
 delete mode 100644 example/dummyschema.yaml

(limited to 'bh20sequploader/main.py')

diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 2513ea3..78e32c9 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -6,12 +6,14 @@ import subprocess
 import tempfile
 import json
 import logging
+import ruamel.yaml
+from bh20sequploader.qc_metadata import qc_metadata
 
 logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%Y-%m-%d %H:%M:%S",
                     level=logging.INFO)
 logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN)
 
-def validate_upload(api, collection, validated_project, latest_result_uuid):
+def validate_upload(api, collection, validated_project):
     col = arvados.collection.Collection(collection["uuid"])
 
     # validate the collection here.  Check metadata, etc.
@@ -20,9 +22,12 @@ def validate_upload(api, collection, validated_project, latest_result_uuid):
     if "sequence.fasta" not in col:
         valid = False
         logging.warn("Upload '%s' missing sequence.fasta", collection["name"])
-    if "metadata.jsonld" not in col:
-        logging.warn("Upload '%s' missing metadata.jsonld", collection["name"])
+    if "metadata.yaml" not in col:
+        logging.warn("Upload '%s' missing metadata.yaml", collection["name"])
         valid = False
+    else:
+        metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml"))
+        valid = qc_metadata(metadata_content) and valid
 
     dup = api.collections().list(filters=[["owner_uuid", "=", validated_project],
                                           ["portable_data_hash", "=", col.portable_data_hash()]]).execute()
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
new file mode 100644
index 0000000..6e0973a
--- /dev/null
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -0,0 +1,36 @@
+$graph:
+
+- name: sampleInformationSchema
+  type: record
+  fields:
+    location: string
+    host: string
+    sequenceTechnology: string
+    assemblyMethod: string
+
+- name: InstituteInformationSchema
+  type: record
+  fields:
+    OriginatingLab: string
+    SubmittingLab: string
+
+- name: SubmitterInformationSchema
+  type: record
+  fields:
+    Submitter: string
+    submissionDate: string
+
+- name: VirusDetailSchema
+  type: record
+  fields:
+    VirusName: string
+    AccessionId: string
+
+- name: MainSchema
+  type: record
+  documentRoot: true
+  fields:
+    sampleInformation: sampleInformationSchema
+    InstituteInformation: InstituteInformationSchema
+    SubmitterInformation: SubmitterInformationSchema
+    VirusDetail: VirusDetailSchema
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index d3ebc0c..8b8fefe 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,6 +6,7 @@ import json
 import urllib.request
 import socket
 import getpass
+from .qc_metadata import qc_metadata
 
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -19,6 +20,8 @@ def main():
 
     api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
 
+    qc_metadata(args.metadata.name)
+
     col = arvados.collection.Collection(api_client=api)
 
     print("Reading FASTA")
@@ -29,8 +32,8 @@ def main():
             f.write(r)
             r = args.sequence.read(65536)
 
-    print("Reading JSONLD")
-    with col.open("metadata.jsonld", "w") as f:
+    print("Reading metadata")
+    with col.open("metadata.yaml", "w") as f:
         r = args.metadata.read(65536)
         print(r[0:20])
         while r:
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 0632777..78b31b2 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -1,13 +1,21 @@
-import yamale
+import schema_salad.schema
+import logging
+import pkg_resources
 
-## NOTE: this is just a DUMMY. Everything about this can and will change
 def qc_metadata(metadatafile):
-    print("Start metadata validation...")
-    schema = yamale.make_schema('../example/dummyschema.yaml')
-    data = yamale.make_data(metadatafile)
-    # Validate data against the schema. Throws a ValueError if data is invalid.
-    yamale.validate(schema, data)
-    print("...complete!")
+    schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml")
+    cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")}
+    (document_loader,
+     avsc_names,
+     schema_metadata,
+     metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache)
 
-#qc_metadata("../example/metadata.yaml")
+    if not isinstance(avsc_names, schema_salad.avro.schema.Names):
+        print(avsc_names)
+        return False
 
+    try:
+        doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
+        return True
+    except:
+        return False
diff --git a/example/dummyschema.yaml b/example/dummyschema.yaml
deleted file mode 100644
index e428324..0000000
--- a/example/dummyschema.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-#sampleInformation: include('sampleInformation')
-#InstituteInformation: include('InstituteInformation')
----
-sampleInformation:
-  location : str()
-  host : str()
-  sequenceTechnology: str()
-  assemblyMethod: str()
-
-InstituteInformation:
-  OriginatingLab: str()
-  SubmittingLab: str()
-
-VirusDetail:
-  VirusName: str()
-  AccessionId: str()
diff --git a/setup.py b/setup.py
index 0685d37..48c25aa 100644
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,7 @@ try:
 except ImportError:
     tagger = egg_info_cmd.egg_info
 
-install_requires = ["arvados-python-client"]
+install_requires = ["arvados-python-client", "schema-salad"]
 
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
 pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else []
@@ -30,6 +30,7 @@ setup(
     author_email="peter.amstutz@curii.com",
     license="Apache 2.0",
     packages=["bh20sequploader", "bh20seqanalyzer"],
+    package_data={"bh20sequploader": ["bh20seq-schema.yml"]},
     install_requires=install_requires,
     setup_requires=[] + pytest_runner,
     tests_require=["pytest<5"],
-- 
cgit v1.2.3


From 9458ed33da08c787c4bb20af7b4108c93334b351 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Wed, 8 Apr 2020 17:41:19 -0400
Subject: Fastq now runs through fastq2fasta pipeline

then gets added to pangenome analysis.
---
 bh20seqanalyzer/main.py        | 141 ++++++++++++++++++++++++++++++-----------
 bh20sequploader/main.py        |  14 +++-
 bh20sequploader/qc_metadata.py |   6 +-
 3 files changed, 120 insertions(+), 41 deletions(-)

(limited to 'bh20sequploader/main.py')

diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 78e32c9..1a8965b 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -13,21 +13,30 @@ logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%
                     level=logging.INFO)
 logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN)
 
-def validate_upload(api, collection, validated_project):
+def validate_upload(api, collection, validated_project,
+                    fastq_project, fastq_workflow_uuid):
     col = arvados.collection.Collection(collection["uuid"])
 
     # validate the collection here.  Check metadata, etc.
     valid = True
 
-    if "sequence.fasta" not in col:
-        valid = False
-        logging.warn("Upload '%s' missing sequence.fasta", collection["name"])
     if "metadata.yaml" not in col:
         logging.warn("Upload '%s' missing metadata.yaml", collection["name"])
         valid = False
     else:
         metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml"))
-        valid = qc_metadata(metadata_content) and valid
+        #valid = qc_metadata(metadata_content) and valid
+        if not valid:
+            logging.warn("Failed metadata qc")
+
+    if valid:
+        if "sequence.fasta" not in col:
+            if "reads.fastq" in col:
+                start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid)
+                return False
+            else:
+                valid = False
+                logging.warn("Upload '%s' missing sequence.fasta", collection["name"])
 
     dup = api.collections().list(filters=[["owner_uuid", "=", validated_project],
                                           ["portable_data_hash", "=", col.portable_data_hash()]]).execute()
@@ -39,7 +48,9 @@ def validate_upload(api, collection, validated_project):
     if valid:
         logging.info("Added '%s' to validated sequences" % collection["name"])
         # Move it to the "validated" project to be included in the next analysis
-        api.collections().update(uuid=collection["uuid"], body={"owner_uuid": validated_project}).execute()
+        api.collections().update(uuid=collection["uuid"], body={
+            "owner_uuid": validated_project,
+            "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute()
     else:
         # It is invalid, delete it.
         logging.warn("Deleting '%s'" % collection["name"])
@@ -47,28 +58,15 @@ def validate_upload(api, collection, validated_project):
 
     return valid
 
-def start_analysis(api,
-                   analysis_project,
-                   workflow_uuid,
-                   validated_project):
 
+def run_workflow(api, parent_project, workflow_uuid, name, inputobj):
     project = api.groups().create(body={
         "group_class": "project",
-        "name": "Pangenome analysis",
-        "owner_uuid": analysis_project,
+        "name": name,
+        "owner_uuid": parent_project,
     }, ensure_unique_name=True).execute()
 
-    validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]])
-
     with tempfile.NamedTemporaryFile() as tmp:
-        inputobj = {
-            "inputReads": []
-        }
-        for v in validated:
-            inputobj["inputReads"].append({
-                "class": "File",
-                "location": "keep:%s/sequence.fasta" % v["portable_data_hash"]
-            })
         tmp.write(json.dumps(inputobj, indent=2).encode('utf-8'))
         tmp.flush()
         cmd = ["arvados-cwl-runner",
@@ -83,32 +81,95 @@ def start_analysis(api,
     if comp.returncode != 0:
         logging.error(comp.stderr.decode('utf-8'))
 
+    return project
+
+
+def start_fastq_to_fasta(api, collection,
+                         analysis_project,
+                         fastq_workflow_uuid):
+    newproject = run_workflow(api, analysis_project, fastq_workflow_uuid, "FASTQ to FASTA", {
+        "fastq_forward": {
+            "class": "File",
+            "location": "keep:%s/reads.fastq" % collection["portable_data_hash"]
+        },
+        "metadata": {
+            "class": "File",
+            "location": "keep:%s/metadata.yaml" % collection["portable_data_hash"]
+        },
+        "ref_fasta": {
+            "class": "File",
+            "location": "keep:ffef6a3b77e5e04f8f62a7b6f67264d1+556/SARS-CoV2-NC_045512.2.fasta"
+        }
+    })
+    api.collections().update(uuid=collection["uuid"],
+                             body={"owner_uuid": newproject["uuid"]}).execute()
+
+def start_pangenome_analysis(api,
+                             analysis_project,
+                             pangenome_workflow_uuid,
+                             validated_project):
+    validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]])
+    inputobj = {
+        "inputReads": []
+    }
+    for v in validated:
+        inputobj["inputReads"].append({
+            "class": "File",
+            "location": "keep:%s/sequence.fasta" % v["portable_data_hash"]
+        })
+    run_workflow(api, analysis_project, pangenome_workflow_uuid, "Pangenome analysis", inputobj)
+
+
+def get_workflow_output_from_project(api, uuid):
+    cr = api.container_requests().list(filters=[['owner_uuid', '=', uuid],
+                                                ["requesting_container_uuid", "=", None]]).execute()
+    if cr["items"] and cr["items"][0]["output_uuid"]:
+        return cr["items"][0]
+    else:
+        return None
+
 
 def copy_most_recent_result(api, analysis_project, latest_result_uuid):
     most_recent_analysis = api.groups().list(filters=[['owner_uuid', '=', analysis_project]],
                                                   order="created_at desc", limit=1).execute()
     for m in most_recent_analysis["items"]:
-        cr = api.container_requests().list(filters=[['owner_uuid', '=', m["uuid"]],
-                                                    ["requesting_container_uuid", "=", None]]).execute()
-        if cr["items"] and cr["items"][0]["output_uuid"]:
-            wf = cr["items"][0]
+        wf = get_workflow_output_from_project(api, m["uuid"])
+        if wf:
             src = api.collections().get(uuid=wf["output_uuid"]).execute()
             dst = api.collections().get(uuid=latest_result_uuid).execute()
             if src["portable_data_hash"] != dst["portable_data_hash"]:
                 logging.info("Copying latest result from '%s' to %s", m["name"], latest_result_uuid)
                 api.collections().update(uuid=latest_result_uuid,
                                          body={"manifest_text": src["manifest_text"],
-                                               "description": "latest result from %s %s" % (m["name"], wf["uuid"])}).execute()
+                                               "description": "Result from %s %s" % (m["name"], wf["uuid"])}).execute()
             break
 
 
+def move_fastq_to_fasta_results(api, analysis_project, uploader_project):
+    projects = api.groups().list(filters=[['owner_uuid', '=', analysis_project],
+                                          ["properties.moved_output", "!=", True]],
+                                 order="created_at desc",).execute()
+    for p in projects["items"]:
+        wf = get_workflow_output_from_project(api, p["uuid"])
+        if wf:
+            logging.info("Moving completed fastq2fasta result %s back to uploader project", wf["output_uuid"])
+            api.collections().update(uuid=wf["output_uuid"],
+                                     body={"owner_uuid": uploader_project}).execute()
+            p["properties"]["moved_output"] = True
+            api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).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('--pangenome-analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='')
+    parser.add_argument('--fastq-project', type=str, default='lugli-j7d0g-xcjxp4oox2u1w8u', help='')
     parser.add_argument('--validated-project', type=str, default='lugli-j7d0g-5ct8p1i1wrgyjvp', help='')
-    parser.add_argument('--workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='')
-    parser.add_argument('--latest-result-uuid', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='')
+
+    parser.add_argument('--pangenome-workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='')
+    parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='')
+
+    parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='')
     args = parser.parse_args()
 
     api = arvados.api()
@@ -116,16 +177,24 @@ def main():
     logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project))
 
     while True:
+        move_fastq_to_fasta_results(api, args.fastq_project, args.uploader_project)
+
         new_collections = api.collections().list(filters=[['owner_uuid', '=', args.uploader_project]]).execute()
         at_least_one_new_valid_seq = False
         for c in new_collections["items"]:
-            at_least_one_new_valid_seq = validate_upload(api, c, args.validated_project) or at_least_one_new_valid_seq
+            at_least_one_new_valid_seq = validate_upload(api, c,
+                                                         args.validated_project,
+                                                         args.fastq_project,
+                                                         args.fastq_workflow_uuid) or at_least_one_new_valid_seq
 
         if at_least_one_new_valid_seq:
-            start_analysis(api, args.analysis_project,
-                           args.workflow_uuid,
-                           args.validated_project)
+            start_pangenome_analysis(api,
+                                     args.pangenome_analysis_project,
+                                     args.pangenome_workflow_uuid,
+                                     args.validated_project)
 
-        copy_most_recent_result(api, args.analysis_project, args.latest_result_uuid)
+        copy_most_recent_result(api,
+                                args.pangenome_analysis_project,
+                                args.latest_result_collection)
 
-        time.sleep(10)
+        time.sleep(15)
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 8b8fefe..56cbe22 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -20,12 +20,18 @@ def main():
 
     api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
 
-    qc_metadata(args.metadata.name)
+    if not qc_metadata(args.metadata.name):
+        print("Failed metadata qc")
+        exit(1)
 
     col = arvados.collection.Collection(api_client=api)
 
-    print("Reading FASTA")
-    with col.open("sequence.fasta", "w") as f:
+    if args.sequence.name.endswith("fasta") or args.sequence.name.endswith("fa"):
+        target = "sequence.fasta"
+    elif args.sequence.name.endswith("fastq") or args.sequence.name.endswith("fq"):
+        target = "reads.fastq"
+
+    with col.open(target, "w") as f:
         r = args.sequence.read(65536)
         print(r[0:20])
         while r:
@@ -52,5 +58,7 @@ def main():
                  (properties['upload_user'], properties['upload_ip']),
                  properties=properties, ensure_unique_name=True)
 
+    print("Done")
+
 if __name__ == "__main__":
     main()
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 78b31b2..ebe4dfc 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -1,6 +1,7 @@
 import schema_salad.schema
 import logging
 import pkg_resources
+import logging
 
 def qc_metadata(metadatafile):
     schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml")
@@ -17,5 +18,6 @@ def qc_metadata(metadatafile):
     try:
         doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
         return True
-    except:
-        return False
+    except Exception as e:
+        logging.warn(e)
+    return False
-- 
cgit v1.2.3


From bf93a6a2fec690eee4bff4891469cd5947102b3a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 9 Apr 2020 17:02:38 -0500
Subject: Moved Guix documentation into separate file (as it confused people ;)

---
 README.md               | 21 +++++----------------
 bh20sequploader/main.py |  2 +-
 doc/INSTALL.md          | 31 +++++++++++++++++++++++++++++++
 3 files changed, 37 insertions(+), 17 deletions(-)
 create mode 100644 doc/INSTALL.md

(limited to 'bh20sequploader/main.py')

diff --git a/README.md b/README.md
index a6fe052..3a8e5f0 100644
--- a/README.md
+++ b/README.md
@@ -122,19 +122,7 @@ It should print some instructions about how to use the uploader.
 
 ## Installation with GNU Guix
 
-Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system.
-
-1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run:
-
-```sh
-~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs
-```
-   
-2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief:
-
-```sh
-pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master
-```
+For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL.md)
 
 # Usage
 
@@ -148,7 +136,7 @@ bh20-seq-uploader example/sequence.fasta example/metadata.json
 
 All these uploaded sequences are being fed into a workflow to generate a [pangenome](https://academic.oup.com/bib/article/19/1/118/2566735) for the virus. You can replicate this workflow yourself.
 
-Get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run:
+An example is to get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run a series of commands
 
 ```sh
 minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf
@@ -157,6 +145,7 @@ odgi build -g seqs.gfa -s -o seqs.odgi
 odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5
 ```
 
-For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes).
-
+Here we convert such a pipeline into the Common Workflow Language (CWL) and
+sources can be found [here](https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate).
 
+For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes).
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 56cbe22..bf74ea5 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,7 +6,7 @@ import json
 import urllib.request
 import socket
 import getpass
-from .qc_metadata import qc_metadata
+import qc_metadata
 
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
diff --git a/doc/INSTALL.md b/doc/INSTALL.md
new file mode 100644
index 0000000..c5c486c
--- /dev/null
+++ b/doc/INSTALL.md
@@ -0,0 +1,31 @@
+# INSTALLATION
+
+Other options for running this tool.
+
+## GNU Guix
+
+Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system.
+
+1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run:
+
+```sh
+~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs
+```
+
+2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief:
+
+```sh
+pip3 install --user schema-salad  arvados-python-client
+```
+
+Pip installed the following modules
+
+```
+arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-client-1.6.7 httplib2-0.17.1 oauth2client-4.1.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 rsa-4.0 ruamel.yaml-0.15.77 six-1.14.0 uritemplate-3.0.1 ws4py-0.5.1
+```
+
+3. Run the tool directly with
+
+```sh
+~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py
+```
-- 
cgit v1.2.3


From bef2a43185f9494398f5d5a8cdb6c5f34352f912 Mon Sep 17 00:00:00 2001
From: Alex Kanitz
Date: Fri, 10 Apr 2020 18:27:44 +0200
Subject: validate seq format with magic file

---
 bh20sequploader/main.py                |  29 +++++++++++++++++++++++++----
 bh20sequploader/validation/Makefile    |   4 ++++
 bh20sequploader/validation/formats     |   4 ++++
 bh20sequploader/validation/formats.mgc | Bin 0 -> 1032 bytes
 4 files changed, 33 insertions(+), 4 deletions(-)
 create mode 100644 bh20sequploader/validation/Makefile
 create mode 100644 bh20sequploader/validation/formats
 create mode 100644 bh20sequploader/validation/formats.mgc

(limited to 'bh20sequploader/main.py')

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index bf74ea5..1d5b9c3 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -3,6 +3,8 @@ import time
 import arvados
 import arvados.collection
 import json
+import magic
+from pathlib import Path
 import urllib.request
 import socket
 import getpass
@@ -14,7 +16,7 @@ UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
 
 def main():
     parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis')
-    parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA')
+    parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA/FASTQ')
     parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json')
     args = parser.parse_args()
 
@@ -26,10 +28,27 @@ def main():
 
     col = arvados.collection.Collection(api_client=api)
 
-    if args.sequence.name.endswith("fasta") or args.sequence.name.endswith("fa"):
-        target = "sequence.fasta"
-    elif args.sequence.name.endswith("fastq") or args.sequence.name.endswith("fq"):
+    magic_file = Path(__file__).parent / "validation" / "formats.mgc"
+    val = magic.Magic(magic_file=magic_file.resolve().as_posix(),
+                      uncompress=False, mime=True)
+    seq_type = val.from_file(args.sequence.name).lower()
+    print(f"Sequence type: {seq_type}")
+    if seq_type == "text/fasta":
+        # ensure that contains only one entry
+        entries = 0
+        for line in args.sequence:
+            if line.startswith(">"):
+                entries += 1
+            if entries > 1:
+                raise ValueError("FASTA file contains multiple entries")
+                break
+        args.sequence.close()
+        args.sequence = open(args.sequence.name, "r")
         target = "reads.fastq"
+    elif seq_type == "text/fastq":
+        target = "sequence.fasta"
+    else:
+        raise ValueError("Sequence file does not look like FASTA or FASTQ")
 
     with col.open(target, "w") as f:
         r = args.sequence.read(65536)
@@ -37,6 +56,7 @@ def main():
         while r:
             f.write(r)
             r = args.sequence.read(65536)
+    args.sequence.close()
 
     print("Reading metadata")
     with col.open("metadata.yaml", "w") as f:
@@ -45,6 +65,7 @@ def main():
         while r:
             f.write(r)
             r = args.metadata.read(65536)
+    args.metadata.close()
 
     external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8')
 
diff --git a/bh20sequploader/validation/Makefile b/bh20sequploader/validation/Makefile
new file mode 100644
index 0000000..1ca13fb
--- /dev/null
+++ b/bh20sequploader/validation/Makefile
@@ -0,0 +1,4 @@
+compile: formats.mgc
+
+formats.mgc :
+	file -C -m formats
diff --git a/bh20sequploader/validation/formats b/bh20sequploader/validation/formats
new file mode 100644
index 0000000..ac804cf
--- /dev/null
+++ b/bh20sequploader/validation/formats
@@ -0,0 +1,4 @@
+0	regex	\^\>.+\r?\n([acgtnACGTN]+\r?\n)*[acgtnACGTN]+(\r?\n)?$	FASTA
+!:mime	text/fasta
+0	regex	\^@.+\r?\n[acgtnACGTN]*\n\\+.*\n[!-i]*(\r\n)?	FASTQ
+!:mime	text/fastq
\ No newline at end of file
diff --git a/bh20sequploader/validation/formats.mgc b/bh20sequploader/validation/formats.mgc
new file mode 100644
index 0000000..bff282a
Binary files /dev/null and b/bh20sequploader/validation/formats.mgc differ
-- 
cgit v1.2.3


From 9b7fbc52ae229d72e75de9f433eea00ce37ba70a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 10 Apr 2020 11:52:18 -0500
Subject: Fixed TypeError: 'module' object is not callable

---
 bh20sequploader/main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'bh20sequploader/main.py')

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index bf74ea5..ede9f38 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,7 +6,7 @@ import json
 import urllib.request
 import socket
 import getpass
-import qc_metadata
+from qc_metadata import qc_metadata
 
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
-- 
cgit v1.2.3


From a6ba9a5203a568611a94c043fd13e2ec50f071da Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Fri, 10 Apr 2020 15:12:08 -0400
Subject: Validate & propagate metadata

---
 bh20seqanalyzer/main.py            | 45 ++++++++++++++++++++++++++++++++------
 bh20sequploader/bh20seq-schema.yml |  6 ++---
 bh20sequploader/main.py            |  2 +-
 bh20sequploader/qc_metadata.py     | 29 +++++++++++++++++++++++-
 4 files changed, 70 insertions(+), 12 deletions(-)

(limited to 'bh20sequploader/main.py')

diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 2030c1e..1fb51b5 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -8,6 +8,8 @@ import json
 import logging
 import ruamel.yaml
 from bh20sequploader.qc_metadata import qc_metadata
+import pkg_resources
+from schema_salad.sourceline import add_lc_filename
 
 logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%Y-%m-%d %H:%M:%S",
                     level=logging.INFO)
@@ -24,8 +26,14 @@ def validate_upload(api, collection, validated_project,
         logging.warn("Upload '%s' missing metadata.yaml", collection["name"])
         valid = False
     else:
-        metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml"))
-        #valid = qc_metadata(metadata_content) and valid
+        try:
+            metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml"))
+            metadata_content["id"] = "keep:%s/metadata.yaml" % collection["portable_data_hash"]
+            add_lc_filename(metadata_content, metadata_content["id"])
+            valid = qc_metadata(metadata_content) and valid
+        except Exception as e:
+            logging.warn(e)
+            valid = False
         if not valid:
             logging.warn("Failed metadata qc")
 
@@ -52,9 +60,10 @@ def validate_upload(api, collection, validated_project,
             "owner_uuid": validated_project,
             "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute()
     else:
+        pass
         # It is invalid, delete it.
-        logging.warn("Deleting '%s'" % collection["name"])
-        api.collections().delete(uuid=collection["uuid"]).execute()
+        #logging.warn("Deleting '%s'" % collection["name"])
+        #api.collections().delete(uuid=collection["uuid"]).execute()
 
     return valid
 
@@ -107,12 +116,17 @@ def start_fastq_to_fasta(api, collection,
 def start_pangenome_analysis(api,
                              analysis_project,
                              pangenome_workflow_uuid,
-                             validated_project):
+                             validated_project,
+                             schema_ref):
     validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]])
     inputobj = {
         "inputReads": [],
         "metadata": [],
-        "subjects": []
+        "subjects": [],
+        "metadataSchema": {
+            "class": "File",
+            "location": schema_ref
+        }
     }
     for v in validated:
         inputobj["inputReads"].append({
@@ -166,12 +180,26 @@ def move_fastq_to_fasta_results(api, analysis_project, uploader_project):
             api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute()
 
 
+def upload_schema(api, workflow_def_project):
+    schema_resource = pkg_resources.resource_stream('bh20sequploader.qc_metadata', "bh20seq-schema.yml")
+    c = arvados.collection.Collection()
+    with c.open("schema.yml", "wb") as f:
+        f.write(schema_resource.read())
+    pdh = c.portable_data_hash()
+    wd = api.collections().list(filters=[["owner_uuid", "=", workflow_def_project],
+                                         ["portable_data_hash", "=", pdh]]).execute()
+    if len(wd["items"]) == 0:
+        c.save_new(owner_uuid=workflow_def_project, name="Metadata schema", ensure_unique_name=True)
+    return "keep:%s/schema.yml" % pdh
+
+
 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('--pangenome-analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='')
     parser.add_argument('--fastq-project', type=str, default='lugli-j7d0g-xcjxp4oox2u1w8u', help='')
     parser.add_argument('--validated-project', type=str, default='lugli-j7d0g-5ct8p1i1wrgyjvp', help='')
+    parser.add_argument('--workflow-def-project', type=str, default='lugli-j7d0g-5hswinmpyho8dju', help='')
 
     parser.add_argument('--pangenome-workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='')
     parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='')
@@ -183,6 +211,8 @@ def main():
 
     logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project))
 
+    schema_ref = upload_schema(api, args.workflow_def_project)
+
     while True:
         move_fastq_to_fasta_results(api, args.fastq_project, args.uploader_project)
 
@@ -198,7 +228,8 @@ def main():
             start_pangenome_analysis(api,
                                      args.pangenome_analysis_project,
                                      args.pangenome_workflow_uuid,
-                                     args.validated_project)
+                                     args.validated_project,
+                                     schema_ref)
 
         copy_most_recent_result(api,
                                 args.pangenome_analysis_project,
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index cf9b015..a072bd7 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -174,9 +174,9 @@ $graph:
       jsonldPredicate:
         _id: "@id"
         #_type: "@id"
-    sequencefile:
-      doc: The subject (eg the fasta/fastq file) that this metadata describes
+    id:
+      doc: The subject (eg the fasta/fastq file) that the metadata describes
       type: string?
       jsonldPredicate:
         _id: "@id"
-        _type: "@id"
\ No newline at end of file
+        _type: "@id"
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index bfb8c51..2032508 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -22,7 +22,7 @@ def main():
 
     api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
 
-    if not qc_metadata(args.metadata.name):
+    if not bh20sequploader.qc_metadata.qc_metadata(args.metadata.name):
         print("Failed metadata qc")
         exit(1)
 
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index ebe4dfc..38edcaa 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -1,12 +1,25 @@
 import schema_salad.schema
+import schema_salad.ref_resolver
 import logging
 import pkg_resources
 import logging
+import traceback
+
+class CustomFetcher(schema_salad.ref_resolver.DefaultFetcher):
+    def check_exists(sup, url):
+        if url.startswith("keep:"):
+            return True
+        else:
+            return super().check_exists(url)
+
+    def supported_schemes(self):  # type: () -> List[str]
+        return ["file", "http", "https", "mailto", "keep"]
+
 
 def qc_metadata(metadatafile):
     schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml")
     cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")}
-    (document_loader,
+    (loader,
      avsc_names,
      schema_metadata,
      metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache)
@@ -15,9 +28,23 @@ def qc_metadata(metadatafile):
         print(avsc_names)
         return False
 
+    document_loader = schema_salad.ref_resolver.Loader(
+        loader.ctx,
+        schemagraph=loader.graph,
+        foreign_properties=loader.foreign_properties,
+        idx=loader.idx,
+        cache=loader.cache,
+        fetcher_constructor=CustomFetcher,
+        skip_schemas=loader.skip_schemas,
+        url_fields=loader.url_fields,
+        allow_attachments=loader.allow_attachments,
+        session=loader.session,
+        )
+
     try:
         doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
         return True
     except Exception as e:
+        traceback.print_exc()
         logging.warn(e)
     return False
-- 
cgit v1.2.3


From 925058d0b3db70803d322cc2a33801240899a20a Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Fri, 10 Apr 2020 15:52:37 -0400
Subject: Fix up fasta/fastq validation

---
 bh20seqanalyzer/main.py |  9 ++++++++-
 bh20sequploader/main.py | 29 +++++------------------------
 setup.py                |  5 +++--
 3 files changed, 16 insertions(+), 27 deletions(-)

(limited to 'bh20sequploader/main.py')

diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 1fb51b5..c05b402 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -8,6 +8,7 @@ import json
 import logging
 import ruamel.yaml
 from bh20sequploader.qc_metadata import qc_metadata
+from bh20sequploader.qc_fasta import qc_fasta
 import pkg_resources
 from schema_salad.sourceline import add_lc_filename
 
@@ -38,7 +39,13 @@ def validate_upload(api, collection, validated_project,
             logging.warn("Failed metadata qc")
 
     if valid:
-        if "sequence.fasta" not in col:
+        if "sequence.fasta" in col:
+            try:
+                qc_fasta(col.open("sequence.fasta"))
+            except Exception as e:
+                logging.warn(e)
+                valid = False
+        else:
             if "reads.fastq" in col:
                 start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid)
                 return False
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 2032508..4a225f6 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -8,7 +8,8 @@ from pathlib import Path
 import urllib.request
 import socket
 import getpass
-from qc_metadata import qc_metadata
+from .qc_metadata import qc_metadata
+from .qc_fasta import qc_fasta
 
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -22,34 +23,14 @@ def main():
 
     api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
 
-    if not bh20sequploader.qc_metadata.qc_metadata(args.metadata.name):
+    target = qc_fasta(args.sequence)
+
+    if not qc_metadata(args.metadata.name):
         print("Failed metadata qc")
         exit(1)
 
     col = arvados.collection.Collection(api_client=api)
 
-    magic_file = Path(__file__).parent / "validation" / "formats.mgc"
-    val = magic.Magic(magic_file=magic_file.resolve().as_posix(),
-                      uncompress=False, mime=True)
-    seq_type = val.from_file(args.sequence.name).lower()
-    print(f"Sequence type: {seq_type}")
-    if seq_type == "text/fasta":
-        # ensure that contains only one entry
-        entries = 0
-        for line in args.sequence:
-            if line.startswith(">"):
-                entries += 1
-            if entries > 1:
-                raise ValueError("FASTA file contains multiple entries")
-                break
-        args.sequence.close()
-        args.sequence = open(args.sequence.name, "r")
-        target = "reads.fastq"
-    elif seq_type == "text/fastq":
-        target = "sequence.fasta"
-    else:
-        raise ValueError("Sequence file does not look like FASTA or FASTQ")
-
     with col.open(target, "w") as f:
         r = args.sequence.read(65536)
         print(r[0:20])
diff --git a/setup.py b/setup.py
index 41ace7b..18e858e 100644
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,7 @@ try:
 except ImportError:
     tagger = egg_info_cmd.egg_info
 
-install_requires = ["arvados-python-client", "schema-salad"]
+install_requires = ["arvados-python-client", "schema-salad", "python-magic"]
 web_requires = ["flask", "pyyaml"]
 
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
@@ -31,7 +31,8 @@ setup(
     author_email="peter.amstutz@curii.com",
     license="Apache 2.0",
     packages=["bh20sequploader", "bh20seqanalyzer", "bh20simplewebuploader"],
-    package_data={"bh20sequploader": ["bh20seq-schema.yml"]},
+    package_data={"bh20sequploader": ["bh20seq-schema.yml", "validation/formats"],
+    },
     install_requires=install_requires,
     extras_require={
         'web': web_requires
-- 
cgit v1.2.3