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--- bh20simplewebuploader/main.py | 86 ++++++++++++++++------------- bh20simplewebuploader/static/main.css | 17 ++++-- bh20simplewebuploader/templates/footer.html | 5 +- 3 files changed, 64 insertions(+), 44 deletions(-) (limited to 'bh20simplewebuploader/static') diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 3173d60..62b68d9 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 +50,8 @@ 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) @@ -78,7 +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. @@ -101,9 +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 @@ -131,14 +133,25 @@ 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 + optional = False + is_list = False + + 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): # It may have documentation docstring = field_type.get('doc', None) @@ -161,25 +174,13 @@ def generate_form(schema, options): 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] + 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 @@ -227,15 +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 -if os.path.isfile("bh20sequploader/bh20seq-schema.yml"): - METADATA_SCHEMA = yaml.safe_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.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml")) - METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml")) -# print(METADATA_SCHEMA,file=sys.stderr) -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(): @@ -543,10 +553,10 @@ def status_page(): for s in (("passed", "/download"), ("pending", "#pending"), ("rejected", "#rejected")): output.write("

" % (s[1], status.get(s[0], 0), s[0])) - output.write("

Pending

") + output.write("

Pending

") pending_table(output, out) - output.write("

Rejected

") + output.write("

Rejected

") rejected_table(output, out) return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS') diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css index 47fb408..b28ee9c 100644 --- a/bh20simplewebuploader/static/main.css +++ b/bh20simplewebuploader/static/main.css @@ -178,7 +178,7 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; } .about { 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 { diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html index 37a6b64..5a1f3c9 100644 --- a/bh20simplewebuploader/templates/footer.html +++ b/bh20simplewebuploader/templates/footer.html @@ -21,11 +21,14 @@

-- cgit 1.4.1 From 2c1a907cbfe222d1deed8c31a44d3ea4c382bc3c Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 17 Jul 2020 08:00:48 +0100 Subject: Add Curii svg --- bh20simplewebuploader/static/image/curii.logo.ai.svg | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 bh20simplewebuploader/static/image/curii.logo.ai.svg (limited to 'bh20simplewebuploader/static') diff --git a/bh20simplewebuploader/static/image/curii.logo.ai.svg b/bh20simplewebuploader/static/image/curii.logo.ai.svg new file mode 100644 index 0000000..e87ea05 --- /dev/null +++ b/bh20simplewebuploader/static/image/curii.logo.ai.svg @@ -0,0 +1,3 @@ + + + \ No newline at end of file -- cgit 1.4.1 From d3fa51ee16d902fc0bfa414611d5e0bae6618009 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 17 Jul 2020 09:09:23 +0100 Subject: Refactoring map code --- bh20simplewebuploader/main.py | 7 +- bh20simplewebuploader/static/main.js | 149 ++++++++------------------ bh20simplewebuploader/static/map.js | 67 ++++++++++++ bh20simplewebuploader/templates/demo-run.html | 26 ----- bh20simplewebuploader/templates/demo.html | 30 +++++- bh20simplewebuploader/templates/footer.html | 3 + bh20simplewebuploader/templates/header.html | 18 ---- bh20simplewebuploader/templates/map.html | 24 ++++- 8 files changed, 164 insertions(+), 160 deletions(-) create mode 100644 bh20simplewebuploader/static/map.js (limited to 'bh20simplewebuploader/static') diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 1147176..e8bb507 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -628,7 +628,7 @@ def validated_page(): @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(): @@ -644,11 +644,6 @@ def about_page(): 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/main.js b/bh20simplewebuploader/static/main.js index 4703047..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: '© OpenStreetMap', - 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("" + label + "
" + "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="" - - // 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" - } - htmlString=htmlString+"

"+data[i]["label"]+"

"+data[i]["count"]+"

" - - 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="" + + // 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" + } +*/ + for (var i=0; i" + } + htmlString=htmlString+"

"+data[i]["label"]+"	"+data[i]["count"]+"
"+data[i]["label"]+"	"+data[i]["count"]+"

" + + 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"); } @@ -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: '© OpenStreetMap contributors' -}).addTo(mymap); - -fetch(scriptRoot + "api/getCountByGPS") - .then(response => { - console.log(response) - return response.json(); - }) - .then(data => { - - for (var i=0; iOpenStreetMap', + subdomains: ['a','b','c'] +}).addTo( map ); + +let markers = L.markerClusterGroup().addTo(map) + + +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: '© OpenStreetMap contributors' +}).addTo(mymap); + +fetch(scriptRoot + "api/getCountByGPS") + .then(response => { + console.log(response) + return response.json(); + }) + .then(data => { + + for (var i=0; i" + label + "
" + "FastaCount: " +fastaCount); + markers.addLayer(marker) + }} + // Reload the map + map.invalidateSize(); + document.getElementById("map_view").classList.add("invisible"); + document.getElementById("loader").classList.add("invisible"); +} diff --git a/bh20simplewebuploader/templates/demo-run.html b/bh20simplewebuploader/templates/demo-run.html index a8f9edc..e69de29 100644 --- a/bh20simplewebuploader/templates/demo-run.html +++ b/bh20simplewebuploader/templates/demo-run.html @@ -1,26 +0,0 @@ -

- - -

- -

diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html index 44aded0..2e290c6 100644 --- a/bh20simplewebuploader/templates/demo.html +++ b/bh20simplewebuploader/templates/demo.html @@ -5,8 +5,34 @@ {% include 'banner.html' %} {% include 'menu.html' %} {% include 'search.html' %} -

The Virtuoso database contains public sequences!

- {% include 'demo-run.html' %} +

The Virtuoso database contains public sequences!

+ +

+ + +

+ +

+ {% include 'footer.html' %} +{% endif %} - - diff --git a/bh20simplewebuploader/templates/map.html b/bh20simplewebuploader/templates/map.html index 595af0c..4aa22b9 100644 --- a/bh20simplewebuploader/templates/map.html +++ b/bh20simplewebuploader/templates/map.html @@ -1,7 +1,26 @@ {% include 'header.html' %} - + + + + + + + + + @@ -11,9 +30,6 @@ {% include 'footer.html' %} - - - -- cgit 1.4.1 From 7565f72b1bf0d70426947a50d1b9a62edc48071d Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 17 Jul 2020 09:45:58 +0100 Subject: Map is back --- bh20simplewebuploader/static/main.css | 2 +- bh20simplewebuploader/static/map.js | 71 +++++++++++++++---------------- bh20simplewebuploader/templates/demo.html | 27 +++++++++++- bh20simplewebuploader/templates/map.html | 49 --------------------- 4 files changed, 61 insertions(+), 88 deletions(-) (limited to 'bh20simplewebuploader/static') diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css index b28ee9c..9f89045 100644 --- a/bh20simplewebuploader/static/main.css +++ b/bh20simplewebuploader/static/main.css @@ -47,7 +47,7 @@ h2 > svg { float: right; } -#map { +#mapid { width: 800px; height: 440px; border: 1px solid #AAA; diff --git a/bh20simplewebuploader/static/map.js b/bh20simplewebuploader/static/map.js index afc6c3f..e1a4289 100644 --- a/bh20simplewebuploader/static/map.js +++ b/bh20simplewebuploader/static/map.js @@ -1,43 +1,40 @@ -let map = L.map( 'map', { - center: [37.0902, -95.7129], // Default to U.S.A - minZoom: 3, - zoom: 0 + +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: '© OpenStreetMap', - subdomains: ['a','b','c'] -}).addTo( map ); + attribution: '© OpenStreetMap', + subdomains: ['a','b','c'] +}).addTo(map); -let markers = L.markerClusterGroup().addTo(map) +var markers = L.markerClusterGroup().addTo(mapid) function drawMap(){ + var mymap = map; -// 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: '© OpenStreetMap contributors' -}).addTo(mymap); - -fetch(scriptRoot + "api/getCountByGPS") - .then(response => { - console.log(response) - return response.json(); - }) - .then(data => { - - for (var i=0; i { + console.log(response) + return response.json(); + }) + .then(data => { + for (var i=0; i" + label + "
" + "FastaCount: " +fastaCount); - markers.addLayer(marker) + // markers.addLayer(marker) }} + */ // Reload the map map.invalidateSize(); - document.getElementById("map_view").classList.add("invisible"); - document.getElementById("loader").classList.add("invisible"); + // document.getElementById("map_view").classList.add("invisible"); + // document.getElementById("loader").classList.add("invisible"); } diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html index 2e290c6..3a80abf 100644 --- a/bh20simplewebuploader/templates/demo.html +++ b/bh20simplewebuploader/templates/demo.html @@ -1,10 +1,30 @@ {% include 'header.html' %} + + + + + + + + + {% include 'banner.html' %} {% include 'menu.html' %} {% include 'search.html' %} +

The Virtuoso database contains public sequences!

@@ -26,14 +46,14 @@