diff options
| -rw-r--r-- | bh20simplewebuploader/api.py | 40 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/ebi-sample.xml | 4 | ||||
| -rw-r--r-- | test/rest-api.org | 14 |
3 files changed, 52 insertions, 6 deletions
diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py index 29fa2b8..ff82b72 100644 --- a/bh20simplewebuploader/api.py +++ b/bh20simplewebuploader/api.py @@ -7,13 +7,51 @@ import sys from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify from bh20simplewebuploader.main import app, baseURL +# Helper functions + +def fetch_sample_metadata(id): + query = """ + PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> + PREFIX sio: <http://semanticscience.org/resource/> + PREFIX edam: <http://edamontology.org/> + PREFIX efo: <http://www.ebi.ac.uk/efo/> + select distinct ?id ?seq ?info ?sequencer + { + ?sample sio:SIO_000115 "%s" . + ?sample sio:SIO_000115 ?id . + ?seq pubseq:technology ?tech . + ?seq pubseq:sample ?sample . + ?sample edam:data_2091 ?info . + ?tech efo:EFO_0002699 ?sequencer . + } limit 5 + """ % id + payload = {'query': query, 'format': 'json'} + r = requests.get(baseURL, params=payload) + return r.json()['results']['bindings'] + +# Main API routes + @app.route('/api/version') def version(): return jsonify({ 'service': 'PubSeq', 'version': 0.10 }) +@app.route('/api/sample/<id>.json') +def sample(id): + # metadata = file.name(seq)+"/metadata.yaml" + meta = fetch_sample_metadata(id) + return jsonify([{ + 'id': x['id']['value'], + 'fasta': x['seq']['value'], + 'collection': os.path.dirname(x['seq']['value']), + 'info': x['info']['value'], + 'sequencer': x['sequencer']['value'], + } for x in meta]) + @app.route('/api/ebi/sample-<id>.xml', methods=['GET']) def ebi_sample(id): - page = render_template('ebi-sample.xml',**locals()) + meta = fetch_sample_metadata(id)[0] + print("HERE",meta,file=sys.stderr) + page = render_template('ebi-sample.xml',sampleid=id,sequencer=meta['sequencer']['value']) return page @app.route('/api/search', methods=['GET']) diff --git a/bh20simplewebuploader/templates/ebi-sample.xml b/bh20simplewebuploader/templates/ebi-sample.xml index 441e29e..0b6b39e 100644 --- a/bh20simplewebuploader/templates/ebi-sample.xml +++ b/bh20simplewebuploader/templates/ebi-sample.xml @@ -1,6 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <SAMPLE_SET> - <SAMPLE alias="{{ id }}" center_name="COVID-19 PubSeq"> + <SAMPLE alias="{{ sampleid }}" center_name="COVID-19 PubSeq"> <TITLE>COVID-19 PubSeq Sample</TITLE> <SAMPLE_NAME> <TAXON_ID>2697049</TAXON_ID> @@ -14,7 +14,7 @@ </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>sequencing method</TAG> - <VALUE>{{ sequence_method }}</VALUE> + <VALUE>{{ sequencer }}</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>collection date</TAG> diff --git a/test/rest-api.org b/test/rest-api.org index 1930d8b..6dd6616 100644 --- a/test/rest-api.org +++ b/test/rest-api.org @@ -53,12 +53,11 @@ When you use the search box on PubSeq it queries the REST end point for information on the search items. For example #+begin_src python :session :exports both -requests.get(baseURL+"/api/search?s=MT326090.1").json() +requests.get(baseURL+"/api/search?s=MT533203.1").json() #+end_src #+RESULTS: -| collection | : | http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126/sequence.fasta | id | : | MT326090.1 | info | : | http://identifiers.org/insdc/MT326090.1#sequence | -| collection | : | http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126/sequence.fasta | id | : | MT326090.1 | info | : | http://identifiers.org/insdc/MT326090.1#sequence | +| collection | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta | id | : | MT533203.1 | info | : | http://identifiers.org/insdc/MT533203.1#sequence | where collection is the raw uploaded data. The hash value in ~c=~ is computed on the contents of the Arvados keep [[https://doc.arvados.org/v2.0/user/tutorials/tutorial-keep-mount-gnu-linux.html][collection]] and effectively @@ -66,10 +65,19 @@ acts as a deduplication uuid. ** Fetch metadata +Using above collection link you can fetch the metadata in JSON as it +was uploaded originally from the SHeX expression, e.g. using +https://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/ + +But better to use the more advanced sample metadata fetcher +because is does a bit more in terms of expansion #+begin_src python :session :exports both +requests.get(baseURL+"/api/sample/MT533203.1.json").json() #+end_src +#+RESULTS: + ** Fetch EBI XML |