diff options
| -rw-r--r-- | Dockerfile | 2 | ||||
| -rw-r--r-- | bh20seqanalyzer/main.py | 41 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 27 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 15 | ||||
| -rw-r--r-- | bh20simplewebuploader/main.py | 119 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/main.css | 26 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/footer.html | 14 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 49 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/home.html | 50 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/menu.html | 4 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/resource.html | 27 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/status.html | 17 |
12 files changed, 296 insertions, 95 deletions
diff --git a/Dockerfile b/Dockerfile index 43fa8f2..1901ac7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,7 +13,7 @@ ADD bh20seqanalyzer /app/bh20simplewebuploader ADD bh20sequploader /app/bh20sequploader ADD bh20simplewebuploader /app/bh20simplewebuploader -RUN pip3 install -e . +RUN pip3 install -e .[web] ENV PORT 8080 CMD ["gunicorn", "-w", "4", "-b", "0.0.0.0:8080", "bh20simplewebuploader.main:app"] diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 1746587..0b52e6b 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -17,10 +17,11 @@ logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="% logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN) def validate_upload(api, collection, validated_project, - fastq_project, fastq_workflow_uuid): + fastq_project, fastq_workflow_uuid, + revalidate): col = arvados.collection.Collection(collection["uuid"]) - if collection.get("status") in ("validated", "rejected"): + if not revalidate and collection["properties"].get("status") in ("validated", "rejected"): return False # validate the collection here. Check metadata, etc. @@ -28,11 +29,12 @@ def validate_upload(api, collection, validated_project, errors = [] - 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 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: @@ -70,12 +72,15 @@ def validate_upload(api, collection, validated_project, if not errors: - logging.info("Added '%s' to validated sequences" % collection["name"]) # 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()))}).execute() + "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 @@ -155,7 +160,9 @@ def start_pangenome_analysis(api, validated_project, schema_ref, exclude_list): - validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]]) + validated = arvados.util.list_all(api.collections().list, filters=[ + ["owner_uuid", "=", validated_project], + ["properties.status", "=", "validated"]]) inputobj = { "inputReads": [], "metadata": [], @@ -187,14 +194,15 @@ def get_workflow_output_from_project(api, uuid): cr = api.container_requests().list(filters=[['owner_uuid', '=', uuid], ["requesting_container_uuid", "=", None]]).execute() if cr["items"] and cr["items"][0]["output_uuid"]: - return cr["items"][0] - else: - return None + 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", limit=1).execute() + order="created_at desc").execute() for m in most_recent_analysis["items"]: wf = get_workflow_output_from_project(api, m["uuid"]) if wf: @@ -220,6 +228,7 @@ def move_fastq_to_fasta_results(api, analysis_project, uploader_project): body={"owner_uuid": uploader_project}).execute() p["properties"]["moved_output"] = True api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute() + break def upload_schema(api, workflow_def_project): @@ -297,6 +306,7 @@ def main(): parser.add_argument('--no-start-analysis', action="store_true") parser.add_argument('--once', action="store_true") parser.add_argument('--print-status', type=str, default=None) + parser.add_argument('--revalidate', action="store_true", default=None) args = parser.parse_args() api = arvados.api() @@ -330,7 +340,8 @@ def main(): at_least_one_new_valid_seq = validate_upload(api, c, args.validated_project, args.fastq_project, - args.fastq_workflow_uuid) or at_least_one_new_valid_seq + 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, diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index fd0278d..f744a8c 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -19,8 +19,10 @@ log = logging.getLogger(__name__ ) log.debug("Entering sequence uploader") ARVADOS_API_HOST='lugli.arvadosapi.com' -ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' +UPLOADER_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' +ANONYMOUS_API_TOKEN='5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh' UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' +VALIDATED_PROJECT='lugli-j7d0g-5ct8p1i1wrgyjvp' def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): failed = False @@ -67,9 +69,14 @@ def main(): parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, nargs='?', help='sequence FASTQ pair') parser.add_argument("--validate", action="store_true", help="Dry run, validate only") parser.add_argument("--skip-qc", action="store_true", help="Skip local qc check") + parser.add_argument("--trusted", action="store_true", help="Trust local validation and add directly to validated project") args = parser.parse_args() - api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) + if args.trusted: + # Use credentials from environment + api = arvados.api() + else: + api = arvados.api(host=ARVADOS_API_HOST, token=UPLOADER_API_TOKEN, insecure=True) target = qc_stuff(args.metadata, args.sequence_p1, args.sequence_p2, not args.skip_qc) seqlabel = target[0][1] @@ -106,7 +113,21 @@ def main(): "upload_user": "%s@%s" % (username, socket.gethostname()) } - col.save_new(owner_uuid=UPLOAD_PROJECT, name="%s uploaded by %s from %s" % + api2 = arvados.api(host=ARVADOS_API_HOST, token=ANONYMOUS_API_TOKEN, insecure=True) + dup = api2.collections().list(filters=[["owner_uuid", "in", [VALIDATED_PROJECT, UPLOAD_PROJECT]], + ["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"]])) + exit(1) + + if args.trusted: + properties["status"] = "validated" + owner_uuid = VALIDATED_PROJECT + else: + owner_uuid = UPLOAD_PROJECT + + col.save_new(owner_uuid=owner_uuid, name="%s uploaded by %s from %s" % (seqlabel, properties['upload_user'], properties['upload_ip']), properties=properties, ensure_unique_name=True) diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index 2b57991..27657b1 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -8,15 +8,20 @@ import traceback from rdflib import Graph, Namespace from pyshex.evaluate import evaluate +metadata_schema = None def qc_metadata(metadatafile): + global metadata_schema log = logging.getLogger(__name__ ) - schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") - cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")} + if metadata_schema is None: + schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") + cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")} + metadata_schema = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache) + (document_loader, avsc_names, schema_metadata, - metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache) + metaschema_loader) = metadata_schema shex = pkg_resources.resource_stream(__name__, "bh20seq-shex.rdf").read().decode("utf-8") @@ -27,6 +32,10 @@ def qc_metadata(metadatafile): g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx) rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape") + # As part of QC make sure serialization works too, this will raise + # an exception if there are invalid URIs. + g.serialize(format="ntriples") + if not rslt: raise Exception(reason) diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 3100dfd..9132453 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -13,12 +13,20 @@ import pkg_resources from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify import os.path import requests +import io +import arvados +from markupsafe import Markup + +ARVADOS_API = 'lugli.arvadosapi.com' +ANONYMOUS_TOKEN = '5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh' +UPLOADER_PROJECT = 'lugli-j7d0g-n5clictpuvwk8aa' +VALIDATED_PROJECT = 'lugli-j7d0g-5ct8p1i1wrgyjvp' logging.basicConfig(level=logging.DEBUG) log = logging.getLogger(__name__ ) log.debug("Entering web uploader") -if not os.path.isfile('bh20sequploader/mainx.py'): +if not os.path.isfile('bh20sequploader/main.py'): print("WARNING: run FLASK from the root of the source repository!", file=sys.stderr) app = Flask(__name__, static_url_path='/static', static_folder='static') @@ -224,12 +232,21 @@ METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20 FORM_ITEMS = generate_form(METADATA_SCHEMA, METADATA_OPTION_DEFINITIONS) @app.route('/') +def send_home(): + """ + Send the front page. + """ + + return render_template('home.html', menu='HOME') + + +@app.route('/upload') def send_form(): """ Send the file upload form/front page. """ - return render_template('form.html', fields=FORM_ITEMS, menu='HOME') + return render_template('form.html', fields=FORM_ITEMS, menu='UPLOAD') class FileTooBigError(RuntimeError): """ @@ -405,7 +422,7 @@ def receive_files(): # Try and upload files to Arvados using the sequence uploader CLI - cmd = ['python3','bh20sequploader/main.py', fasta_dest, metadata_dest] + cmd = ['python3','bh20sequploader/main.py', metadata_dest, fasta_dest] print(" ".join(cmd),file=sys.stderr) result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) @@ -439,7 +456,83 @@ def get_html_body(fn): @app.route('/download') def download_page(): buf = get_html_body('doc/web/download.html') - return render_template('about.html',menu='DOWNLOAD',embed=buf) + return render_template('resource.html',menu='DOWNLOAD',embed=buf) + +def pending_table(output, items): + output.write( +""" +<table> +<tr><th>Collection</th> +<th>Sequence label</th></tr> +""") + 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>") + output.write( +""" +</table> +""") + +def rejected_table(output, items): + output.write( +""" +<table> +<tr><th>Collection</th> +<th>Sequence label</th> +<th>Errors</th></tr> +""") + for r in items: + 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["sequence_label"])) + output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", [])))) + output.write("</tr>") + output.write( +""" +</table> +""") + + +@app.route('/status') +def status_page(): + """ + Processing status + """ + + api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN) + 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 + + 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")): + 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>") + pending_table(output, out) + + output.write("<a id='rejected'><h1>Rejected</h1>") + rejected_table(output, out) + + return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS') @app.route('/demo') def demo_page(): @@ -474,20 +567,10 @@ baseURL='http://sparql.genenetwork.org/sparql/' @app.route('/api/getCount', methods=['GET']) def getCount(): - query=""" -PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> -select (COUNT(distinct ?dataset) as ?num) -{ - ?dataset pubseq:submitter ?id . - ?id ?p ?submitter -} -""" - payload = {'query': query, 'format': 'json'} - r = requests.get(baseURL, params=payload) - result = r.json()['results']['bindings'] - # [{'num': {'type': 'typed-literal', 'datatype': 'http://www.w3.org/2001/XMLSchema#integer', 'value': '1352'}}] - # print(result, file=sys.stderr) - return jsonify({'sequences': int(result[0]["num"]["value"])}) + api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN) + c = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute() + + return jsonify({'sequences': c["items_available"]}) @app.route('/api/getAllaccessions', methods=['GET']) def getAllaccessions(): diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css index 5a9f231..b9b27f4 100644 --- a/bh20simplewebuploader/static/main.css +++ b/bh20simplewebuploader/static/main.css @@ -168,11 +168,11 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; } grid-template-rows: auto; row-gap:5px; grid-template-areas: - "a a b b" - "a a c c" - "a a d d" - "e e e e" - "f f f f"; + "b b a a" + "b b c c" + "b b d d" + "e e e e" + "f f f f"; grid-auto-flow: column; } @@ -361,3 +361,19 @@ footer { .blog-table-body { display: table-row-group; } + +div.status { + margin: 1em; +} + +.status table { + display: table; + width: 100%; +} + +.status td, th { + padding-left: 1em; + padding-right: 1em; + vertical-align: top; + border-bottom: 1px solid #ddd; +} diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html index 9326b1e..a1dd4fd 100644 --- a/bh20simplewebuploader/templates/footer.html +++ b/bh20simplewebuploader/templates/footer.html @@ -41,3 +41,17 @@ </div> </section> <script type="text/javascript" src="/static/main.js"></script> + +<script type="text/javascript"> + document.addEventListener("DOMContentLoaded", function(){ + var count = fetch("/api/getCount") + .then((resp) => resp.json()) + .then(function (data) { + count = data["sequences"]; + console.log(count); + span = document.getElementById("Counter"); + txt = document.createTextNode(count); + span.appendChild(txt); + }); + }); +</script> diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html index 0ad2080..b9b3776 100644 --- a/bh20simplewebuploader/templates/form.html +++ b/bh20simplewebuploader/templates/form.html @@ -7,43 +7,6 @@ <section> <form action="/submit" method="POST" enctype="multipart/form-data" id="main_form" class="grid-container"> - <div class="intro"> - <p> - Make your sequence - data <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR</a>. Upload - your SARS-CoV-2 sequence (FASTA or FASTQ - formats) with metadata (JSONLD) to - the <a href="/about">public sequence - resource</a>. The upload will trigger a - recompute with all available sequences into a - Pangenome available for - <a href="/download">download</a>! - </p> - <p> - Your uploaded sequence will automatically be - processed and incorporated into the public - pangenome with metadata using worklows from - the High Performance Open Biology Lab - defined <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. All - data is published under - a <a href="https://creativecommons.org/licenses/by/4.0/">Creative - Commons license</a> You can take the published - (GFA/RDF/FASTA) data and store it in a triple - store for further processing. Clinical - data can be stored - securely - at <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>. - </p> - <p> - Note that form fields contain - web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">ontology - URI's</a> - for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a> - and machine readable metadata. For examples of - use, see the <a href="/blog">BLOG</a>. - </p> - </div> - <div class="fasta-file-select"> <h2><svg class="bi bi-cloud-upload" width="1.2em" height="1.2em" viewBox="0 0 16 16" fill="currentColor" xmlns="http://www.w3.org/2000/svg"> <path d="M4.887 6.2l-.964-.165A2.5 2.5 0 103.5 11H6v1H3.5a3.5 3.5 0 11.59-6.95 5.002 5.002 0 119.804 1.98A2.501 2.501 0 0113.5 12H10v-1h3.5a1.5 1.5 0 00.237-2.981L12.7 7.854l.216-1.028a4 4 0 10-7.843-1.587l-.185.96z"/> @@ -160,18 +123,6 @@ setMode() - document.addEventListener("DOMContentLoaded", function(){ - var count = fetch("/api/getCount") - .then((resp) => resp.json()) - .then(function (data) { - count = data["sequences"]; - console.log(count); - span = document.getElementById("Counter"); - txt = document.createTextNode(count); - span.appendChild(txt); - }); -}); - </script> </body> diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html new file mode 100644 index 0000000..b90a18d --- /dev/null +++ b/bh20simplewebuploader/templates/home.html @@ -0,0 +1,50 @@ +<!DOCTYPE html> +<html> + {% include 'header.html' %} + <body> + {% include 'banner.html' %} + {% include 'menu.html' %} + + <section> + <div class="intro"> + <p> + Make your sequence + data <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR</a>. Upload + your SARS-CoV-2 sequence (FASTA or FASTQ + formats) with metadata (JSONLD) to + the <a href="/about">public sequence + resource</a>. The upload will trigger a + recompute with all available sequences into a + Pangenome available for + <a href="/download">download</a>! + </p> + <p> + Your uploaded sequence will automatically be + processed and incorporated into the public + pangenome with metadata using worklows from + the High Performance Open Biology Lab + defined <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. All + data is published under + a <a href="https://creativecommons.org/licenses/by/4.0/">Creative + Commons license</a> You can take the published + (GFA/RDF/FASTA) data and store it in a triple + store for further processing. Clinical + data can be stored + securely + at <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>. + </p> + <p> + Note that form fields contain + web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">ontology + URI's</a> + for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a> + and machine readable metadata. For examples of + use, see the <a href="/blog">BLOG</a>. + </p> + </div> + </section> + +{% include 'footer.html' %} + + </body> +</html> diff --git a/bh20simplewebuploader/templates/menu.html b/bh20simplewebuploader/templates/menu.html index 6f97e19..0f6003f 100644 --- a/bh20simplewebuploader/templates/menu.html +++ b/bh20simplewebuploader/templates/menu.html @@ -1,7 +1,9 @@ <section class="menu"> <div class="topnav" id="myTopnav"> - <a href="/" class="{{ 'active' if menu=='HOME' }}">COVID-19</a> + <a href="/" class="{{ 'active' if menu=='HOME' }}">PUBSEQ</a> <a href="/download" class="{{ 'active' if menu=='DOWNLOAD' }}">DOWNLOAD</a> + <a href="/upload" class="{{ 'active' if menu=='UPLOAD' }}">UPLOAD</a> + <a href="/status" class="{{ 'active' if menu=='STATUS' }}">STATUS</a> <a href="/demo" class="{{ 'active' if menu=='DEMO' }}">DEMO</a> <a href="/blog" class="{{ 'active' if menu=='BLOG' }}">BLOG</a> <a href="/about" class="{{ 'active' if menu=='ABOUT' }}">ABOUT</a> diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html new file mode 100644 index 0000000..91b6c20 --- /dev/null +++ b/bh20simplewebuploader/templates/resource.html @@ -0,0 +1,27 @@ +<!DOCTYPE html> +<html> + {% include 'header.html' %} + <body> + {% include 'banner.html' %} + {% include 'menu.html' %} + + <div class="status"> + <p><img src="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.png" height="300px"></p> + <p><a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-5ct8p1i1wrgyjvp#Data_collections">All sequences project</a></p> + <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup.fasta">All sequences (FASTA) relabled and deduplicated</a></p> + <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">Metadata (RDF) for all sequences</a></p> + <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p> + <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.gfa">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p> + <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.ttl.xz">All sequences in RDF using spodgi</a> - <a href="https://github.com/pangenome/spodgi">More about spodgi</a></p> + + + <p><a href="http://sparql.genenetwork.org/sparql/">SPARQL endpoint</a> - <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=SELECT+DISTINCT+%3Ffasta+%3Fvalue+WHERE+%7B%3Ffasta+%3Fx%5B+%3Chttp%3A%2F%2Fedamontology.org%2Fdata_2091%3E+%3Fvalue+%5D%7D%0D%0A&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+">Sample query for accessions</a> + + {{ embed|safe }} + + </div> + +{% include 'footer.html' %} + + </body> +</html> diff --git a/bh20simplewebuploader/templates/status.html b/bh20simplewebuploader/templates/status.html new file mode 100644 index 0000000..a1cf28f --- /dev/null +++ b/bh20simplewebuploader/templates/status.html @@ -0,0 +1,17 @@ +<!DOCTYPE html> +<html> + {% include 'header.html' %} + <body> + {% include 'banner.html' %} + {% include 'menu.html' %} + + <h1>Sequence upload processing status</h1> + + <div class="status"> + {{ table }} + </div> + +{% include 'footer.html' %} + + </body> +</html> |