diff options
| -rw-r--r-- | bh20simplewebuploader/main.py | 211 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/main.css | 18 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/main.js | 84 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/demo.html | 22 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/menu.html | 2 |
5 files changed, 325 insertions, 12 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 0495613..27dcd4b 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -949,8 +949,8 @@ def getSEQCountbyLocation(): @app.route('/api/getSEQCountbyContinent', methods=['GET']) def getSEQCountbyContinent(): query="""SELECT DISTINCT ?continent ?continent_label (count(?fasta) as ?fastaCount) WHERE { - ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] . - ?location <http://www.wikidata.org/prop/direct/P17> ?country . + ?fasta ?x [ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] . + ?location <http://www.wikidata.org/prop/direct/P17> ?country . ?country <http://www.wikidata.org/prop/direct/P30> ?continent . OPTIONAL { ?continent rdfs:label ?key_tmp_label } BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?continent_label) @@ -1064,3 +1064,210 @@ def getSEQbyLocationAndSpecimenSource(): r = requests.get(sparqlURL, params=payload) result = r.json()['results']['bindings'] return str(result) + + +################## SPARQL PLAYGORUND API function ################ + +@app.route('/api/demoGetSEQCountbySpecimenSource', methods=['GET']) +def demoGetSEQCountbySpecimenSource(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" + + query="""SELECT ?specimen_source ?specimen_source_label (count(?seq) as ?seqCount) WHERE + { + ?seq ?x [obo:OBI_0001479 ?specimen_source] . + ?specimen_source rdfs:label ?specimen_source_label + } + GROUP BY ?specimen_source ?specimen_source_label + ORDER BY DESC (?seqCount) + """ + + description="Get the count of all sequences, grouped by specimen source and specimen label (This is a 1-to-1 relationship). In addition we want to order by the sequence count descending." + payload = {'query': prefix+query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + + return jsonify([{'description' : description},{'prefix' : prefix}, {'query': query}],[{'count': x['seqCount']['value'], + 'key': x['specimen_source']['value'], + 'label': x['specimen_source_label']['value']} for x in result]) + + +@app.route('/api/demoGetSEQCountbyLocation', methods=['GET']) +def demoGetSEQCountbyLocation(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" + + query=""" + SELECT ?geoLocation ?geoLocation_label (count(?seq) as ?seqCount) WHERE + { + ?seq ?x [obo:GAZ_00000448 ?geoLocation] . + ?geoLocation rdfs:label ?geoLocation_label + } + GROUP BY ?geoLocation ?geoLocation_label + """ + description = "Get count of all sequences grouped by geoLocation and geoLocation_label (1-to-1 relationship)" + payload = {'query': prefix+query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description' : description},{'prefix' : prefix}, {'query': query}],[{'count': x['seqCount']['value'], + 'key': x['geoLocation']['value'], + 'label': x['geoLocation_label']['value']} for x in result]) + + + +@app.route('/api/demoGetAuthors', methods=['GET']) +def demoGetAuthors(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX wiki: <http://www.wikidata.org/prop/direct/>""" + + query = """SELECT DISTINCT ?author ?country_label ?continent_label WHERE { + ?fasta ?x [ obo:GAZ_00000448 ?location] . + ?fasta ?y [ obo:NCIT_C42781 ?author] . + + ?location wiki:P17 ?country . + ?country wiki:P30 ?continent . + ?country rdfs:label ?country_label . + ?continent rdfs:label ?continent_label + } + ORDER BY ?author + LIMIT 500 + """ + + description = "Get all autors (obo:NCIT_C42781) that are in the DB and the country/continent where their samples were taken. The result is limited to 500." + payload = {'query': prefix+query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description' : description},{'prefix' : prefix}, {'query': query}],[{'author': x['author']['value'], + 'country_label': x['country_label']['value'], + 'continent_label': x['continent_label']['value']} for x in result]) + + +@app.route('/api/demoInstitutesPublications', methods=['GET']) +def demoInstitutesPublications(): + prefix="PREFIX obo: <http://purl.obolibrary.org/obo/>" + query=""" + SELECT DISTINCT ?originating_lab ?publication WHERE { + ?seq ?x [ obo:NCIT_C37984 ?originating_lab] . + ?seq ?y [ obo:NCIT_C19026 ?publication] . + } + """ + + description = "List institutes (originating_lab, obo:NCIT_C37984) associated their publications in the DB" + payload = {'query': prefix+query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description' : description},{'prefix' : prefix}, {'query': query}],[{'originating_lab': x['originating_lab']['value'], + 'publication': x['publication']['value']} for x in result]) + + + +@app.route('/api/demoGetSEQCountbytechContinent', methods=['GET']) +def demoGetSEQCountbytechContinent(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX wiki: <http://www.wikidata.org/prop/direct/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" + + query="""SELECT DISTINCT ?continent_label ?tech_label (count(?seq) as ?seqCount) WHERE + { + ?seq ?x [ obo:OBI_0600047 ?tech] . + ?seq ?y [ obo:GAZ_00000448 ?location] . + + ?tech rdfs:label ?tech_label . + + ?location wiki:P17 ?country . + ?country wiki:P30 ?continent . + ?continent rdfs:label ?continent_label + } + + GROUP BY ?tech_label ?continent_label + ORDER BY ?continent_label ?seqCount + """ + + description = "List institutes (originating_lab, obo:NCIT_C37984) and their associated publications in the DB" + payload = {'query': prefix+query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description' : description},{'prefix' : prefix}, {'query': query}],[{'continent_label': x['continent_label']['value'], + 'tech_label': x['tech_label']['value'], 'seqCount': x['seqCount']['value']} for x in result]) + + +@app.route('/api/demoGetSEQCountbytech', methods=['GET']) +def dempGetSEQCountbytech(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" + + query="""SELECT ?tech ?tech_label (count(?seq) as ?seqCount) WHERE + { + ?seq ?x [obo:OBI_0600047 ?tech] . + ?tech rdfs:label ?tech_label + } + GROUP BY ?tech ?tech_label ORDER BY DESC (?seqCount) + """ + description = "Show count per sequence technology" + payload = {'query': prefix + query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}], + [{'tech_label': x['tech_label']['value'], + 'tech': x['tech']['value'], 'seqCount': x['seqCount']['value']} for x in result]) + + +@app.route('/api/demoGetSequencePerDate', methods=['GET']) +def demoGetSequencePerDate(): + prefix="" + query="""SELECT ?seq ?date WHERE { + ?seq ?a [<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date] + FILTER ( xsd:date(?date) < xsd:date("2020-03-01") ) + } + ORDER BY ?date""" + description = "Show all sequences with a submission date before 2020-03-01! To accomplish this a FILTER expression is used. Since date is a string, we cast xsd:date(...)" + payload = {'query': prefix + query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}], + [{'seq': x['seq']['value'], + 'date': x['date']['value']} for x in result]) + +@app.route('/api/demoLocationGps', methods=['GET']) +def demoLocationGps(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX wiki: <http://www.wikidata.org/prop/direct/>""" + + query="""SELECT distinct ?location ?GPS WHERE { + ?seq ?a [ obo:GAZ_00000448 ?location] . + ?location wiki:P625 ?GPS + } + """ + description = "Show all locations with their GPS coordinates that we have in the database. GPS coordinates are encoded as Point tuple." + payload = {'query': prefix + query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}], + [{'location': x['location']['value'], + 'GPS': x['GPS']['value']} for x in result]) + +@app.route('/api/getNYsamples', methods=['GET']) +def getNYsamples(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX wikiE: <http://www.wikidata.org/entity/>""" + + query="""SELECT DISTINCT ?seq ?key_label ?key ?value_label ?value WHERE { + ?seq ?x [ obo:GAZ_00000448 wikiE:Q1384] . + ?seq ?y [?key ?value] . + + ?key rdfs:label ?key_label . + ?value rdfs:label ?value_label + } + ORDER BY ?seq""" + + description = "Get all samples and their information (key, values) that were taken in New York (Q1384)!" + payload = {'query': prefix + query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}], + [{'seq': x['seq']['value'], + 'key_label': x['key_label']['value'], + 'key': x['key']['value'], + 'value_label': x['value_label']['value'], + 'value': x['value']['value']} for x in result])
\ No newline at end of file diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css index 76a1755..36c1a33 100644 --- a/bh20simplewebuploader/static/main.css +++ b/bh20simplewebuploader/static/main.css @@ -533,3 +533,21 @@ div.status { border-bottom: 2px solid white; padding-bottom: 20px; } + + + +/* SPARQL playground CSS*/ +#playground { +margin-left: 20px; +} + +#playground table{ +border: 1px solid black; +min-height: 400px; +} + +#playground td{ +border: 1px solid black; +padding-left:10px; +padding-right:10px; +} diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js index 6cc0d9f..0e642c1 100644 --- a/bh20simplewebuploader/static/main.js +++ b/bh20simplewebuploader/static/main.js @@ -83,6 +83,48 @@ function fetchHTMLTable(apiEndPoint) { }); } + + +// changing access for Demo page +function demofetchHTMLTable(apiEndPoint) { + fetch(scriptRoot + apiEndPoint) + .then(response => { + return response.json(); + }) + .then(data => { + htmlString="<h3>Description</h3><p>"+data[0][0]["description"]+"</p>" + prefix=data[0][1]["prefix"].replaceAll("<","<") + htmlString+="<h4>Namespace</h4><pre>"+prefix+"</pre>"//prefix to construct correct query @data[0][1]["prefix"] + htmlString+="<h3>SPARQL query</h3><pre>"+data[0][2]["query"]+"</pre>" + htmlString+="<h3>SPARQL results table</h3><table>" + + keys=Object.keys(data[1][0]) + // Add keys as table headers + htmlString+="<tr>" + for (var j=0; j<keys.length;j++){ + htmlString+="<td style='font-weight: bold;'>"+keys[j]+"</bold></td>" + } + + //Go through the results set given the keys and fill the tail of the table + for (var i=0; i<data[1].length;i++) { + htmlString+="</tr><tr>" + for (var j=0; j<keys.length;j++){ + htmlString+="<td>"+data[1][i][keys[j]]+"</td>" + } + htmlString+="</tr>" + } + htmlString=htmlString+"</table>" + + //Something like this would be nice, hm + //htmlString+="Execute this query <a href='http://sparql.genenetwork.org/sparql?query='"+encodeURIComponent(encodeURIComponent(data[0][1]["prefix"]+data[0][2]["query"]))+"'>here</a>" + + document.getElementById("playground").innerHTML = htmlString + }); +} + + + + /* Fetch record info using a 'global search'. Returns for example [ @@ -122,14 +164,50 @@ let fetchCountDB = () => { fetchAPI("/api/getCountDB"); } -let fetchSEQCountBySpecimen = () => { - fetchHTMLTable("/api/getSEQCountbySpecimenSource"); + +//****** SPARQL playground functions // keep old functionality as comments for now, might be transfered elsewhere +let fetchSEQCountBySpecimen = (toHTML) => { + //fetchHTMLTable("/api/getSEQCountbySpecimenSource"); + demofetchHTMLTable("/api/demoGetSEQCountbySpecimenSource") } let fetchSEQCountByLocation = () => { - fetchHTMLTable("/api/getSEQCountbyLocation"); + //fetchHTMLTable("/api/getSEQCountbyLocation"); + demofetchHTMLTable("/api/demoGetSEQCountbyLocation") +} + +//Get authors and there country/contitent where they come from +let fetchAuthors = () => { + demofetchHTMLTable("/api/demoGetAuthors") +} + +// Fetch all institutes/originating labs and their associeted publications +let fetchInstitutesPublications = () => { + demofetchHTMLTable("/api/demoInstitutesPublications") +} + +//Fetch seqeenctechnologies used by continent +let demoGetSEQCountbytechContinent = () => { + demofetchHTMLTable("/api/demoGetSEQCountbytechContinent") +} + +let demoGetSEQCountbytech = () => { + demofetchHTMLTable("/api/demoGetSEQCountbytech") +} + +let demoGetSequencePerDate = () => { + demofetchHTMLTable('/api/demoGetSequencePerDate') +} + +let demoLocationGps = () => { + demofetchHTMLTable("/api/demoLocationGps") +} + +let getNYsamples = () => { + demofetchHTMLTable("/api/getNYsamples") } +//old/unused functions let fetchSEQCountByTech = () => { fetchHTMLTable("/api/getSEQCountbytech"); } diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html index 1edca00..ffebc91 100644 --- a/bh20simplewebuploader/templates/demo.html +++ b/bh20simplewebuploader/templates/demo.html @@ -5,7 +5,7 @@ {% include 'banner.html' %} {% include 'menu.html' %} - <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences! The examples here should provide a starting point to explore our data in our public <a href="http://sparql.genenetwork.org/sparql">SPARQL endpoint</a> or via <a href="https://covid-19-sparql.expasy.org/">SIB COVID-19 Integrated Knowledgebase</a>. See also our documentation <a href="http://127.0.0.1:5000/blog?id=using-covid-19-pubseq-part1">here</a> for more information!</p> + <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences! The examples here should provide a starting point to explore our data in our public <a href="http://sparql.genenetwork.org/sparql">SPARQL endpoint</a> or via <a href="https://covid-19-sparql.expasy.org/">SIB COVID-19 Integrated Knowledgebase</a>. See also our documentation <a href="http://covid-19.genenetwork.org/blog?id=using-covid-19-pubseq-part1">here</a> for more information!</p> <!-- <div class="search"> <input id="search-input" type="search" placeholder="FASTA uri" required> @@ -21,11 +21,21 @@ <section class="search-section"> <div class="filter-options" action="#"> <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="demoGetSEQCountbytech()">Count by Sequencer</button> + <button class="button" onclick="fetchInstitutesPublications()">Get list of publications</button> + <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button> + <button class="button" onclick="demoGetSEQCountbytechContinent()">Sequence Technologies used by continent</button> + <button class="button" onclick="getNYsamples()">Get all NY samples</button> + <button class="button" onclick="fetchAuthors()">Get authors</button> + <button class="button" onclick="demoGetSequencePerDate()">Show Sequences before submission date</button> + <button class="button" onclick="demoLocationGps()">Locations and their GPS</button> + + + + + <!-- <button class="button" onclick="fetchAllaccessions()">Show All accessions</button> + <button class="button" onclick="fetchSEQCountbyContinent()">Count by Continent</button>--> </div> </div> @@ -36,7 +46,7 @@ <section> - <div id="table"></div> + <div id="playground"></div> </section> {% include 'footer.html' %} diff --git a/bh20simplewebuploader/templates/menu.html b/bh20simplewebuploader/templates/menu.html index 8e6ef52..cf32fec 100644 --- a/bh20simplewebuploader/templates/menu.html +++ b/bh20simplewebuploader/templates/menu.html @@ -4,7 +4,7 @@ <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="/demo" class="{{ 'active' if menu=='DEMO' }}">SPARQL-PLAYGROUND</a> <a href="/export" class="{{ 'active' if menu=='EXPORT' }}">EXPORT</a> <a href="/blog" class="{{ 'active' if menu=='BLOG' }}">DOCS</a> <a href="/about" class="{{ 'active' if menu=='ABOUT' }}">ABOUT</a> |