diff options
43 files changed, 1227 insertions, 785 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 0b52e6b..b3a439d 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -16,277 +16,308 @@ 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, - fastq_project, fastq_workflow_uuid, - revalidate): - col = arvados.collection.Collection(collection["uuid"]) - - if not revalidate and collection["properties"].get("status") in ("validated", "rejected"): - return False - - # validate the collection here. Check metadata, etc. - logging.info("Validating upload '%s' (%s)" % (collection["name"], collection["uuid"])) - - errors = [] - - if collection["owner_uuid"] != validated_project: - dup = api.collections().list(filters=[["owner_uuid", "=", validated_project], - ["portable_data_hash", "=", col.portable_data_hash()]]).execute() - if dup["items"]: - # This exact collection has been uploaded before. - errors.append("Duplicate of %s" % ([d["uuid"] for d in dup["items"]])) - - if not errors: - if "metadata.yaml" not in col: - errors.append("Missing metadata.yaml", collection["name"]) - else: +class SeqAnalyzer: + + def __init__(self, api, keepclient, + uploader_project, + pangenome_analysis_project, + fastq_project, + validated_project, + workflow_def_project, + pangenome_workflow_uuid, + fastq_workflow_uuid, + exclude_list, + latest_result_collection): + self.api = api + self.keepclient = keepclient + self.uploader_project = uploader_project + self.pangenome_analysis_project = pangenome_analysis_project + self.fastq_project = fastq_project + self.validated_project = validated_project + self.workflow_def_project = workflow_def_project + self.pangenome_workflow_uuid = pangenome_workflow_uuid + self.fastq_workflow_uuid = fastq_workflow_uuid + self.exclude_list = exclude_list + self.latest_result_uuid = latest_result_collection + self.schema_ref = None + + def validate_upload(self, collection, revalidate): + col = arvados.collection.Collection(collection["uuid"], api_client=self.api, keep_client=self.keepclient) + + if not revalidate and collection["properties"].get("status") in ("validated", "rejected"): + return False + + # validate the collection here. Check metadata, etc. + logging.info("Validating upload '%s' (%s)" % (collection["name"], collection["uuid"])) + + errors = [] + + if collection["owner_uuid"] != self.validated_project: + dup = self.api.collections().list(filters=[["owner_uuid", "=", self.validated_project], + ["portable_data_hash", "=", col.portable_data_hash()]]).execute() + if dup["items"]: + # This exact collection has been uploaded before. + errors.append("Duplicate of %s" % ([d["uuid"] for d in dup["items"]])) + + if not errors: + if "metadata.yaml" not in col: + errors.append("Missing metadata.yaml", collection["name"]) + else: + try: + with col.open("metadata.yaml") as md: + metadata_content = ruamel.yaml.round_trip_load(md) + metadata_content["id"] = "http://arvados.org/keep:%s/metadata.yaml" % collection["portable_data_hash"] + sample_id = metadata_content["sample"]["sample_id"] + add_lc_filename(metadata_content, metadata_content["id"]) + valid = qc_metadata(metadata_content) + if not valid: + errors.append("Failed metadata qc") + except Exception as e: + errors.append(str(e)) + + if not errors: try: - metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) - metadata_content["id"] = "http://arvados.org/keep:%s/metadata.yaml" % collection["portable_data_hash"] - sample_id = metadata_content["sample"]["sample_id"] - add_lc_filename(metadata_content, metadata_content["id"]) - valid = qc_metadata(metadata_content) - if not valid: - errors.append("Failed metadata qc") - except Exception as e: - errors.append(str(e)) - - if not errors: - try: - tgt = None - paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"} - for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): - if n not in col: - continue - with col.open(n, 'rb') as qf: - tgt = qc_fasta(qf)[0] - if tgt != n and tgt != paired.get(n): - errors.append("Expected %s but magic says it should be %s", n, tgt) - elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): - start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n, sample_id) - return False - if tgt is None: - errors.append("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"]) - except Exception as v: - errors.append(str(v)) - - - if not errors: - # Move it to the "validated" project to be included in the next analysis - if "errors" in collection["properties"]: - del collection["properties"]["errors"] - collection["properties"]["status"] = "validated" - api.collections().update(uuid=collection["uuid"], body={ - "owner_uuid": validated_project, - "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime())), - "properties": collection["properties"]}).execute() - logging.info("Added '%s' to validated sequences" % collection["name"]) - return True - else: - # It is invalid - logging.warn("'%s' (%s) has validation errors: %s" % ( - collection["name"], collection["uuid"], "\n".join(errors))) - collection["properties"]["status"] = "rejected" - collection["properties"]["errors"] = errors - api.collections().update(uuid=collection["uuid"], body={"properties": collection["properties"]}).execute() - return False - - -def run_workflow(api, parent_project, workflow_uuid, name, inputobj): - project = api.groups().create(body={ - "group_class": "project", - "name": name, - "owner_uuid": parent_project, - }, ensure_unique_name=True).execute() - - with tempfile.NamedTemporaryFile() as tmp: - tmp.write(json.dumps(inputobj, indent=2).encode('utf-8')) - tmp.flush() - cmd = ["arvados-cwl-runner", - "--submit", - "--no-wait", - "--project-uuid=%s" % project["uuid"], - "arvwf:%s" % workflow_uuid, - tmp.name] - logging.info("Running %s" % ' '.join(cmd)) - comp = subprocess.run(cmd, capture_output=True) - logging.info("Submitted %s", comp.stdout) - 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, - tgt, - sample_id): - - params = { - "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" - }, - "sample_id": sample_id - } - - if tgt.startswith("reads.fastq"): - params["fastq_forward"] = { - "class": "File", - "location": "keep:%s/%s" % (collection["portable_data_hash"], tgt) - } - elif tgt.startswith("reads_1.fastq"): - params["fastq_forward"] = { - "class": "File", - "location": "keep:%s/reads_1.%s" % (collection["portable_data_hash"], tgt[8:]) - } - params["fastq_reverse"] = { - "class": "File", - "location": "keep:%s/reads_2.%s" % (collection["portable_data_hash"], tgt[8:]) + tgt = None + paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"} + for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): + if n not in col: + continue + with col.open(n, 'rb') as qf: + tgt = qc_fasta(qf)[0] + if tgt != n and tgt != paired.get(n): + errors.append("Expected %s but magic says it should be %s", n, tgt) + elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): + self.start_fastq_to_fasta(collection, n, sample_id) + return False + if tgt is None: + errors.append("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"]) + except Exception as v: + errors.append(str(v)) + + + if not errors: + # Move it to the "validated" project to be included in the next analysis + if "errors" in collection["properties"]: + del collection["properties"]["errors"] + collection["properties"]["status"] = "validated" + self.api.collections().update(uuid=collection["uuid"], body={ + "owner_uuid": self.validated_project, + "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime())), + "properties": collection["properties"]}).execute() + logging.info("Added '%s' to validated sequences" % collection["name"]) + return True + else: + # It is invalid + logging.warn("'%s' (%s) has validation errors: %s" % ( + collection["name"], collection["uuid"], "\n".join(errors))) + collection["properties"]["status"] = "rejected" + collection["properties"]["errors"] = errors + self.api.collections().update(uuid=collection["uuid"], body={"properties": collection["properties"]}).execute() + return False + + + def run_workflow(self, parent_project, workflow_uuid, name, inputobj): + project = self.api.groups().create(body={ + "group_class": "project", + "name": name, + "owner_uuid": parent_project, + }, ensure_unique_name=True).execute() + + with tempfile.NamedTemporaryFile() as tmp: + tmp.write(json.dumps(inputobj, indent=2).encode('utf-8')) + tmp.flush() + cmd = ["arvados-cwl-runner", + "--submit", + "--no-wait", + "--project-uuid=%s" % project["uuid"], + "arvwf:%s" % workflow_uuid, + tmp.name] + logging.info("Running %s" % ' '.join(cmd)) + comp = subprocess.run(cmd, capture_output=True) + logging.info("Submitted %s", comp.stdout) + if comp.returncode != 0: + logging.error(comp.stderr.decode('utf-8')) + + return project + + + def start_fastq_to_fasta(self, collection, + tgt, + sample_id): + + params = { + "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" + }, + "sample_id": sample_id } - newproject = run_workflow(api, analysis_project, fastq_workflow_uuid, "FASTQ to FASTA", params) - api.collections().update(uuid=collection["uuid"], - body={"owner_uuid": newproject["uuid"]}).execute() - -def start_pangenome_analysis(api, - analysis_project, - pangenome_workflow_uuid, - validated_project, - schema_ref, - exclude_list): - validated = arvados.util.list_all(api.collections().list, filters=[ - ["owner_uuid", "=", validated_project], - ["properties.status", "=", "validated"]]) - inputobj = { - "inputReads": [], - "metadata": [], - "subjects": [], - "metadataSchema": { - "class": "File", - "location": schema_ref - }, - "exclude": { - "class": "File", - "location": exclude_list + if tgt.startswith("reads.fastq"): + params["fastq_forward"] = { + "class": "File", + "location": "keep:%s/%s" % (collection["portable_data_hash"], tgt) + } + elif tgt.startswith("reads_1.fastq"): + params["fastq_forward"] = { + "class": "File", + "location": "keep:%s/reads_1.%s" % (collection["portable_data_hash"], tgt[8:]) + } + params["fastq_reverse"] = { + "class": "File", + "location": "keep:%s/reads_2.%s" % (collection["portable_data_hash"], tgt[8:]) + } + + newproject = self.run_workflow(self.fastq_project, self.fastq_workflow_uuid, "FASTQ to FASTA", params) + self.api.collections().update(uuid=collection["uuid"], + body={"owner_uuid": newproject["uuid"]}).execute() + + def start_pangenome_analysis(self): + + if self.schema_ref is None: + self.upload_schema() + + validated = arvados.util.list_all(self.api.collections().list, filters=[ + ["owner_uuid", "=", self.validated_project], + ["properties.status", "=", "validated"]]) + inputobj = { + "inputReads": [], + "metadata": [], + "subjects": [], + "metadataSchema": { + "class": "File", + "location": self.schema_ref + }, + "exclude": { + "class": "File", + "location": self.exclude_list + } } - } - validated.sort(key=lambda v: v["portable_data_hash"]) - for v in validated: - inputobj["inputReads"].append({ - "class": "File", - "location": "keep:%s/sequence.fasta" % v["portable_data_hash"] - }) - inputobj["metadata"].append({ - "class": "File", - "location": "keep:%s/metadata.yaml" % v["portable_data_hash"] - }) - inputobj["subjects"].append("http://collections.lugli.arvadosapi.com/c=%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"]: - container = api.containers().get(uuid=cr["items"][0]["container_uuid"]).execute() - if container["state"] == "Complete" and container["exit_code"] == 0: - return cr["items"][0] - 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").execute() - for m in most_recent_analysis["items"]: - 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": "Result from %s %s" % (m["name"], wf["uuid"])}).execute() - break - + validated.sort(key=lambda v: v["portable_data_hash"]) + for v in validated: + inputobj["inputReads"].append({ + "class": "File", + "location": "keep:%s/sequence.fasta" % v["portable_data_hash"] + }) + inputobj["metadata"].append({ + "class": "File", + "location": "keep:%s/metadata.yaml" % v["portable_data_hash"] + }) + inputobj["subjects"].append("http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % v["portable_data_hash"]) + self.run_workflow(self.pangenome_analysis_project, self.pangenome_workflow_uuid, "Pangenome analysis", inputobj) + + + def get_workflow_output_from_project(self, uuid): + cr = self.api.container_requests().list(filters=[['owner_uuid', '=', uuid], + ["requesting_container_uuid", "=", None]]).execute() + if cr["items"] and cr["items"][0]["output_uuid"]: + container = self.api.containers().get(uuid=cr["items"][0]["container_uuid"]).execute() + if container["state"] == "Complete" and container["exit_code"] == 0: + return cr["items"][0] + return None + + + def copy_most_recent_result(self): + most_recent_analysis = self.api.groups().list(filters=[['owner_uuid', '=', self.pangenome_analysis_project]], + order="created_at desc").execute() + for m in most_recent_analysis["items"]: + wf = self.get_workflow_output_from_project(m["uuid"]) + if wf: + src = self.api.collections().get(uuid=wf["output_uuid"]).execute() + dst = self.api.collections().get(uuid=self.latest_result_uuid).execute() + if src["portable_data_hash"] != dst["portable_data_hash"]: + logging.info("Copying latest result from '%s' to %s", m["name"], self.latest_result_uuid) + self.api.collections().update(uuid=self.latest_result_uuid, + body={"manifest_text": src["manifest_text"], + "description": "Result from %s %s" % (m["name"], wf["uuid"])}).execute() + break + + + def move_fastq_to_fasta_results(self): + projects = self.api.groups().list(filters=[['owner_uuid', '=', self.fastq_project], + ["properties.moved_output", "!=", True]], + order="created_at asc",).execute() + for p in projects["items"]: + wf = self.get_workflow_output_from_project(p["uuid"]) + if not wf: + continue -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() - break + col = arvados.collection.Collection(wf["output_uuid"], api_client=self.api, keep_client=self.keepclient) + with col.open("metadata.yaml") as md: + metadata_content = ruamel.yaml.round_trip_load(md) + + colprop = col.get_properties() + colprop["sequence_label"] = metadata_content["sample"]["sample_id"] + self.api.collections().update(uuid=wf["output_uuid"], + body={"owner_uuid": self.uploader_project, + "properties": colprop}).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 print_status(api, uploader_project, fmt): - pending = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", uploader_project]]) - out = [] - status = {} - for p in pending: - prop = p["properties"] - out.append(prop) - if "status" not in prop: - prop["status"] = "pending" - prop["created_at"] = p["created_at"] - prop["uuid"] = p["uuid"] - status[prop["status"]] = status.get(prop["status"], 0) + 1 - if fmt == "html": - print( -""" -<html> -<body> -""") - print("<p>Total collections in upload project %s</p>" % len(out)) - print("<p>Status %s</p>" % status) - print( -""" -<table> -<tr><th>Collection</th> -<th>Sequence label</th> -<th>Status</th> -<th>Errors</th></tr> -""") - for r in out: - print("<tr valign='top'>") - print("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"])) - print("<td>%s</td>" % r["sequence_label"]) - print("<td>%s</td>" % r["status"]) - print("<td><pre>%s</pre></td>" % "\n".join(r.get("errors", []))) - print("</tr>") - print( -""" -</table> -</body> -</html> -""") - else: - print(json.dumps(out, indent=2)) + p["properties"]["moved_output"] = True + self.api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute() + + + def upload_schema(self): + schema_resource = pkg_resources.resource_stream('bh20sequploader.qc_metadata', "bh20seq-schema.yml") + c = arvados.collection.Collection(api_client=self.api, keep_client=self.keepclient) + with c.open("schema.yml", "wb") as f: + f.write(schema_resource.read()) + pdh = c.portable_data_hash() + wd = self.api.collections().list(filters=[["owner_uuid", "=", self.workflow_def_project], + ["portable_data_hash", "=", pdh]]).execute() + if len(wd["items"]) == 0: + c.save_new(owner_uuid=self.workflow_def_project, name="Metadata schema", ensure_unique_name=True) + self.schema_ref = "keep:%s/schema.yml" % pdh + + + def print_status(self, fmt): + pending = arvados.util.list_all(self.api.collections().list, filters=[["owner_uuid", "=", self.uploader_project]]) + out = [] + status = {} + for p in pending: + prop = p["properties"] + out.append(prop) + if "status" not in prop: + prop["status"] = "pending" + prop["created_at"] = p["created_at"] + prop["uuid"] = p["uuid"] + status[prop["status"]] = status.get(prop["status"], 0) + 1 + if fmt == "html": + print( + """ + <html> + <body> + """) + print("<p>Total collections in upload project %s</p>" % len(out)) + print("<p>Status %s</p>" % status) + print( + """ + <table> + <tr><th>Collection</th> + <th>Sequence label</th> + <th>Status</th> + <th>Errors</th></tr> + """) + for r in out: + print("<tr valign='top'>") + print("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"])) + print("<td>%s</td>" % r["sequence_label"]) + print("<td>%s</td>" % r["status"]) + print("<td><pre>%s</pre></td>" % "\n".join(r.get("errors", []))) + print("</tr>") + print( + """ + </table> + </body> + </html> + """) + else: + print(json.dumps(out, indent=2)) def main(): parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project') @@ -310,50 +341,45 @@ def main(): args = parser.parse_args() api = arvados.api() - - - - schema_ref = upload_schema(api, args.workflow_def_project) + keepclient = arvados.keep.KeepClient(api_client=api) + + seqanalyzer = SeqAnalyzer(api, keepclient, + args.uploader_project, + args.pangenome_analysis_project, + args.fastq_project, + args.validated_project, + args.workflow_def_project, + args.pangenome_workflow_uuid, + args.fastq_workflow_uuid, + args.exclude_list, + args.latest_result_collection) if args.kickoff: logging.info("Starting a single analysis run") - start_pangenome_analysis(api, - args.pangenome_analysis_project, - args.pangenome_workflow_uuid, - args.validated_project, - schema_ref, - args.exclude_list) + seqanalyzer.start_pangenome_analysis() return if args.print_status: - print_status(api, args.uploader_project, args.print_status) + seqanalyzer.print_status(args.print_status) exit(0) 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 = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", args.uploader_project]]) - at_least_one_new_valid_seq = False - for c in new_collections: - at_least_one_new_valid_seq = validate_upload(api, c, - args.validated_project, - args.fastq_project, - args.fastq_workflow_uuid, - args.revalidate) or at_least_one_new_valid_seq - - if at_least_one_new_valid_seq and not args.no_start_analysis: - start_pangenome_analysis(api, - args.pangenome_analysis_project, - args.pangenome_workflow_uuid, - args.validated_project, - schema_ref, - args.exclude_list) - - copy_most_recent_result(api, - args.pangenome_analysis_project, - args.latest_result_collection) + try: + seqanalyzer.move_fastq_to_fasta_results() + + new_collections = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", args.uploader_project]]) + at_least_one_new_valid_seq = False + for c in new_collections: + at_least_one_new_valid_seq = seqanalyzer.validate_upload(c, args.revalidate) or at_least_one_new_valid_seq + + if at_least_one_new_valid_seq and not args.no_start_analysis: + seqanalyzer.start_pangenome_analysis() + + seqanalyzer.copy_most_recent_result() + except Exception as e: + logging.exeception("Error in main loop") if args.once: break diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index b3d4d12..0aead3b 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -1,6 +1,7 @@ $base: http://biohackathon.org/bh20-seq-schema $namespaces: cc: http://creativecommons.org/ns# + dc: http://purl.org/metadata/dublin_core_elements# sch: https://schema.org/ efo: http://www.ebi.ac.uk/efo/ obo: http://purl.obolibrary.org/obo/ @@ -15,24 +16,29 @@ $graph: fields: license_type: doc: License types as defined in https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf - type: string? + type: string jsonldPredicate: _id: https://creativecommons.org/ns#License title: doc: Attribution title related to data license type: string? jsonldPredicate: - _id: http://semanticscience.org/resource/SIO_001167 + _id: http://purl.org/metadata/dublin_core_elements#Title + attribution_name: + doc: Attribution NAME related to data license + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#attributionName attribution_url: doc: Attribution URL related to data license type: string? jsonldPredicate: - _id: https://creativecommons.org/ns#Work + _id: https://creativecommons.org/ns#attributionURL attribution_source: doc: Attribution source URL related to data license type: string? jsonldPredicate: - _id: https://creativecommons.org/ns#Work + _id: https://creativecommons.org/ns#attributionSource - name: hostSchema type: record @@ -258,6 +264,7 @@ $graph: virus: virusSchema technology: technologySchema submitter: submitterSchema + license: ["null", licenseSchema] id: doc: The subject (eg the fasta/fastq file) that the metadata describes type: string diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 965229c..bbc7309 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -1,6 +1,8 @@ PREFIX : <https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#> PREFIX MainSchema: <http://biohackathon.org/bh20-seq-schema#MainSchema/> PREFIX hostSchema: <http://biohackathon.org/bh20-seq-schema#hostSchema/> +PREFIX cc: <http://creativecommons.org/ns#> +PREFIX dc: <http://purl.org/metadata/dublin_core_elements#> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX sio: <http://semanticscience.org/resource/> @@ -15,10 +17,11 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> MainSchema:submitter @:submitterShape ; MainSchema:technology @:technologyShape ; MainSchema:virus @:virusShape; + MainSchema:license @:licenseShape ?; } :hostShape { - efo:EFO_0000532 [ obo:NCBITaxon_~ ] ; + efo:EFO_0000532 [ obo:NCBITaxon_~ ] ; sio:SIO_000115 xsd:string ?; obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 obo:PATO_0001340] ?; obo:PATO_0000011 xsd:integer ?; @@ -32,14 +35,14 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> :sampleShape { sio:SIO_000115 xsd:string; - evs:C25164 xsd:string; - obo:GAZ_00000448 [wikidata:~] ; + evs:C25164 xsd:string; + obo:GAZ_00000448 [wikidata:~] ; obo:OBI_0001895 xsd:string ?; obo:NCIT_C41206 xsd:string ?; obo:OBI_0001479 IRI {0,2}; obo:OBI_0001472 xsd:string ?; sio:SIO_001167 xsd:string ?; - edam:data_2091 IRI {0,3}; + edam:data_2091 IRI {0,3}; } :submitterShape { @@ -47,7 +50,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> sio:SIO_000116 xsd:string *; sio:SIO_000172 xsd:string ?; obo:NCIT_C37984 xsd:string ?; - obo:NCIT_C37900 xsd:string ?; + obo:NCIT_C37900 xsd:string ?; efo:EFO_0001741 xsd:string ?; obo:NCIT_C42781 xsd:string ?; obo:NCIT_C19026 xsd:string ?; @@ -63,6 +66,14 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> } :virusShape{ - edam:data_1875 [ obo:NCBITaxon_~ ] ; - sio:SIO_010055 xsd:string ?; + edam:data_1875 [ obo:NCBITaxon_~ ] ; + sio:SIO_010055 xsd:string ?; } + +:licenseShape{ + cc:License xsd:string ; + dc:Title xsd:string ?; + cc:attributionName xsd:string ?; + cc:attributionURL xsd:string ?; + cc:attributionSource xsd:string ?; +} \ No newline at end of file diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index f744a8c..6049bf9 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -29,11 +29,10 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): try: log.debug("Checking metadata" if do_qc else "Skipping metadata check") if do_qc and not qc_metadata(metadata.name): - log.warning("Failed metadata qc") + log.warning("Failed metadata QC") failed = True except Exception as e: - log.debug(e) - print(e) + log.exception("Failed metadata QC") failed = True target = [] @@ -45,8 +44,7 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): target[0] = ("reads_1."+target[0][0][6:], target[0][1]) target[1] = ("reads_2."+target[1][0][6:], target[0][1]) except Exception as e: - log.debug(e) - print(e) + log.exception("Failed sequence QC") failed = True if failed: @@ -82,7 +80,7 @@ def main(): seqlabel = target[0][1] if args.validate: - print("Valid") + log.info("Valid") exit(0) col = arvados.collection.Collection(api_client=api) @@ -91,10 +89,10 @@ def main(): if args.sequence_p2: upload_sequence(col, target[1], args.sequence_p2) - print("Reading metadata") + log.info("Reading metadata") with col.open("metadata.yaml", "w") as f: r = args.metadata.read(65536) - print(r[0:20]) + log.info(r[0:20]) while r: f.write(r) r = args.metadata.read(65536) @@ -118,7 +116,7 @@ def main(): ["portable_data_hash", "=", col.portable_data_hash()]]).execute() if dup["items"]: # This exact collection has been uploaded before. - print("Duplicate of %s" % ([d["uuid"] for d in dup["items"]])) + log.error("Duplicate of %s" % ([d["uuid"] for d in dup["items"]])) exit(1) if args.trusted: @@ -131,9 +129,9 @@ def main(): (seqlabel, properties['upload_user'], properties['upload_ip']), properties=properties, ensure_unique_name=True) - print("Saved to %s" % col.manifest_locator()) - - print("Done") + log.info("Saved to %s" % col.manifest_locator()) + log.info("Done") + exit(0) if __name__ == "__main__": main() diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index 37eb4e8..0c7e16d 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -84,10 +84,8 @@ def qc_fasta(arg_sequence, check_with_clustalw=True): except Exception as e: logging.warn("QC against reference sequence using 'minimap2': %s", e, exc_info=e) - if similarity and similarity < 70.0: + if similarity < 70.0: raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity)) - if similarity == 0: - raise ValueError("QC fail") return ("sequence.fasta"+gz, seqlabel) elif seq_type == "text/fastq": diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 77e345b..206f884 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -8,7 +8,7 @@ import os import sys import re import string -import yaml +import ruamel.yaml as yaml import pkg_resources from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify import os.path @@ -16,6 +16,9 @@ import requests import io import arvados from markupsafe import Markup +from schema_salad.sourceline import add_lc_filename +from schema_salad.schema import shortname +from typing import MutableSequence, MutableMapping ARVADOS_API = 'lugli.arvadosapi.com' ANONYMOUS_TOKEN = '5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh' @@ -47,6 +50,9 @@ def type_to_heading(type_name): Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading. """ + type_name = shortname(type_name) + + print(type_name,file=sys.stderr) # Remove camel case decamel = re.sub('([A-Z])', r' \1', type_name) # Split @@ -77,7 +83,7 @@ def is_iri(string): return string.startswith('http') -def generate_form(schema, options): +def generate_form(components, options): """ Linearize the schema into a list of dicts. @@ -100,9 +106,6 @@ def generate_form(schema, options): IRI. """ - # Get the list of form components, one of which is the root - components = schema.get('$graph', []) - # Find the root root_name = None # And also index components by type name @@ -130,55 +133,54 @@ def generate_form(schema, options): # First make a heading, if we aren't the very root of the form yield {'heading': type_to_heading(type_name)} - for field_name, field_type in by_name.get(type_name, {}).get('fields', {}).items(): + for field in by_name.get(type_name, {}).get('fields', []): + field_name = shortname(field["name"]) + field_type = field["type"] # For each field ref_iri = None docstring = None - if not isinstance(field_type, str): - # If the type isn't a string - - # It may have documentation - docstring = field_type.get('doc', None) - - # See if it has a more info/what goes here URL - predicate = field_type.get('jsonldPredicate', {}) - # Predicate may be a URL, a dict with a URL in _id, maybe a - # dict with a URL in _type, or a dict with _id and _type but no - # URLs anywhere. Some of these may not technically be allowed - # by the format, but if they occur, we might as well try to - # handle them. - if isinstance(predicate, str): - if is_iri(predicate): - ref_iri = predicate - else: - # Assume it's a dict. Look at the fields we know about. - for field in ['_id', 'type']: - field_value = predicate.get(field, None) - if isinstance(field_value, str) and is_iri(field_value) and ref_iri is None: - # Take the first URL-looking thing we find - ref_iri = field_value - break - - # Now overwrite the field type with the actual type string - field_type = field_type.get('type', '') - - # Decide if the field is optional (type ends in ?) optional = False - if field_type.endswith('?'): - # It's optional - optional = True - # Drop the ? - field_type = field_type[:-1] - - # Decide if the field is a list (type ends in []) is_list = False - if field_type.endswith('[]'): - # It's a list - is_list = True - # Reduce to the normal type - field_type = field_type[:-2] + + # It may have documentation + docstring = field.get('doc', None) + + # See if it has a more info/what goes here URL + predicate = field.get('jsonldPredicate', {}) + # Predicate may be a URL, a dict with a URL in _id, maybe a + # dict with a URL in _type, or a dict with _id and _type but no + # URLs anywhere. Some of these may not technically be allowed + # by the format, but if they occur, we might as well try to + # handle them. + if isinstance(predicate, str): + if is_iri(predicate): + ref_iri = predicate + else: + # Assume it's a dict. Look at the fields we know about. + for field in ['_id', 'type']: + field_value = predicate.get(field, None) + if isinstance(field_value, str) and is_iri(field_value) and ref_iri is None: + # Take the first URL-looking thing we find + ref_iri = field_value + break + + if isinstance(field_type, MutableSequence): + if field_type[0] == "null" and len(field_type) == 2: + optional = True + field_type = field_type[1] + else: + raise Exception("Can't handle it") + + if isinstance(field_type, MutableMapping): + if field_type["type"] == "array": + # Now replace the field type with the actual type string + is_list = True + field_type = field_type.get('items', '') + else: + field_type = field_type.get('type', '') + pass if field_type in by_name: # This is a subrecord. We need to recurse @@ -226,10 +228,24 @@ def generate_form(schema, options): return list(walk_fields(root_name)) -# At startup, we need to load the metadata schema from the uploader module, so we can make a form for it -METADATA_SCHEMA = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml")) -METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml")) -FORM_ITEMS = generate_form(METADATA_SCHEMA, METADATA_OPTION_DEFINITIONS) +import schema_salad.schema +def load_schema_generate_form(): + # At startup, we need to load the metadata schema from the uploader module, so we can make a form for it + if os.path.isfile("bh20sequploader/bh20seq-schema.yml"): + METADATA_SCHEMA = yaml.round_trip_load(open("bh20sequploader/bh20seq-schema.yml","r").read()) + METADATA_OPTION_DEFINITIONS = yaml.safe_load(open("bh20sequploader/bh20seq-options.yml","r").read()) + else: + METADATA_SCHEMA = yaml.round_trip_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml")) + METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml")) + + METADATA_SCHEMA["name"] = "bh20seq-schema.yml" + add_lc_filename(METADATA_SCHEMA, "bh20seq-schema.yml") + metaschema_names, _metaschema_doc, metaschema_loader = schema_salad.schema.get_metaschema() + schema_doc, schema_metadata = metaschema_loader.resolve_ref(METADATA_SCHEMA, "") + + return generate_form(schema_doc, METADATA_OPTION_DEFINITIONS) + +FORM_ITEMS = load_schema_generate_form() @app.route('/') def send_home(): @@ -237,7 +253,7 @@ def send_home(): Send the front page. """ - return render_template('home.html', menu='HOME') + return render_template('home.html', menu='HOME', load_map=True) @app.route('/upload') @@ -429,17 +445,21 @@ def receive_files(): if result.returncode != 0: # It didn't work. Complain. - error_message="Uploader returned value {} and said:".format(result.returncode) + str(result.stderr.decode('utf-8')) + error_message="Uploader returned value {} and said:\n".format(result.returncode) + str(result.stderr.decode('utf-8')) print(error_message, file=sys.stderr) return (render_template('error.html', error_message=error_message), 403) else: # It worked. Say so. - return render_template('success.html', log=result.stdout.decode('utf-8', errors='replace')) + return render_template('success.html', log=result.stderr.decode('utf-8', errors='replace')) finally: shutil.rmtree(dest_dir) -def get_html_body(fn): - buf = "" + +def edit_button(url,text="Edit text!"): + return '<p class="editbutton"><a href="'+url+'">'+text+'<img src="static/image/edit.png"></a></p>' + +def get_html_body(fn,source="https://github.com/arvados/bh20-seq-resource/tree/master/doc"): + buf = edit_button(source) in_body = False begin_body = re.compile(r"<body>",re.IGNORECASE) end_body = re.compile(r"(</body>|.*=\"postamble\")",re.IGNORECASE) @@ -451,11 +471,12 @@ def get_html_body(fn): buf += line elif begin_body.match(line): in_body = True + buf += edit_button(source) return buf @app.route('/download') def download_page(): - buf = get_html_body('doc/web/download.html') + buf = get_html_body('doc/web/download.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/download.org') return render_template('resource.html',menu='DOWNLOAD',embed=buf) def pending_table(output, items): @@ -468,10 +489,13 @@ def pending_table(output, items): for r in items: if r["status"] != "pending": continue - output.write("<tr>") - output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"])) - output.write("<td>%s</td>" % Markup.escape(r["sequence_label"])) - output.write("</tr>") + try: + output.write("<tr>") + output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"])) + output.write("<td>%s</td>" % Markup.escape(r.get("sequence_label"))) + output.write("</tr>") + except: + pass output.write( """ </table> @@ -486,18 +510,69 @@ def rejected_table(output, items): <th>Errors</th></tr> """) for r in items: - if r["status"] != "rejected": - continue + try: + if r["status"] != "rejected": + continue + output.write("<tr>") + output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"])) + output.write("<td>%s</td>" % Markup.escape(r.get("sequence_label"))) + output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", [])))) + output.write("</tr>") + except: + pass + output.write( +""" +</table> +""") + +def workflows_table(output, items): + output.write( +""" +<table> +<tr> +<th>Name</th> +<th>Sample id</th> +<th>Started</th> +<th>Container request</th> +</tr> +""") + for r in items: output.write("<tr>") - output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"])) - output.write("<td>%s</td>" % Markup.escape(r["sequence_label"])) - output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", [])))) + try: + sid = r["mounts"]["/var/lib/cwl/cwl.input.json"]["content"]["sample_id"] + output.write("<td>%s</td>" % Markup.escape(r["name"])) + output.write("<td>%s</td>" % Markup.escape(sid)) + output.write("<td>%s</td>" % Markup.escape(r["created_at"])) + output.write("<td><a href='https://workbench.lugli.arvadosapi.com/container_requests/%s'>%s</a></td>" % (r["uuid"], r["uuid"])) + except: + pass output.write("</tr>") output.write( """ </table> """) +def validated_table(output, items): + output.write( +""" +<table> +<tr> +<th>Collection</th> +<th>Sequence label</th> +</tr> +""") + for r in items: + try: + output.write("<tr>") + output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"])) + output.write("<td>%s</td>" % Markup.escape(r["properties"].get("sequence_label"))) + output.write("</tr>") + except: + pass + output.write( +""" +</table> +""") @app.route('/status') def status_page(): @@ -518,46 +593,57 @@ def status_page(): prop["uuid"] = p["uuid"] status[prop["status"]] = status.get(prop["status"], 0) + 1 + workflows = arvados.util.list_all(api.container_requests().list, + filters=[["name", "in", ["fastq2fasta.cwl"]], ["state", "=", "Committed"]], + order="created_at asc") + output = io.StringIO() validated = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute() status["passed"] = validated["items_available"] - for s in (("passed", "/download"), ("pending", "#pending"), ("rejected", "#rejected")): + for s in (("passed", "/validated"), ("pending", "#pending"), ("rejected", "#rejected")): output.write("<p><a href='%s'>%s sequences QC %s</a></p>" % (s[1], status.get(s[0], 0), s[0])) - output.write("<a id='pending'><h1>Pending</h1>") + output.write("<p><a href='%s'>%s analysis workflows running</a></p>" % ('#workflows', len(workflows))) + + output.write("<a id='pending'><h1>Pending</h1></a>") pending_table(output, out) - output.write("<a id='rejected'><h1>Rejected</h1>") + output.write("<a id='rejected'><h1>Rejected</h1></a>") rejected_table(output, out) + output.write("<a id='workflows'><h1>Running Workflows</h1></a>") + workflows_table(output, workflows) + return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS') +@app.route('/validated') +def validated_page(): + api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN, insecure=True) + output = io.StringIO() + validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", VALIDATED_PROJECT]]) + validated_table(output, validated) + return render_template('validated.html', table=Markup(output.getvalue()), menu='STATUS') + @app.route('/demo') def demo_page(): - return render_template('demo.html',menu='DEMO') + return render_template('demo.html',menu='DEMO',load_map=True) @app.route('/blog',methods=['GET']) def blog_page(): blog_content = request.args.get('id') # e.g. using-covid-19-pubseq-part3 buf = None; if blog_content: - buf = get_html_body('doc/blog/'+blog_content+'.html') + buf = get_html_body('doc/blog/'+blog_content+'.html',"https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/"+blog_content+".org") return render_template('blog.html',menu='BLOG',embed=buf,blog=blog_content) @app.route('/about') def about_page(): - buf = get_html_body('doc/web/about.html') + buf = get_html_body('doc/web/about.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/about.org') return render_template('about.html',menu='ABOUT',embed=buf) -## -@app.route('/map') -def map_page(): - return render_template('map.html',menu='DEMO') - - ## Dynamic API functions starting here ## This is quick and dirty for now, just to get something out and demonstrate the queries diff --git a/bh20simplewebuploader/static/blog.css b/bh20simplewebuploader/static/blog.css index 82a7c51..3ee8c44 100644 --- a/bh20simplewebuploader/static/blog.css +++ b/bh20simplewebuploader/static/blog.css @@ -4,12 +4,13 @@ .timestamp { font-family: monospace; color: darkgreen; } h1,h2 { font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,monospace; color:black;background-color:#F0F8FF; } -h2 { color: darkblue; } -h3,h4 { color: black; } +h2 { color: black; } +h3,h4 { color: black; margin:0; } code { color: darkblue; } -body {font-family: Palatino, 'Palatino Linotype', serif; color:black;background-color:#e5d8f0; font-size: large } +body {font-family: Palatino, 'Palatino Linotype', serif; color:black; background-color:white; font-size: large } -div.verbatim { margin: 30px; color: black; background-color: white; border-style:outset; font-family: palatino font, monospace; font-size:80%; font-weight:bold; } +div.verbatim { margin: 30px; color: black; background-color: white; border-style:outset; + font-family: palatino font, monospace; font-size:80%; font-weight:bold; } div.quote { font-family: palatino font, monospace; font-size:80%; } div.quotation { font-family: palatino font, monospace; font-size:80%; } pre.example { margin: 30px; font-family: prestige, monospace; color:black; font-size:70%; background-color: lightyellow; } @@ -23,10 +24,10 @@ div[id="text-table-of-contents"]{ } div[class^="outline-text"] { margin: 10px; - background-color:#ebe6f0; - border-style: dotted; - border-color: #98bf21; - border-width: 1px; + // background-color:white; + // border-style: dotted; + // border-color: #98bf21; + // border-width: 1px; font-family: Palatino, 'Palatino Linotype', serif; color:black; font-size: large } span[class="todo TESTING"] { diff --git a/bh20simplewebuploader/static/image/CWL.png b/bh20simplewebuploader/static/image/CWL.png new file mode 100644 index 0000000..81d1807 --- /dev/null +++ b/bh20simplewebuploader/static/image/CWL.png Binary files differdiff --git a/bh20simplewebuploader/static/image/ESR.png b/bh20simplewebuploader/static/image/ESR.png new file mode 100644 index 0000000..557c798 --- /dev/null +++ b/bh20simplewebuploader/static/image/ESR.png Binary 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display: grid; - grid-template-columns: repeat(2, 1fr); + grid-template-columns: 1fr 1fr; grid-auto-flow: row; } @@ -229,7 +229,7 @@ a { #metadata_fill_form { column-count: 4; margin-top: 0.5em; - column-width: 250px; + column-width: 15em; } .record, .record .field-group, .record .field-group .field { @@ -238,6 +238,8 @@ a { -webkit-column-break-inside: avoid; /* Chrome, Safari, Opera */ page-break-inside: avoid; /* Firefox */ break-inside: avoid; + display: block; + width: 90%; } .record { @@ -258,6 +260,10 @@ a { width: max-content; } +.control { + width: 100%; +} + .filter-options { width: 100%; } @@ -304,9 +310,10 @@ footer { } .sponsors img { - width: 80%; - display:block; - margin:auto; + width: auto; + display: block; + margin: auto; + height: 4em; } .loader { @@ -377,3 +384,22 @@ div.status { vertical-align: top; border-bottom: 1px solid #ddd; } + +.map { + padding: 20px 32px; + // display: inline-block; +} + +.editbutton { + float: right; + text-align: right; + background-color: lightgrey; + border: 2px solid #4CAF50; + border-radius: 12px; + color: black; + padding: 5px 32px; + // text-decoration: none; + display: inline-block; + font-size: 16px; + box-shadow: 0 8px 16px 0 rgba(0,0,0,0.2), 0 6px 20px 0 rgba(0,0,0,0.19); +} diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js index 751e478..1633c25 100644 --- a/bh20simplewebuploader/static/main.js +++ b/bh20simplewebuploader/static/main.js @@ -13,70 +13,41 @@ function myFunction() { } } -let map = L.map( 'map', { - center: [37.0902, -95.7129], // Default to U.S.A - minZoom: 3, - zoom: 0 -}); -L.tileLayer( 'http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', { - attribution: '© <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a>', - subdomains: ['a','b','c'] -}).addTo( map ); - -let markers = L.markerClusterGroup().addTo(map) - - function fetchAPI(apiEndPoint) { - fetch(scriptRoot + apiEndPoint) - .then(response => { - return response.json(); - }) - .then(data => { - console.log(data); - markers.clearLayers(); - document.getElementById("results").classList.remove("invisible"); - document.getElementById("loader").classList.add("invisible"); - if (!(apiEndPoint === "/api/getAllaccessions")) { - for (let i = 0; i < data.length; i++) { - let {"count": fastaCount, GPS, LocationLabel: label } = data[i]; - let coordinates = GPS.split(" "); - if (!(coordinates == null)) { - let lat, lon; - [lon, lat] = coordinates.map(parseFloat); - let point = L.point() - let marker = L.marker([lat, lon]); - marker.bindPopup("<b>" + label + "</b><br/>" + "FastaCount: " +fastaCount); - markers.addLayer(marker) - }} - } - // Reload the map - map.invalidateSize(); - }); - document.getElementById("results").classList.add("invisible"); - document.getElementById("loader").classList.remove("invisible"); - -} - -// Copy from function above but now added as table instead of plain json -function fetchAPIV2(apiEndPoint) { - fetch(scriptRoot + apiEndPoint) - .then(response => { - return response.json(); - }) - .then(data => { - console.log(data) - htmlString="<table>" - - // Depending on what we want to explore we'd have to call a different function ....? But how to Include that? - for (var i=0; i<data.length;i++) { - htmlString=htmlString+"<tr><td><a href='#' onclick='fetchSEQByLocation(\""+data[i]["key"]+"\");'>"+data[i]["label"]+"</a></td><td>"+data[i]["count"]+"<td></tr>" - } - htmlString=htmlString+"</table>" - - document.getElementById("table").innerHTML = htmlString - }); - - document.getElementById("results").classList.add("invisible"); + fetch(scriptRoot + apiEndPoint) + .then(response => { + return response.json(); + }) + .then(data => { + console.log(data); + }); + document.getElementById("map_view").classList.add("invisible"); + document.getElementById("loader").classList.remove("invisible"); +} + +// Copy from function above but now output HTML table instead of plain json +function fetchHTMLTable(apiEndPoint) { + fetch(scriptRoot + apiEndPoint) + .then(response => { + return response.json(); + }) + .then(data => { + console.log(data) + htmlString="<table>" + + // Depending on what we want to explore we'd have to call a different function ....? But how to Include that? + /* + for (var i=0; i<data.length;i++) { + htmlString=htmlString+"<tr><td><a href='#' onclick='fetchSEQByLocation(\""+data[i]["key"]+"\");'>"+data[i]["label"]+"</a></td><td>"+data[i]["count"]+"<td></tr>" + } +*/ + for (var i=0; i<data.length;i++) { + htmlString=htmlString+"<tr><td>"+data[i]["label"]+"</td><td>"+data[i]["count"]+"<td></tr>" + } + htmlString=htmlString+"</table>" + + document.getElementById("table").innerHTML = htmlString + }); } @@ -85,36 +56,39 @@ let search = () => { fetchAPI(scriptRoot + "/api/getDetailsForSeq?seq=" + encodeURIComponent(m)); } +// Get count from Arvados let fetchCount = () => { fetchAPI("/api/getCount"); } +// Get count from Virtuoso let fetchCountDB = () => { fetchAPI("/api/getCountDB"); } let fetchSEQCountBySpecimen = () => { - fetchAPIV2("/api/getSEQCountbySpecimenSource"); + fetchHTMLTable("/api/getSEQCountbySpecimenSource"); } let fetchSEQCountByLocation = () => { - fetchAPIV2("/api/getSEQCountbyLocation"); + fetchHTMLTable("/api/getSEQCountbyLocation"); } let fetchSEQCountByTech = () => { - fetchAPIV2("/api/getSEQCountbytech"); + fetchHTMLTable("/api/getSEQCountbytech"); } let fetchAllaccessions = () => { - fetchAPI("/api/getAllaccessions"); + fetchHTMLTable("/api/getAllaccessions"); }; -let fetchCountByGPS = () => { - fetchAPI("/api/getCountByGPS"); +let fetchMap = () => { + fetchAPI("/api/getCountByGPS"); + updateMapMarkers(); }; let fetchSEQCountbyLocation = () => { - fetchAPIV2("/api/getSEQCountbyLocation"); + fetchHTMLTable("/api/getSEQCountbyLocation"); }; let fetchSEQByLocation = () => { @@ -122,7 +96,7 @@ let fetchSEQByLocation = () => { }; let fetchSEQCountbyContinent = () => { - fetchAPIV2("/api/getSEQCountbyContinent"); + fetchHTMLTable("/api/getSEQCountbyContinent"); } @@ -195,7 +169,7 @@ function addField(e) { // Increment the number and use the keypath and number to set IDs and cross // references. // TODO: Heavily dependent on the form field HTML. Maybe we want custom - // elements for the labeled controlsd that know how to be list items? + // elements for the labeled controls that know how to be list items? fieldNumber++ newField.dataset.number = fieldNumber let newID = keypath + '[' + fieldNumber + ']' @@ -252,36 +226,3 @@ function on_submit_button() { return false; } } - - - -// - -function drawMap(){ - -// initialize the map on the "map" div with a given center and zoom -var mymap = L.map('mapid').setView([51.505, -0.09], 1); - -L.tileLayer('https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', { - attribution: '© <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a> contributors' -}).addTo(mymap); - -fetch(scriptRoot + "api/getCountByGPS") - .then(response => { - console.log(response) - return response.json(); - }) - .then(data => { - - for (var i=0; i<data.length;i++) { - gps=data[i]["GPS"].split(" ") - var circle = L.circle([gps[1], gps[0]], { - color: 'red', - fillColor: '#f03', - fillOpacity: 0.5, - radius: parseInt(data[i]["count"]) //not working for whatever reason - }).addTo(mymap); - } - - }); -} diff --git a/bh20simplewebuploader/static/map.js b/bh20simplewebuploader/static/map.js new file mode 100644 index 0000000..1003f7d --- /dev/null +++ b/bh20simplewebuploader/static/map.js @@ -0,0 +1,50 @@ + +var map = L.map( 'mapid', { + center: [51.505, -0.09], // Default to U.S.A + minZoom: 2, + zoom: 0 +}); + +L.tileLayer( 'http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', { + attribution: '© <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a> | <a href="http://covid19.genenetwork.org/">COVID-19 PubSeq</a>', + subdomains: ['a','b','c'] +}).addTo(map); + + +function drawMap(){ + var mymap = map; + + fetch(scriptRoot + "api/getCountByGPS") + .then(response => { + console.log(response) + return response.json(); + }) + .then(data => { + updateMapMarkers(data); + + }); + document.getElementById("map_view").classList.remove("invisible"); + map.invalidateSize(); +} + + + +/* This function updates the map with markers + * +*/ +function updateMapMarkers(data) { + let markers = L.markerClusterGroup(); + for (let i = 0; i < data.length; i++) { + let {"count": fastaCount, GPS, LocationLabel: label } = data[i]; + let coordinates = GPS.split(" "); + if (!(coordinates == null)) { + let lat, lon; + [lon, lat] = coordinates.map(parseFloat); + let point = L.point() + marker = (L.marker([lat, lon])); + marker.bindPopup("<b>" + label + "</b><br/>" + "SARS-CoV-2<br/>sequences: " +fastaCount); + markers.addLayer(marker); + } + } + map.addLayer(markers); +} diff --git a/bh20simplewebuploader/templates/blog.html b/bh20simplewebuploader/templates/blog.html index dbc0b99..823f8a1 100644 --- a/bh20simplewebuploader/templates/blog.html +++ b/bh20simplewebuploader/templates/blog.html @@ -9,9 +9,7 @@ {{ embed|safe }} <hr> - <p> - Other blog entries: - </p> + <h1>Other blog entries</h1> {% else %} {% include 'blurb.html' %} diff --git a/bh20simplewebuploader/templates/blurb.html b/bh20simplewebuploader/templates/blurb.html index 80fd384..9eef7c2 100644 --- a/bh20simplewebuploader/templates/blurb.html +++ b/bh20simplewebuploader/templates/blurb.html @@ -2,7 +2,7 @@ This is the COVID-19 Public Sequence Resource (COVID-19 PubSeq) for SARS-CoV-2 virus sequences. COVID-19 PubSeq is a repository for sequences with a low barrier to entry for uploading sequence data - using best practices. I.e., data published with a creative commons + using best practices, including <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR data</a>. I.e., data published with a creative commons CC0 or CC-4.0 license with metadata using state-of-the art standards and, perhaps most importantly, providing standardised workflows that get triggered on upload, so that results are immediately available diff --git a/bh20simplewebuploader/templates/demo-run.html b/bh20simplewebuploader/templates/demo-run.html deleted file mode 100644 index a8f9edc..0000000 --- a/bh20simplewebuploader/templates/demo-run.html +++ /dev/null @@ -1,26 +0,0 @@ -<section class="search-section"> - <div class="filter-options" action="#"> - <p>[Demo] Display content sequences by: </p> - <div> - <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button> - <button class="button" onclick="fetchSEQCountByLocation()">Count by Location</button> - <button class="button" onclick="fetchSEQCountByTech()">Count by Sequencer</button> - <button class="button" onclick="fetchAllaccessions()">Show All accessions</button> - <button class="button" onclick="fetchSEQCountbyContinent()">Count by Continent</button> - <button class="button" onclick="fetchCountByGPS()">Map</button> - - </div> - - </div> - -</section> -<div id="loader" class="loader invisible"> -</div> - -<section id="results" class="invisible"> - <div id="map"></div> -</section> - - <section> - <div id="table"></div> - </section> diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html index 44aded0..75bc0e2 100644 --- a/bh20simplewebuploader/templates/demo.html +++ b/bh20simplewebuploader/templates/demo.html @@ -1,13 +1,51 @@ <!DOCTYPE html> <html> {% include 'header.html' %} + {% include 'mapheader.html' %} <body> {% include 'banner.html' %} {% include 'menu.html' %} - {% include 'search.html' %} - <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences!</p> - {% include 'demo-run.html' %} - {% include 'footer.html' %} + + <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences!</p> + + <!-- + <div class="search"> + <input id="search-input" type="search" placeholder="FASTA uri" required> + <button class="button search-button" type="submit" onclick="search()"> + <span class="icon ion-search"> + <span class="sr-only">Search</span> + </span> + </button> + <span class="dropt" title="http://collections.lugli.arvadosapi.com/c=00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta">(example)<span style="width:500px;"></span></span> + </div> + --> + + <section class="search-section"> + <div class="filter-options" action="#"> + <p>[Demo] Display content sequences by: </p> + <div> + <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button> + <button class="button" onclick="fetchSEQCountByLocation()">Count by Location</button> + <button class="button" onclick="fetchSEQCountByTech()">Count by Sequencer</button> + <!-- <button class="button" onclick="fetchAllaccessions()">Show All accessions</button> --> + <button class="button" onclick="fetchSEQCountbyContinent()">Count by Continent</button> + </div> + + </div> + + </section> + <div id="loader" class="loader invisible"> + </div> + + <section id="map_view" class="map"> + <div id="mapid"></div> + </section> + + <section> + <div id="table"></div> + </section> + + {% include 'footer.html' %} <script type="text/javascript"> let scriptRoot = {{ request.script_root|tojson|safe }}; // examples @@ -24,7 +62,10 @@ }); }); + drawMap() + </script> + </body> </html> diff --git a/bh20simplewebuploader/templates/error.html b/bh20simplewebuploader/templates/error.html index b1d9402..fc08aed 100644 --- a/bh20simplewebuploader/templates/error.html +++ b/bh20simplewebuploader/templates/error.html @@ -15,7 +15,7 @@ </pre> </p> <p> - <a href="/">Click here to try again.</a> + <a href="/upload">Click here to try again.</a> </p> <hr> </body> diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html index a1dd4fd..f84cef5 100644 --- a/bh20simplewebuploader/templates/footer.html +++ b/bh20simplewebuploader/templates/footer.html @@ -21,14 +21,21 @@ <img src="static/image/covid19biohackathon.png"></a> </div> <div class="sponsorimg"> - <a href="https://www.commonwl.org/"><img src="static/image/CWL-Logo-Header.png"></a> + <a href="https://www.curii.com/"><img src="static/image/curii.logo.ai.png"></a> </div> <div class="sponsorimg"> <a href="https://arvados.org/"><img src="static/image/arvados-logo.png"></a> </div> <div class="sponsorimg"> + <a href="https://www.commonwl.org/"><img src="static/image/CWL.png"></a> + </div> + <div class="sponsorimg"> <a href="https://uthsc.edu/"><img src="static/image/UTHSC-primary-stacked-logo-4c.png"></a> </div> + <div class="sponsorimg"> + <a href="https://www.esr.cri.nz/"><img src="static/image/ESR.png"></a> + </div> + </div> </div> <div class="footer"> @@ -40,6 +47,9 @@ </center> </div> </section> +{% if load_map %} +<script type="text/javascript" src="/static/map.js"></script> +{% endif %} <script type="text/javascript" src="/static/main.js"></script> <script type="text/javascript"> diff --git a/bh20simplewebuploader/templates/header.html b/bh20simplewebuploader/templates/header.html index 0ac5157..1d66590 100644 --- a/bh20simplewebuploader/templates/header.html +++ b/bh20simplewebuploader/templates/header.html @@ -6,22 +6,4 @@ {% if blog %} <link rel="Blog stylesheet" type="text/css" href="/static/blog.css" /> {% endif %} - <link rel="stylesheet" href="https://unpkg.com/leaflet@1.6.0/dist/leaflet.css" - integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ==" - crossorigin=""/> - <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.css" - integrity="sha512-RLEjtaFGdC4iQMJDbMzim/dOvAu+8Qp9sw7QE4wIMYcg2goVoivzwgSZq9CsIxp4xKAZPKh5J2f2lOko2Ze6FQ==" - crossorigin=""/> - - <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.Default.css" - integrity="sha512-BBToHPBStgMiw0lD4AtkRIZmdndhB6aQbXpX7omcrXeG2PauGBl2lzq2xUZTxaLxYz5IDHlmneCZ1IJ+P3kYtQ==" - crossorigin=""/> - - <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js" - integrity="sha512-gZwIG9x3wUXg2hdXF6+rVkLF/0Vi9U8D2Ntg4Ga5I5BZpVkVxlJWbSQtXPSiUTtC0TjtGOmxa1AJPuV0CPthew==" - crossorigin=""></script> - - <script src="https://unpkg.com/leaflet.markercluster@1.4.1/dist/leaflet.markercluster.js" - integrity="sha512-MQlyPV+ol2lp4KodaU/Xmrn+txc1TP15pOBF/2Sfre7MRsA/pB4Vy58bEqe9u7a7DczMLtU5wT8n7OblJepKbg==" - crossorigin=""></script> </head> diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html index b90a18d..bede611 100644 --- a/bh20simplewebuploader/templates/home.html +++ b/bh20simplewebuploader/templates/home.html @@ -1,6 +1,7 @@ <!DOCTYPE html> <html> {% include 'header.html' %} + {% include 'mapheader.html' %} <body> {% include 'banner.html' %} {% include 'menu.html' %} @@ -44,7 +45,19 @@ </div> </section> -{% include 'footer.html' %} + <section id="map_view" class="map"> + <div id="mapid"></div> + </section> + + {% include 'footer.html' %} + + + <script type="text/javascript"> + let scriptRoot = {{ request.script_root|tojson|safe }}; // examples + + drawMap() + + </script> </body> </html> diff --git a/bh20simplewebuploader/templates/map.html b/bh20simplewebuploader/templates/map.html deleted file mode 100644 index 595af0c..0000000 --- a/bh20simplewebuploader/templates/map.html +++ /dev/null @@ -1,33 +0,0 @@ -<!DOCTYPE html> -<html> - {% include 'header.html' %} -<link rel="stylesheet" href="https://unpkg.com/leaflet@1.6.0/dist/leaflet.css" - integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ==" - crossorigin=""/> - - {% include 'banner.html' %} - {% include 'menu.html' %} - <div id="mapid" style="height: 500px;"></div> - - {% include 'footer.html' %} - - - - - <script type="text/javascript"> - let scriptRoot = {{ request.script_root|tojson|safe }}; // examples - </script> - -<!-- Make sure you put this AFTER Leaflet's CSS --> - <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js" - integrity="sha512-gZwIG9x3wUXg2hdXF6+rVkLF/0Vi9U8D2Ntg4Ga5I5BZpVkVxlJWbSQtXPSiUTtC0TjtGOmxa1AJPuV0CPthew==" - crossorigin=""></script> - - <script> - //drawMap - drawMap() - </script> - - </body> - -</html> diff --git a/bh20simplewebuploader/templates/mapheader.html b/bh20simplewebuploader/templates/mapheader.html new file mode 100644 index 0000000..ca62051 --- /dev/null +++ b/bh20simplewebuploader/templates/mapheader.html @@ -0,0 +1,16 @@ + <link rel="stylesheet" href="https://unpkg.com/leaflet@1.6.0/dist/leaflet.css" + integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ==" + crossorigin=""/> + <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.css" + integrity="sha512-RLEjtaFGdC4iQMJDbMzim/dOvAu+8Qp9sw7QE4wIMYcg2goVoivzwgSZq9CsIxp4xKAZPKh5J2f2lOko2Ze6FQ==" + crossorigin=""/> + <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.Default.css" + integrity="sha512-BBToHPBStgMiw0lD4AtkRIZmdndhB6aQbXpX7omcrXeG2PauGBl2lzq2xUZTxaLxYz5IDHlmneCZ1IJ+P3kYtQ==" + crossorigin=""/> + + <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js" + integrity="sha512-gZwIG9x3wUXg2hdXF6+rVkLF/0Vi9U8D2Ntg4Ga5I5BZpVkVxlJWbSQtXPSiUTtC0TjtGOmxa1AJPuV0CPthew==" + crossorigin=""></script> + <script src="https://unpkg.com/leaflet.markercluster@1.4.1/dist/leaflet.markercluster.js" + integrity="sha512-MQlyPV+ol2lp4KodaU/Xmrn+txc1TP15pOBF/2Sfre7MRsA/pB4Vy58bEqe9u7a7DczMLtU5wT8n7OblJepKbg==" + crossorigin=""></script> diff --git a/bh20simplewebuploader/templates/search.html b/bh20simplewebuploader/templates/search.html index dbdca90..e69de29 100644 --- a/bh20simplewebuploader/templates/search.html +++ b/bh20simplewebuploader/templates/search.html @@ -1,10 +0,0 @@ -<div class="search"> - <input id="search-input" type="search" placeholder="FASTA uri" required> - <button class="button search-button" type="submit" onclick="search()"> - <span class="icon ion-search"> - <span class="sr-only">Search</span> - </span> - </button> - <span class="dropt" title="http://collections.lugli.arvadosapi.com/c=00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta">(example)<span style="width:500px;"></span></span> -</div> - diff --git a/bh20simplewebuploader/templates/status.html b/bh20simplewebuploader/templates/status.html index a1cf28f..e89437e 100644 --- a/bh20simplewebuploader/templates/status.html +++ b/bh20simplewebuploader/templates/status.html @@ -7,7 +7,8 @@ <h1>Sequence upload processing status</h1> - <div class="status"> + <div class="status"> + {{ table }} </div> diff --git a/bh20simplewebuploader/templates/success.html b/bh20simplewebuploader/templates/success.html index 9f0987c..c2302fa 100644 --- a/bh20simplewebuploader/templates/success.html +++ b/bh20simplewebuploader/templates/success.html @@ -9,7 +9,7 @@ <h1>Upload Successful</h1> <hr> <p> - Your files have been uploaded. They should soon appear as output of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>. + Your files have been uploaded. You can track their <a href="/status">QC status</a>, once validated they will be part of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>. </p> <p> The upload log was: diff --git a/bh20simplewebuploader/templates/validated.html b/bh20simplewebuploader/templates/validated.html new file mode 100644 index 0000000..cee94bd --- /dev/null +++ b/bh20simplewebuploader/templates/validated.html @@ -0,0 +1,17 @@ +<!DOCTYPE html> +<html> + {% include 'header.html' %} + <body> + {% include 'banner.html' %} + {% include 'menu.html' %} + + <h1>Validated sequences</h1> + + <div class="status"> + {{ table }} + </div> + +{% include 'footer.html' %} + + </body> +</html> diff --git a/doc/INSTALL.md b/doc/INSTALL.md index 6dcd72b..3b270dd 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -42,7 +42,7 @@ repository. ### Using the Web Uploader -To run the web uploader in a GNU Guix environment/container +To run the web uploader in a GNU Guix environment/container run it with something like ``` guix environment guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs --network openssl -- env FLASK_ENV=development PYTHONPATH=$PYTHONPATH:./bh20sequploader FLASK_APP=bh20simplewebuploader/main.py flask run @@ -59,7 +59,7 @@ WIP: add gunicorn container Currently the full webserver container deploy command looks like ``` -penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc clustalw python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run -`` +penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-oinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc clustalw python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run +``` Note: see above on GUIX_PACKAGE_PATH. diff --git a/doc/blog/using-covid-19-pubseq-part1.html b/doc/blog/using-covid-19-pubseq-part1.html index 1959fac..0e6136c 100644 --- a/doc/blog/using-covid-19-pubseq-part1.html +++ b/doc/blog/using-covid-19-pubseq-part1.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-05-29 Fri 12:06 --> +<!-- 2020-07-17 Fri 05:05 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>COVID-19 PubSeq (part 1)</title> @@ -248,20 +248,20 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org9afe6ab">1. What does this mean?</a></li> -<li><a href="#orgf4bc3d4">2. Fetch sequence data</a></li> -<li><a href="#org9d7d482">3. Predicates</a></li> -<li><a href="#orgc6046bb">4. Fetch submitter info and other metadata</a></li> -<li><a href="#orgdcb216b">5. Fetch all sequences from Washington state</a></li> -<li><a href="#org7060f51">6. Discussion</a></li> -<li><a href="#orgdc51ccc">7. Acknowledgements</a></li> +<li><a href="#org0db5db0">1. What does this mean?</a></li> +<li><a href="#orge5267fd">2. Fetch sequence data</a></li> +<li><a href="#orgfbd3adc">3. Predicates</a></li> +<li><a href="#org08e70e1">4. Fetch submitter info and other metadata</a></li> +<li><a href="#org9194557">5. Fetch all sequences from Washington state</a></li> +<li><a href="#org76317ad">6. Discussion</a></li> +<li><a href="#orgeb871a1">7. Acknowledgements</a></li> </ul> </div> </div> -<div id="outline-container-org9afe6ab" class="outline-2"> -<h2 id="org9afe6ab"><span class="section-number-2">1</span> What does this mean?</h2> +<div id="outline-container-org0db5db0" class="outline-2"> +<h2 id="org0db5db0"><span class="section-number-2">1</span> What does this mean?</h2> <div class="outline-text-2" id="text-1"> <p> This means that when someone uploads a SARS-CoV-2 sequence using one @@ -274,24 +274,24 @@ expressed in a <a href="https://github.com/arvados/bh20-seq-resource/blob/master type: record fields: host_species: - doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_<span style="color: #8bc34a;">9606</span> for Homo sapiens + doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens type: string jsonldPredicate: - _id: http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0000532</span> - _type: <span style="color: #9ccc65;">"@id"</span> - noLinkCheck: <span style="color: #8bc34a;">true</span> + _id: http://www.ebi.ac.uk/efo/EFO_0000532 + _type: "@id" + noLinkCheck: true host_sex: - doc: Sex of the host as defined in PATO, expect male <span style="color: #e91e63;">()</span> or female <span style="color: #e91e63;">()</span> + doc: Sex of the host as defined in PATO, expect male () or female () type: string? jsonldPredicate: - _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000047</span> - _type: <span style="color: #9ccc65;">"@id"</span> - noLinkCheck: <span style="color: #8bc34a;">true</span> + _id: http://purl.obolibrary.org/obo/PATO_0000047 + _type: "@id" + noLinkCheck: true host_age: - doc: Age of the host as number <span style="color: #e91e63;">(</span>e.g. <span style="color: #8bc34a;">50</span><span style="color: #e91e63;">)</span> + doc: Age of the host as number (e.g. 50) type: int? jsonldPredicate: - _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000011</span> + _id: http://purl.obolibrary.org/obo/PATO_0000011 </pre> </div> @@ -314,8 +314,8 @@ initiative! </div> -<div id="outline-container-orgf4bc3d4" class="outline-2"> -<h2 id="orgf4bc3d4"><span class="section-number-2">2</span> Fetch sequence data</h2> +<div id="outline-container-orge5267fd" class="outline-2"> +<h2 id="orge5267fd"><span class="section-number-2">2</span> Fetch sequence data</h2> <div class="outline-text-2" id="text-2"> <p> The latest run of the pipeline can be viewed <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">here</a>. Each of these @@ -339,8 +339,8 @@ these identifiers throughout. </div> </div> -<div id="outline-container-org9d7d482" class="outline-2"> -<h2 id="org9d7d482"><span class="section-number-2">3</span> Predicates</h2> +<div id="outline-container-orgfbd3adc" class="outline-2"> +<h2 id="orgfbd3adc"><span class="section-number-2">3</span> Predicates</h2> <div class="outline-text-2" id="text-3"> <p> To explore an RDF dataset, the first query we can do is open and gets @@ -350,10 +350,10 @@ the following in a SPARQL end point </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">select distinct ?p +{ ?o ?p ?s -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -364,10 +364,10 @@ To get a <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&q </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?g -<span style="color: #e91e63;">{</span> - GRAPH ?g <span style="color: #2196F3;">{</span>?s ?p ?o<span style="color: #2196F3;">}</span> -<span style="color: #e91e63;">}</span> +<pre class="src src-sql">select distinct ?g +{ + GRAPH ?g {?s ?p ?o} +} </pre> </div> @@ -383,10 +383,10 @@ To list all submitters, try </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s -<span style="color: #e91e63;">{</span> - ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter></a> ?s -<span style="color: #e91e63;">}</span> +<pre class="src src-sql">select distinct ?s +{ + ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?s +} </pre> </div> @@ -397,11 +397,11 @@ and by </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s -<span style="color: #e91e63;">{</span> - ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter></a> ?id . +<pre class="src src-sql">select distinct ?s +{ + ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?id . ?id ?p ?s -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -415,12 +415,12 @@ To lift the full URL out of the query you can use a header like </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -438,32 +438,32 @@ Now we got this far, lets <a href="http://sparql.genenetwork.org/sparql/?default </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #e91e63;">(</span><span style="color: #ff8A65;">COUNT</span><span style="color: #2196F3;">(</span><span style="color: #fff59d;">distinct</span> ?dataset<span style="color: #2196F3;">)</span> <span style="color: #fff59d;">as</span> ?num<span style="color: #e91e63;">)</span> -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select (COUNT(distinct ?dataset) as ?num) +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> </div> </div> -<div id="outline-container-orgc6046bb" class="outline-2"> -<h2 id="orgc6046bb"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2> +<div id="outline-container-org08e70e1" class="outline-2"> +<h2 id="org08e70e1"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2> <div class="outline-text-2" id="text-4"> <p> To get dataests with submitters we can do the above </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?p ?submitter -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?p ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -480,13 +480,13 @@ Let's focus on one sample with </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter . - FILTER<span style="color: #2196F3;">(</span><span style="color: #fff59d;">CONTAINS</span><span style="color: #EF6C00;">(</span>?submitter,"Roychoudhury"<span style="color: #EF6C00;">)</span><span style="color: #2196F3;">)</span> . -<span style="color: #e91e63;">}</span> + FILTER(CONTAINS(?submitter,"Roychoudhury")) . +} </pre> </div> @@ -496,12 +496,12 @@ see if we can get a sample ID by listing sample predicates </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?p +{ ?dataset ?p ?o . ?dataset pubseq:submitter ?id . -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -513,15 +513,15 @@ Let's zoom in on those of Roychoudhury with <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sid ?sample ?p1 ?dataset ?submitter -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?sid ?sample ?p1 ?dataset ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter . - FILTER<span style="color: #2196F3;">(</span><span style="color: #fff59d;">CONTAINS</span><span style="color: #EF6C00;">(</span>?submitter,"Roychoudhury"<span style="color: #EF6C00;">)</span><span style="color: #2196F3;">)</span> . + FILTER(CONTAINS(?submitter,"Roychoudhury")) . ?dataset pubseq:sample ?sid . ?sid ?p1 ?sample -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -532,18 +532,13 @@ this database. Let's focus on one sample "MT326090.1" with predicate </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/">#MainSchema/> -</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/">PREFIX</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/"> sio: <http://semanticscience.org/resource/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sample ?p ?o -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?p ?o +{ ?sample sio:SIO_000115 "MT326090.1" . ?sample ?p ?o . -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -561,8 +556,8 @@ to view/query the database. </div> </div> -<div id="outline-container-orgdcb216b" class="outline-2"> -<h2 id="orgdcb216b"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2> +<div id="outline-container-org9194557" class="outline-2"> +<h2 id="org9194557"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2> <div class="outline-text-2" id="text-5"> <p> Now we know how to get at the origin we can do it the other way round @@ -570,15 +565,11 @@ and fetch all sequences referring to Washington state </p> <div class="org-src-container"> -<pre class="src src-sql"> -<span style="color: #fff59d;">select</span> ?seq ?sample -<span style="color: #e91e63;">{</span> - ?seq <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223">#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223></a> -<span style="color: #e91e63;">}</span> +<pre class="src src-sql">select ?seq ?sample +{ + ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> +} </pre> </div> @@ -586,11 +577,26 @@ and fetch all sequences referring to Washington state which lists 300 sequences originating from Washington state! Which is almost half of the set coming out of GenBank. </p> + +<p> +Likewise to list all sequences from Turkey we can find the wikidata +entity is <a href="https://www.wikidata.org/wiki/Q43">Q43</a>: +</p> + +<div class="org-src-container"> +<pre class="src src-sql">select ?seq ?sample +{ + ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q43> +} +</pre> </div> </div> +</div> + -<div id="outline-container-org7060f51" class="outline-2"> -<h2 id="org7060f51"><span class="section-number-2">6</span> Discussion</h2> +<div id="outline-container-org76317ad" class="outline-2"> +<h2 id="org76317ad"><span class="section-number-2">6</span> Discussion</h2> <div class="outline-text-2" id="text-6"> <p> The public sequence uploader collects sequences, raw data and @@ -601,8 +607,8 @@ referenced in publications and origins are citeable. </div> </div> -<div id="outline-container-orgdc51ccc" class="outline-2"> -<h2 id="orgdc51ccc"><span class="section-number-2">7</span> Acknowledgements</h2> +<div id="outline-container-orgeb871a1" class="outline-2"> +<h2 id="orgeb871a1"><span class="section-number-2">7</span> Acknowledgements</h2> <div class="outline-text-2" id="text-7"> <p> The overall effort was due to magnificent freely donated input by a @@ -617,7 +623,7 @@ Garrison this initiative would not have existed! </div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-29 Fri 12:06</small>. +<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-17 Fri 05:02</small>. </div> </body> </html> diff --git a/doc/blog/using-covid-19-pubseq-part4.html b/doc/blog/using-covid-19-pubseq-part4.html index b5a05ca..c975c21 100644 --- a/doc/blog/using-covid-19-pubseq-part4.html +++ b/doc/blog/using-covid-19-pubseq-part4.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-07-12 Sun 06:24 --> +<!-- 2020-07-17 Fri 05:04 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>COVID-19 PubSeq (part 4)</title> @@ -161,6 +161,19 @@ .footdef { margin-bottom: 1em; } .figure { padding: 1em; } .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } .inlinetask { padding: 10px; border: 2px solid gray; @@ -186,7 +199,7 @@ @licstart The following is the entire license notice for the JavaScript code in this tag. -Copyright (C) 2012-2018 Free Software Foundation, Inc. +Copyright (C) 2012-2020 Free Software Foundation, Inc. The JavaScript code in this tag is free software: you can redistribute it and/or modify it under the terms of the GNU @@ -235,15 +248,16 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org8f8b64a">1. What does this mean?</a></li> -<li><a href="#orgcc7a403">2. Modify Workflow</a></li> +<li><a href="#orgc2ee09f">1. What does this mean?</a></li> +<li><a href="#org0d37881">2. Where can I find the workflows?</a></li> +<li><a href="#orgddb0531">3. Modify Workflow</a></li> </ul> </div> </div> -<div id="outline-container-org8f8b64a" class="outline-2"> -<h2 id="org8f8b64a"><span class="section-number-2">1</span> What does this mean?</h2> +<div id="outline-container-orgc2ee09f" class="outline-2"> +<h2 id="orgc2ee09f"><span class="section-number-2">1</span> What does this mean?</h2> <div class="outline-text-2" id="text-1"> <p> This means that when someone uploads a SARS-CoV-2 sequence using one @@ -253,18 +267,28 @@ which triggers a rerun of our workflows. </div> </div> - -<div id="outline-container-orgcc7a403" class="outline-2"> -<h2 id="orgcc7a403"><span class="section-number-2">2</span> Modify Workflow</h2> +<div id="outline-container-org0d37881" class="outline-2"> +<h2 id="org0d37881"><span class="section-number-2">2</span> Where can I find the workflows?</h2> <div class="outline-text-2" id="text-2"> <p> +Workflows are written in the common workflow language (CWL) and listed +on <a href="https://github.com/arvados/bh20-seq-resource/tree/master/workflows">github</a>. PubSeq being an open project these workflows can be studied +and modified! +</p> +</div> +</div> + +<div id="outline-container-orgddb0531" class="outline-2"> +<h2 id="orgddb0531"><span class="section-number-2">3</span> Modify Workflow</h2> +<div class="outline-text-2" id="text-3"> +<p> <i>Work in progress!</i> </p> </div> </div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-12 Sun 06:24</small>. +<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-17 Fri 01:47</small>. </div> </body> </html> diff --git a/doc/blog/using-covid-19-pubseq-part4.org b/doc/blog/using-covid-19-pubseq-part4.org index 5fe71d1..8ad5e2d 100644 --- a/doc/blog/using-covid-19-pubseq-part4.org +++ b/doc/blog/using-covid-19-pubseq-part4.org @@ -10,6 +10,7 @@ * Table of Contents :TOC:noexport: - [[#what-does-this-mean][What does this mean?]] + - [[#where-can-i-find-the-workflows][Where can I find the workflows?]] - [[#modify-workflow][Modify Workflow]] * What does this mean? @@ -18,6 +19,11 @@ This means that when someone uploads a SARS-CoV-2 sequence using one of our tools (CLI or web-based) they add a sequence and some metadata which triggers a rerun of our workflows. +* Where can I find the workflows? + +Workflows are written in the common workflow language (CWL) and listed +on [[https://github.com/arvados/bh20-seq-resource/tree/master/workflows][github]]. PubSeq being an open project these workflows can be studied +and modified! * Modify Workflow diff --git a/doc/blog/using-covid-19-pubseq-part5.html b/doc/blog/using-covid-19-pubseq-part5.html index 80bf559..4caa5ac 100644 --- a/doc/blog/using-covid-19-pubseq-part5.html +++ b/doc/blog/using-covid-19-pubseq-part5.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-07-12 Sun 06:24 --> +<!-- 2020-07-17 Fri 05:03 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>COVID-19 PubSeq (part 4)</title> @@ -161,6 +161,19 @@ .footdef { margin-bottom: 1em; } .figure { padding: 1em; } .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } .inlinetask { padding: 10px; border: 2px solid gray; @@ -186,7 +199,7 @@ @licstart The following is the entire license notice for the JavaScript code in this tag. -Copyright (C) 2012-2018 Free Software Foundation, Inc. +Copyright (C) 2012-2020 Free Software Foundation, Inc. The JavaScript code in this tag is free software: you can redistribute it and/or modify it under the terms of the GNU @@ -235,38 +248,40 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org871ad58">1. Modify Metadata</a></li> -<li><a href="#org07e8755">2. What is the schema?</a></li> -<li><a href="#org4857280">3. How is the website generated?</a></li> -<li><a href="#orge709ae2">4. Modifying the schema</a></li> +<li><a href="#org758b923">1. Modify Metadata</a></li> +<li><a href="#orgec32c13">2. What is the schema?</a></li> +<li><a href="#org2e487b2">3. How is the website generated?</a></li> +<li><a href="#orge4dfe84">4. Modifying the schema</a></li> +<li><a href="#org564a7a8">5. Adding fields to the form</a></li> +<li><a href="#org633781a">6. <span class="todo TODO">TODO</span> Testing the license fields</a></li> </ul> </div> </div> -<div id="outline-container-org871ad58" class="outline-2"> -<h2 id="org871ad58"><span class="section-number-2">1</span> Modify Metadata</h2> +<div id="outline-container-org758b923" class="outline-2"> +<h2 id="org758b923"><span class="section-number-2">1</span> Modify Metadata</h2> <div class="outline-text-2" id="text-1"> <p> The public sequence resource uses multiple data formats listed on the -<a href="./download">DOWNLOAD</a> page. One of the most exciting features is the full support +<a href="http://covid19.genenetwork.org/download">download</a> page. One of the most exciting features is the full support for RDF and semantic web/linked data ontologies. This technology allows for querying data in unprescribed ways - that is, you can formulate your own queries without dealing with a preset model of that data (so typical of CSV files and SQL tables). Examples of exploring -data are listed <a href="./blog?id=using-covid-19-pubseq-part1">here</a>. +data are listed <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1">here</a>. </p> <p> In this BLOG we are going to look at the metadata entered on the -<a href="./">COVID-19 PubSeq</a> website (or command line client). It is important to +COVID-19 PubSeq website (or command line client). It is important to understand that anyone, including you, can change that information! </p> </div> </div> -<div id="outline-container-org07e8755" class="outline-2"> -<h2 id="org07e8755"><span class="section-number-2">2</span> What is the schema?</h2> +<div id="outline-container-orgec32c13" class="outline-2"> +<h2 id="orgec32c13"><span class="section-number-2">2</span> What is the schema?</h2> <div class="outline-text-2" id="text-2"> <p> The default metadata schema is listed <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml">here</a>. @@ -274,8 +289,8 @@ The default metadata schema is listed <a href="https://github.com/arvados/bh20-s </div> </div> -<div id="outline-container-org4857280" class="outline-2"> -<h2 id="org4857280"><span class="section-number-2">3</span> How is the website generated?</h2> +<div id="outline-container-org2e487b2" class="outline-2"> +<h2 id="org2e487b2"><span class="section-number-2">3</span> How is the website generated?</h2> <div class="outline-text-2" id="text-3"> <p> Using the schema we use <a href="https://pypi.org/project/PyShEx/">pyshex</a> shex expressions and <a href="https://github.com/common-workflow-language/schema_salad">schema salad</a> to @@ -285,13 +300,13 @@ All from that one metadata schema. </div> </div> -<div id="outline-container-orge709ae2" class="outline-2"> -<h2 id="orge709ae2"><span class="section-number-2">4</span> Modifying the schema</h2> +<div id="outline-container-orge4dfe84" class="outline-2"> +<h2 id="orge4dfe84"><span class="section-number-2">4</span> Modifying the schema</h2> <div class="outline-text-2" id="text-4"> <p> -One of the first things we wanted to do is to add a field for the data -license. Initially we only support CC-4.0 as a license by default, but -now we want to give uploaders the option to make it an even more +One of the first things we want to do is to add a field for the data +license. Initially we only supported CC-4.0 as a license, but +we wanted to give uploaders the option to use an even more liberal CC0 license. The first step is to find a good ontology term for the field. Searching for `creative commons cc0 rdf' rendered this useful <a href="https://creativecommons.org/ns">page</a>. We also find an <a href="https://wiki.creativecommons.org/wiki/CC_License_Rdf_Overview">overview</a> where CC0 is represented as URI @@ -302,13 +317,148 @@ attributionName and attributionURL. </p> <p> -<i>Note: work in progress</i> +A minimal triple should be +</p> + +<pre class="example"> +id xhtml:license <http://creativecommons.org/licenses/by/4.0/> . +</pre> + + +<p> +Other suggestions are +</p> + +<pre class="example"> +id dc:title "Description" . +id cc:attributionName "Your Name" . +id cc:attributionURL <http://resource.org/id> +</pre> + + +<p> +and 'dc:source' which indicates the original source of any modified +work, specified as a URI. +The prefix 'cc:' is an abbreviation for <a href="http://creativecommons.org/ns">http://creativecommons.org/ns</a>#. +</p> + +<p> +Going back to the schema, where does it fit? Under host, sample, +virus, technology or submitter block? It could fit under sample, but +actually the license concerns the whole metadata block and sequence, +so I think we can fit under its own license tag. For example +</p> + + +<p> +id: placeholder +</p> + +<pre class="example"> +license: + license_type: http://creativecommons.org/licenses/by/4.0/ + attribution_title: "Sample ID" + attribution_name: "John doe, Joe Boe, Jonny Oe" + attribution_url: http://covid19.genenetwork.org/id + attribution_source: https://www.ncbi.nlm.nih.gov/pubmed/323088888 +</pre> + + +<p> +So, let's update the example. Notice the license info is optional - if it is missing +we just assume the default CC-4.0. +</p> + +<p> +One thing that is interesting is that in the name space <a href="https://creativecommons.org/ns">https://creativecommons.org/ns</a> there +is no mention of a title. I think it is useful, however, because we have no such field. +So, we'll add it simply as a title field. Now the draft schema is </p> + +<div class="org-src-container"> +<pre class="src src-js">- name: licenseSchema + type: record + fields: + license_type: + doc: License types as refined in https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#License + title: + doc: Attribution title related to license + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + attribution_url: + doc: Attribution URL related to license + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#Work + attribution_source: + doc: Attribution source URL + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#Work +</pre> +</div> + +<p> +Now, we are no ontology experts, right? So, next we submit a patch to +our source tree and ask for feedback before wiring it up in the data +entry form. The pull request was submitted <a href="https://github.com/arvados/bh20-seq-resource/pull/97">here</a> and reviewed on the +gitter channel and I merged it. +</p> +</div> </div> + +<div id="outline-container-org564a7a8" class="outline-2"> +<h2 id="org564a7a8"><span class="section-number-2">5</span> Adding fields to the form</h2> +<div class="outline-text-2" id="text-5"> +<p> +To add the new fields to the form we have to modify it a little. If we +go to the upload form we need to add the license box. The schema is +loaded in <a href="https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229">main.py</a> in the 'generate<sub>form</sub>' function. +</p> + +<p> +With this <a href="https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3">patch</a> the website adds the license input fields on the form. +</p> + +<p> +Finally, to make RDF output work we need to add expressions to bh20seq-shex.rdf. This +was done with this <a href="https://github.com/arvados/bh20-seq-resource/commit/f4ed46dae20abe5147871495ede2d6ac2b0854bc">patch</a>. In the end we decided to use the Dublin core title, +<a href="http://purl.org/metadata/dublin_core_elements#Title">http://purl.org/metadata/dublin_core_elements#Title</a>: +</p> + +<div class="org-src-container"> +<pre class="src src-js">:licenseShape{ + cc:License xsd:string; + dc:Title xsd:string ?; + cc:attributionName xsd:string ?; + cc:attributionURL xsd:string ?; + cc:attributionSource xsd:string ?; +} +</pre> +</div> + +<p> +Note that cc:AttributionSource is not really defined in the cc standard. +</p> + +<p> +When pushing the license info we discovered the workflow broke because +the existing data had no licensing info. So we changed the license +field to be optional - a missing license assumes it is CC-BY-4.0. +</p> +</div> +</div> + +<div id="outline-container-org633781a" class="outline-2"> +<h2 id="org633781a"><span class="section-number-2">6</span> <span class="todo TODO">TODO</span> Testing the license fields</h2> </div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-12 Sun 06:24</small>. +<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-16 Thu 03:27</small>. </div> </body> </html> diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org index 4b0ea64..78eea66 100644 --- a/doc/blog/using-covid-19-pubseq-part5.org +++ b/doc/blog/using-covid-19-pubseq-part5.org @@ -13,19 +13,21 @@ - [[#what-is-the-schema][What is the schema?]] - [[#how-is-the-website-generated][How is the website generated?]] - [[#modifying-the-schema][Modifying the schema]] + - [[#adding-fields-to-the-form][Adding fields to the form]] + - [[#testing-the-license-fields][Testing the license fields]] * Modify Metadata The public sequence resource uses multiple data formats listed on the -[[./download][DOWNLOAD]] page. One of the most exciting features is the full support +[[http://covid19.genenetwork.org/download][download]] page. One of the most exciting features is the full support for RDF and semantic web/linked data ontologies. This technology allows for querying data in unprescribed ways - that is, you can formulate your own queries without dealing with a preset model of that data (so typical of CSV files and SQL tables). Examples of exploring -data are listed [[./blog?id=using-covid-19-pubseq-part1][here]]. +data are listed [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1][here]]. In this BLOG we are going to look at the metadata entered on the -[[./][COVID-19 PubSeq]] website (or command line client). It is important to +COVID-19 PubSeq website (or command line client). It is important to understand that anyone, including you, can change that information! * What is the schema? @@ -41,8 +43,8 @@ All from that one metadata schema. * Modifying the schema One of the first things we want to do is to add a field for the data -license. Initially we only support CC-4.0 as a license by default, but -now we want to give uploaders the option to make it an even more +license. Initially we only supported CC-4.0 as a license, but +we wanted to give uploaders the option to use an even more liberal CC0 license. The first step is to find a good ontology term for the field. Searching for `creative commons cc0 rdf' rendered this useful [[https://creativecommons.org/ns][page]]. We also find an [[https://wiki.creativecommons.org/wiki/CC_License_Rdf_Overview][overview]] where CC0 is represented as URI @@ -113,8 +115,37 @@ So, we'll add it simply as a title field. Now the draft schema is _id: https://creativecommons.org/ns#Work #+END_SRC -Now, we are no ontology experts, right? So, next we submit a patch to our source tree and -ask for feedback before wiring it up in the data entry form. The pull request was -submitted here FIXME. +Now, we are no ontology experts, right? So, next we submit a patch to +our source tree and ask for feedback before wiring it up in the data +entry form. The pull request was submitted [[https://github.com/arvados/bh20-seq-resource/pull/97][here]] and reviewed on the +gitter channel and I merged it. -/Note: work in progress/ +* Adding fields to the form + +To add the new fields to the form we have to modify it a little. If we +go to the upload form we need to add the license box. The schema is +loaded in [[https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229][main.py]] in the 'generate_form' function. + +With this [[https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3][patch]] the website adds the license input fields on the form. + +Finally, to make RDF output work we need to add expressions to bh20seq-shex.rdf. This +was done with this [[https://github.com/arvados/bh20-seq-resource/commit/f4ed46dae20abe5147871495ede2d6ac2b0854bc][patch]]. In the end we decided to use the Dublin core title, +http://purl.org/metadata/dublin_core_elements#Title: + +#+BEGIN_SRC js +:licenseShape{ + cc:License xsd:string; + dc:Title xsd:string ?; + cc:attributionName xsd:string ?; + cc:attributionURL xsd:string ?; + cc:attributionSource xsd:string ?; +} +#+END_SRC + +Note that cc:AttributionSource is not really defined in the cc standard. + +When pushing the license info we discovered the workflow broke because +the existing data had no licensing info. So we changed the license +field to be optional - a missing license assumes it is CC-BY-4.0. + +* TODO Testing the license fields diff --git a/doc/web/about.org b/doc/web/about.org index ad13bc3..1949e2d 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -140,7 +140,8 @@ See the [[http://covid19.genenetwork.org/blog]]! * How do I change the work flows? -See the [[http://covid19.genenetwork.org/blog]]! +Workflows are on [[https://github.com/arvados/bh20-seq-resource/tree/master/workflows][github]] and can be modified. See also the +[[[[http://covid19.genenetwork.org/blog]]][workflow blog]]. * How do I change the source code? diff --git a/example/minimal_metadata_example.yaml b/example/minimal_metadata_example.yaml index 51f8a87..1b46cc7 100644 --- a/example/minimal_metadata_example.yaml +++ b/example/minimal_metadata_example.yaml @@ -1,5 +1,9 @@ id: placeholder + +license: + license_type: http://creativecommons.org/licenses/by/4.0/ + host: host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 @@ -15,4 +19,4 @@ technology: sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] submitter: - authors: [John Doe] \ No newline at end of file + authors: [John Doe] diff --git a/scripts/cleanup.py b/scripts/cleanup.py new file mode 100644 index 0000000..78f34c8 --- /dev/null +++ b/scripts/cleanup.py @@ -0,0 +1,41 @@ +import arvados +import arvados.util + +api = arvados.api() + +delete_patterns = [ + "%missing%`collection_location`%", + "%missing%`technology`%", + "%missing%`host_species`%", + "%QC fail: alignment%", + "%does not look like a valid URI%", + "%Duplicate of%", + "%No matching triples found for predicate obo:NCIT_C42781%", + "%does not look like a valid URI%" + ] + +revalidate_patterns = [ + "%missing%`license`%", + "%QC fail%" +] + +for p in delete_patterns: + c = arvados.util.list_all(api.collections().list, filters=[ + ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"], + ["properties.errors", "like", p]]) + for i in c: + print("trashing %s %s" % (i["uuid"], i["properties"].get("sequence_label"))) + api.collections().delete(uuid=i["uuid"]).execute() + +for p in revalidate_patterns: + c = arvados.util.list_all(api.collections().list, filters=[ + ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"], + ["properties.errors", "like", p]]) + for i in c: + print("clearing status %s %s" % (i["uuid"], i["properties"].get("sequence_label"))) + pr = i["properties"] + if "status" in pr: + del pr["status"] + if "errors" in pr: + del pr["errors"] + api.collections().update(uuid=i["uuid"], body={"properties": pr}).execute() diff --git a/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz b/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz deleted file mode 100644 index 88acb18..0000000 --- a/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz +++ /dev/null Binary files differdiff --git a/scripts/create_sra_metadata/SraExperimentPackage.2020.07.09.xml.gz b/scripts/create_sra_metadata/SraExperimentPackage.2020.07.09.xml.gz new file mode 100644 index 0000000..93ef550 --- /dev/null +++ b/scripts/create_sra_metadata/SraExperimentPackage.2020.07.09.xml.gz Binary files differdiff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index ef0d119..352a30e 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -8,7 +8,7 @@ import gzip dir_yaml = 'yaml' -date = '2020.07.05' +date = '2020.07.09' # Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D) # Query on SRA: 'txid2697049[Organism:noexp] NOT 0[Mbases ' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism:noexp%5D%20NOT%200[Mbases) @@ -50,13 +50,14 @@ sra_metadata_xml_file.close() EXPERIMENT_PACKAGE_SET = tree.getroot() missing_value_list = [] +not_created_accession_list = [] run_accession_set = set() run_accession_to_downloadble_file_url_dict = {} for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): #print(i, EXPERIMENT_PACKAGE) - + # A general default-empty yaml could be read from the definitive one info_for_yaml_dict = { 'id': 'placeholder', @@ -74,17 +75,17 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): #print(accession) info_for_yaml_dict['sample']['sample_id'] = accession - + #SRAFiles = RUN.find('SRAFiles') #if SRAFiles is not None: # url = SRAFiles.find('SRAFile').attrib['url'] # if 'sra-download.ncbi.nlm.nih.gov' in url: # run_accession_to_downloadble_file_url_dict[accession] = url - + SAMPLE = EXPERIMENT_PACKAGE.find('SAMPLE') SAMPLE_ATTRIBUTE_list = SAMPLE.iter('SAMPLE_ATTRIBUTE') - + for SAMPLE_ATTRIBUTE in SAMPLE_ATTRIBUTE_list: VALUE = SAMPLE_ATTRIBUTE.find('VALUE') if VALUE is not None: @@ -101,7 +102,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): missing_value_list.append('\t'.join([accession, 'host_species', VALUE_text])) elif TAG_text in ['host_health_status', 'host health state']: if VALUE_text in term_to_uri_dict: - info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[VALUE_text] + info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[VALUE_text] elif VALUE_text.strip("'") not in ['missing', 'not collected', 'not provided']: missing_value_list.append('\t'.join([accession, 'host_health_status', VALUE_text])) elif TAG_text in ['strain', 'isolate']: @@ -113,12 +114,12 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if value_to_insert in term_to_uri_dict: value_to_insert = term_to_uri_dict[value_to_insert] - - if 'virus_strain' not in info_for_yaml_dict: + + if 'virus_strain' not in info_for_yaml_dict: info_for_yaml_dict['virus']['virus_strain'] = value_to_insert else: info_for_yaml_dict['virus']['virus_strain'] += '; ' + value_to_insert - elif TAG_text in ['isolation_source', 'isolation source host-associated']: + elif TAG_text in ['isolation_source', 'isolation source host-associated']: if VALUE_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[VALUE_text]] else: @@ -145,7 +146,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): elif TAG_text == 'collected_by': if VALUE_text.lower() not in ['not available', 'missing']: name = VALUE_text in ['Dr. Susie Bartlett', 'Ahmed Babiker', 'Aisi Fu', 'Brandi Williamson', 'George Taiaroa', 'Natacha Ogando', 'Tim Dalebout', 'ykut Ozdarendeli'] - + info_for_yaml_dict['sample']['collector_name' if name else 'collecting_institution'] = VALUE_text elif TAG_text == 'collecting institution': if VALUE_text.lower() not in ['not provided', 'na']: @@ -154,11 +155,11 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if VALUE_text.lower() not in ['not applicable', 'missing', 'na']: date_to_write = VALUE_text date_is_estimated = True - + VALUE_text_list = VALUE_text.split('-') if len(VALUE_text_list) == 3: date_is_estimated = False - + if VALUE_text_list[1].isalpha(): date_to_write = parse(VALUE_text).strftime('%Y-%m-%d') elif len(VALUE_text_list) == 2: @@ -170,7 +171,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): date_to_write = "{}-01-15".format(VALUE_text) info_for_yaml_dict['sample']['collection_date'] = date_to_write - + if date_is_estimated: if 'additional_collection_information' in info_for_yaml_dict['sample']: info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(VALUE_text) @@ -188,8 +189,8 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): taxon_id = SAMPLE.find('SAMPLE_NAME').find('TAXON_ID').text info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+taxon_id - - + + EXPERIMENT = EXPERIMENT_PACKAGE.find('EXPERIMENT') INSTRUMENT_MODEL = [x.text for x in EXPERIMENT.find('PLATFORM').iter('INSTRUMENT_MODEL')][0] @@ -206,18 +207,18 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): SUBMISSION = EXPERIMENT_PACKAGE.find('SUBMISSION') info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession'] - + if SUBMISSION.attrib['lab_name'].lower() not in ['na']: info_for_yaml_dict['submitter']['originating_lab'] = SUBMISSION.attrib['lab_name'] - STUDY = EXPERIMENT_PACKAGE.find('STUDY') + STUDY = EXPERIMENT_PACKAGE.find('STUDY') info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias'] - - + + Organization = EXPERIMENT_PACKAGE.find('Organization') Organization_Name = Organization.find('Name') info_for_yaml_dict['submitter']['authors'] = [Organization_Name.text] - + Organization_Contact = Organization.find('Contact') if Organization_Contact is not None: Organization_Contact_Name = Organization_Contact.find('Name') @@ -231,20 +232,33 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): Organization_Address = Organization.find('Address') if Organization_Address is not None: info_for_yaml_dict['submitter']['lab_address'] = '; '.join([x.text for x in Organization_Address] + ['Postal code ' + Organization_Address.attrib['postal_code']]) - + if 'collection_date' not in info_for_yaml_dict['sample']: info_for_yaml_dict['sample']['collection_date'] = '1970-01-01' info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing" if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: - print(accession, ' - technology not found') + #print(accession, ' - technology not found') + not_created_accession_list.append([accession, 'technology not found']) + continue + + if 'host_species' not in info_for_yaml_dict['host']: + #print(accession, ' - technology not found') + not_created_accession_list.append([accession, 'missing host species']) continue with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw: json.dump(info_for_yaml_dict, fw, indent=2) - + if len(missing_value_list) > 0: - path_missing_terms_tsv = 'missing_terms.tsv' + path_missing_terms_tsv = 'missing_terms.sra.tsv' print('Written missing terms in {}'.format(path_missing_terms_tsv)) with open(path_missing_terms_tsv, 'w') as fw: fw.write('\n'.join(missing_value_list)) + +if len(not_created_accession_list) > 0: + path_not_created_accession_tsv = 'not_created_accession.sra.tsv' + print('Written not created accession in {}'.format(path_not_created_accession_tsv)) + with open(path_not_created_accession_tsv, 'w') as fw: + fw.write('\n'.join(['\t'.join(x) for x in not_created_accession_list])) + diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv index 40572a3..0bfc455 100644 --- a/scripts/dict_ontology_standardization/ncbi_host_species.csv +++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv @@ -2,6 +2,7 @@ Homo sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606 human,http://purl.obolibrary.org/obo/NCBITaxon_9606 Human,http://purl.obolibrary.org/obo/NCBITaxon_9606 sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606 +homosapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606 Mustela lutreola,http://purl.obolibrary.org/obo/NCBITaxon_9666 Manis javanica,http://purl.obolibrary.org/obo/NCBITaxon_9974 Felis catus,http://purl.obolibrary.org/obo/NCBITaxon_9685 diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py index 39e401a..dbebfbb 100755 --- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py +++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py @@ -138,6 +138,7 @@ min_len_to_count = 27500 num_seq_with_len_ge_X_bp = 0 missing_value_list = [] +not_created_accession_list = [] accession_with_errors_list = [] for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata) if name_metadata_xxx_xml.endswith('.xml')]: @@ -371,7 +372,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: - print(accession_version, ' - technology not found') + #print(accession_version, ' - technology not found') + not_created_accession_list.append([accession_version, 'technology not found']) continue with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw: @@ -389,15 +391,21 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) continue if len(missing_value_list) > 0: - path_missing_terms_tsv = 'missing_terms.tsv' + path_missing_terms_tsv = 'missing_terms.genbank.tsv' print('Written missing terms in {}'.format(path_missing_terms_tsv)) with open(path_missing_terms_tsv, 'w') as fw: fw.write('\n'.join(missing_value_list)) if len(accession_with_errors_list) > 0: - path_accession_with_errors_tsv = 'accession_with_errors.tsv' + path_accession_with_errors_tsv = 'accession_with_errors.genbank.tsv' print('Written the accession with errors in {}'.format(path_accession_with_errors_tsv)) with open(path_accession_with_errors_tsv, 'w') as fw: fw.write('\n'.join(accession_with_errors_list)) +if len(not_created_accession_list) > 0: + path_not_created_accession_tsv = 'not_created_accession.genbank.tsv' + print('Written not created accession in {}'.format(path_not_created_accession_tsv)) + with open(path_not_created_accession_tsv, 'w') as fw: + fw.write('\n'.join(['\t'.join(x) for x in not_created_accession_list])) + print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp)) |
