Merge branch 'master' into yamlfa2ttl

15 files changed, 348 insertions, 137 deletions

diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py
index b1b505f..761ad03 100644
--- a/bh20simplewebuploader/api.py
+++ b/bh20simplewebuploader/api.py
@@ -3,20 +3,26 @@
 import os
 import requests
 import sys
+import types
 
 from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
 from bh20simplewebuploader.main import app, sparqlURL
 
+PUBSEQ="http://covid19.genenetwork.org"
+ARVADOS="https://collections.lugli.arvadosapi.com/c="
+
 # Helper functions
 
-def fetch_sample_metadata(id):
-    query = """
+def fetch_sample(id, query=None):
+    default_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/>
     PREFIX evs: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
     PREFIX obo: <http://purl.obolibrary.org/obo/>
+
     select distinct ?id ?seq ?date ?info ?specimen ?sequencer ?mapper
     {
       ?sample sio:SIO_000115 "%s" ;
@@ -24,15 +30,49 @@ def fetch_sample_metadata(id):
               evs:C25164 ?date .
       ?seq    pubseq:technology ?tech ;
               pubseq:sample ?sample .
-      ?tech   efo:EFO_0002699 ?mapper ;
-              obo:OBI_0600047 ?sequencer .
+      optional { ?tech   efo:EFO_0002699 ?mapper } .
+      optional { ?tech   obo:OBI_0600047 ?sequencer . }
       optional { ?sample edam:data_2091 ?info } .
       optional { ?sample obo:OBI_0001479 ?specimen } .
     } limit 5
+
     """ % id
+    if not query: query = default_query
+    print(query)
     payload = {'query': query, 'format': 'json'}
     r = requests.get(sparqlURL, params=payload)
-    return r.json()['results']['bindings']
+    res = r.json()
+    print(res)
+    return res['results']['bindings'],res['head']['vars']
+
+def fetch_one_sample(id, query=None):
+    """Get the top sample and return a SimpleNamespace"""
+
+    result,varlist = fetch_sample(id,query)
+    h = {}
+    row = result[0]
+    for key in varlist:
+        if key in row:
+            h[key] = row[key]['value']
+    print(h)
+    h['arv_id'] = os.path.basename(h['seq'])
+    return types.SimpleNamespace(**h)
+
+def fetch_one_record(id):
+    m = fetch_one_sample(id)
+    arv_id = m.arv_id
+    rec = { "id": id,
+            'arv_id': arv_id,
+            "permalink": PUBSEQ+'/resource/'+id,
+            "collection": m.seq,
+            'collection_date': m.date,
+            'fasta': ARVADOS+arv_id+'/sequence.fasta',
+            'metadata': ARVADOS+arv_id+'/metadata.yaml',
+    }
+    h = m.__dict__ # for optional items
+    if 'mapper' in h: rec['mapper'] = m.mapper
+    if 'sequencer' in h: rec['sequencer']= m.sequencer
+    return rec
 
 # Main API routes
 
@@ -42,54 +82,40 @@ def version():
 
 @app.route('/api/sample/<id>.json')
 def sample(id):
-    # metadata = file.name(seq)+"/metadata.yaml"
-    meta = fetch_sample_metadata(id)
-    print(meta)
-    return jsonify([{
-        'id': x['id']['value'],
-        'fasta': x['seq']['value'],
-        'collection': os.path.dirname(x['seq']['value']),
-        'date': x['date']['value'],
-        'info': x['info']['value'],
-        'specimen': x['specimen']['value'],
-        'sequencer': x['sequencer']['value'],
-        'mapper': x['mapper']['value'],
-    } for x in meta])
+    """
+
+API sample should return a record pointing to other resources,
+notably: permalink, original metadata record and the fasta
+data.
+
+curl http://localhost:5067/api/sample/MT533203.1.json
+{
+  "id": "MT533203.1",
+  "permalink": "http://covid19.genenetwork.org/resource/MT533203.1",
+  "collection": "http://covid19.genenetwork.org/resource/lugli-4zz18-uovend31hdwa5ks",
+  "collection_date": "2020-04-27",
+  "fasta": "https://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/sequence.fasta",
+  "metadata": "https://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/metadata.yaml",
+  "mapper": "minimap v. 2.17",
+  "sequencer": "http://www.ebi.ac.uk/efo/EFO_0008632"
+}
+
+"""
+
+    return jsonify([fetch_one_record(id)])
 
 @app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
 def ebi_sample(id):
-    meta = fetch_sample_metadata(id)[0]
+    meta,varlist = fetch_sample(id)[0]
     page = render_template('ebi-sample.xml',sampleid=id,sequencer=meta['sequencer']['value'],date=meta['date']['value'],specimen=meta['specimen']['value'])
     return page
 
 @app.route('/api/search', methods=['GET'])
 def search():
     """
-    Execute a 'global search'
+    Execute a 'global search'. Currently just duplicates fetch one
+    sample. Should be more flexible FIXME.
     """
     s = request.args.get('s')
-    if s == "":
-        s = "MT326090.1"
-    query = """
-    PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
-    PREFIX sio: <http://semanticscience.org/resource/>
-    PREFIX edam: <http://edamontology.org/>
-    select distinct ?id ?seq ?info
-    {
-    ?sample sio:SIO_000115 "%s" .
-    ?sample sio:SIO_000115 ?id .
-    ?seq pubseq:sample ?sample .
-    ?sample edam:data_2091 ?info .
-    } limit 100
-    """ % s
-    payload = {'query': query, 'format': 'json'}
-    r = requests.get(sparqlURL, params=payload)
-    result = r.json()['results']['bindings']
-    # metadata = file.name(seq)+"/metadata.yaml"
-    print(result)
-    return jsonify([{
-        'id': x['id']['value'],
-        'fasta': x['seq']['value'],
-        'collection': os.path.dirname(x['seq']['value']),
-        'info': x['info']['value'],
-    } for x in result])
+    if s == "": s = "MT326090.1"
+    return jsonify([fetch_one_record(s)])
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index b620946..504f03c 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -34,6 +34,7 @@ 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')
+app.config['JSON_SORT_KEYS'] = False
 
 # Limit file upload size. We shouldn't be working with anything over 1 MB; these are small genomes.
 # We will enforce the limit ourselves and set a higher safety limit here.
@@ -252,7 +253,7 @@ FORM_ITEMS = load_schema_generate_form()
 def get_feed_items(name, start=0, stop=9):
     redis_client = redis.Redis(host=os.environ.get('HOST', 'localhost'),
                                port=os.environ.get('PORT', 6379),
-                               db=os.environ.get('REDIS_DB', 0))    
+                               db=os.environ.get('REDIS_DB', 0))
     feed_items = []
     try:
         for el in redis_client.zrevrange(name, start, stop):
@@ -272,12 +273,23 @@ def send_home():
     """
     Send the front page.
     """
+    (tweets,
+     commits,
+     pubmed_articles,
+     arxiv_articles) = [get_feed_items(x) for x in ["bh20-tweet-score:",
+                                                    "bh20-commit-score:",
+                                                    "bh20-pubmed-score:",
+                                                    "bh20-arxiv-score:"]]
     return render_template(
         'home.html', menu='HOME',
-        tweets=get_feed_items("bh20-tweet-score:"),
-        commits=get_feed_items("bh20-commit-score:"),
-        pubmed_articles=get_feed_items("bh20-pubmed-score:"),
-        arxiv_articles=get_feed_items("bh20-arxiv-score:"),
+        all_items=list(itertools.chain(tweets,
+                                       commits,
+                                       pubmed_articles,
+                                       arxiv_articles)),
+        tweets=tweets,
+        commits=commits,
+        pubmed_articles=pubmed_articles,
+        arxiv_articles=arxiv_articles,
         load_map=True)
 
 
@@ -750,8 +762,8 @@ union
     # http://covid19.genenetwork.org/resource/lugli-4zz18-gx0ifousk9yu0ql
     m = re.match(r"http://collections.lugli.arvadosapi.com/c=([^/]*)/sequence.fasta|http://covid19.genenetwork.org/resource/(.*)", sequenceuri)
     collection = m.group(1) or m.group(2)
-    fastauri = f"http://collections.lugli.arvadosapi.com/c={collection}/sequence.fasta"
-    metauri = f"http://collections.lugli.arvadosapi.com/c={collection}/metadata.yaml"
+    fastauri = f"https://collections.lugli.arvadosapi.com/c={collection}/sequence.fasta"
+    metauri = f"https://collections.lugli.arvadosapi.com/c={collection}/metadata.yaml"
     locationuri=sample['geo']['value']
     location=sample['geoname']['value']
     date=sample['date']['value']
diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css
index fbc721e..e2f0c83 100644
--- a/bh20simplewebuploader/static/main.css
+++ b/bh20simplewebuploader/static/main.css
@@ -567,6 +567,7 @@ input[name="feed-tabs"] ~ .tab {
     display: none;
 }
 
+#tab-all-items:checked ~ .tab.content-all-items,
 #tab-pubmed-articles:checked ~ .tab.content-pubmed-articles,
 #tab-arxiv-articles:checked ~ .tab.content-arxiv-articles,
 #tab-tweets:checked ~ .tab.content-tweets,
diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html
index a880f81..23f48bf 100644
--- a/bh20simplewebuploader/templates/home.html
+++ b/bh20simplewebuploader/templates/home.html
@@ -29,7 +29,9 @@
                       </div>
 
                       <div id="feed">
-                          <input name="feed-tabs" type="radio" id="tab-arxiv-articles" checked/>
+                          <input name="feed-tabs" type="radio" id="tab-all-items" checked/>
+                          <label for="tab-all-items">All Items</label>
+                          <input name="feed-tabs" type="radio" id="tab-arxiv-articles"/>
                           <label for="tab-arxiv-articles">Arxiv</label>
                           <input name="feed-tabs" type="radio" id="tab-pubmed-articles"/>
                           <label for="tab-pubmed-articles">Pubmed</label>
@@ -37,6 +39,73 @@
                           <label for="tab-tweets">Tweets</label>
                           <input name="feed-tabs" type="radio" id="tab-commits"/>
                           <label for="tab-commits">Commits</label>
+                          <ul class="tab content-all-items">
+                              <!-- Begin News -->
+                                  {% if all_items %}
+                                  {% for item in all_items|sort(reverse=true, attribute="score")%}
+                                  <li>
+                                      {% if item['authors'] %}
+                                      <!-- Arxiv article -->
+                                      <p>
+                                          <b>[arxiv]</b>
+                                          <a href="{{ item['url'] }}" target="_blank">
+                                              {{item['title']}}
+                                          </a>
+                                          <br/>
+                                          <b>Authors:</b> {{ item['authors'] }}
+                                          <br/>
+                                          <b>Abstract:</b> {{ item['abstract']}}...
+                                          <br/>
+                                          <b>Submitted:</b> {{ item['submission']}}
+                                      </p>
+
+                                      {% elif item['full-authors'] %}
+                                      <!-- Pubmed Article -->
+                                      <p><b>[Pubmed]:</b>
+                                          <a href="https://pubmed.ncbi.nlm.nih.gov/{{ item['docsum-pmid'] }}" target="_blank"><b>Summary:</b>
+                                              {{ item['summary'] }}
+                                          </a> <br/>
+                                          <b>Full Authors:</b> {{ item['full-authors'] }} <br/>
+                                          <b>Short Authors:</b> {{ item['short-authors'] }} <br/>
+                                          <b>Citation:</b> {{ item['citation'] }} <br/>
+                                          <b>Short Journal Citation:</b> {{ item['short-journal-citation'] }} <br/>
+                                      </p>
+
+                                      {% elif item['tweet'] %}
+                                      <!-- Tweets -->
+                                      <p>
+                                          <b>[Tweet]:</b>
+                                          {{ item['tweet']|urlize(40, target="_blank")}}
+                                          <small>
+                                              <a href="{{ item['url'] }}" target="_blank">source</a></small>
+                                          <br/>
+                                          by {{ item['author'] }}
+                                          <br/>
+                                          <small>{{ item['timeposted'] }}</small>
+                                      </p>
+
+                                      {% elif item['repository-url'] %}
+                                      <!-- Commits -->
+                                      <p>
+                                          <b>[Commit]:</b>
+                                          <a href="{{ item.url }}" target="_blank">
+                                              {{ item.hash.split(":")[-1][:7] }}: {{ item.content }}
+                                          </a>
+                                          <br/>
+                                          <small>
+                                              <a href="{{ item['repository-url'] }}" target="_blank"> {{ item.author }}/{{ item.repository }}</a>
+                                              on {{ item.timeposted }}
+                                          </small>
+                                      </p>
+                                      {% endif %}
+                                  </li>
+                                  {%endfor%}
+
+                                  {% else %}
+                                  There are no items to display :(
+                                  {% endif %}
+                              <!-- End News -->
+                          </ul>
                           <ul class="tab content-arxiv-articles">
                               {% if arxiv_articles %}
                               {% for article in arxiv_articles|sort(reverse=true, attribute="score")%}
diff --git a/example/esr_example.yaml b/example/esr_example.yaml
index c97d0bf..c7bdb30 100644
--- a/example/esr_example.yaml
+++ b/example/esr_example.yaml
@@ -15,7 +15,7 @@ sample:
     collection_date: "2020-02-26"
     collection_location: https://www.wikidata.org/wiki/Q37100
     specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831]
-    source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence] ??
+    source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence]
     additional_collection_information: Optional free text field for additional information
 
 virus:
@@ -23,7 +23,7 @@ virus:
     virus_strain: SARS-CoV-2/human/CHN/HS_8/2020
 
 technology:
-    sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION
+    sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] # Nanopore MinION
     alignment_protocol: https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics
     assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
     additional_technology_information: "Artic V3 workflow"
diff --git a/example/uthsc_example.yaml b/example/uthsc_example.yaml
index 661cf60..589a7a5 100644
--- a/example/uthsc_example.yaml
+++ b/example/uthsc_example.yaml
@@ -23,7 +23,7 @@ virus:
     virus_strain: SARS-CoV-2/human/USA/AL_UT14/2020
 
 technology:
-    sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION
+    sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] # Nanopore MinION
     alignment_protocol: guppy
     assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
     additional_technology_information: Optional free text field for additional information
diff --git a/test/rest-api.org b/test/rest-api.org
index 66639c3..2ea2b11 100644
--- a/test/rest-api.org
+++ b/test/rest-api.org
@@ -36,6 +36,35 @@ curl http://covid19.genenetwork.org/api/version
 }
 #+end_src
 
+The current API can fetch data
+
+#+begin_src js
+curl http://covid19.genenetwork.org/api/search?s=MT533203.1
+[
+  {
+    "collection": "http://covid19.genenetwork.org/resource",
+    "fasta": "http://covid19.genenetwork.org/resource/lugli-4zz18-uovend31hdwa5ks",
+    "id": "MT533203.1",
+    "info": "http://identifiers.org/insdc/MT533203.1#sequence"
+  }
+]
+
+curl http://covid19.genenetwork.org/api/sample/MT533203.1.json
+[
+  {
+    "collection": "http://covid19.genenetwork.org/resource",
+    "date": "2020-04-27",
+    "fasta": "http://covid19.genenetwork.org/resource/lugli-4zz18-uovend31hdwa5ks",
+    "id": "MT533203.1",
+    "info": "http://identifiers.org/insdc/MT533203.1#sequence",
+    "mapper": "minimap v. 2.17",
+    "sequencer": "http://www.ebi.ac.uk/efo/EFO_0008632",
+    "specimen": "http://purl.obolibrary.org/obo/NCIT_C155831"
+  }
+]
+#+end_src
+
+
 The Python3 version is
 
 #+begin_src python :session :exports both
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md
index 5464d1d..188ff6f 100644
--- a/workflows/pull-data/genbank/README.md
+++ b/workflows/pull-data/genbank/README.md
@@ -11,7 +11,8 @@ The following workflow sends GenBank data into PubSeq
 
 ```sh
 # --- get list of IDs already in PubSeq
-../../tools/sparql-fetch-ids > pubseq_ids.txt
+../../tools/pubseq-fetch-ids > pubseq_ids.txt
+
 # --- get list of missing genbank IDs
 python3 genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt
 
@@ -26,6 +27,13 @@ python3 ../../workflows/tools/normalize-yamlfa.py -s ~/tmp/yamlfa/state.json --s
 
 ```
 
+## Validate GenBank data
+
+To pull the data from PubSeq use the list of pubseq ids generated
+above.
+
+
+
 # TODO
 
-- [ ] Add id for GenBank accession - i.e. how can we tell a record is from GenBank
+- [X] Add id for GenBank accession - i.e. how can we tell a record is from GenBank
diff --git a/workflows/pull-data/genbank/genbank-fetch-ids.py b/workflows/pull-data/genbank/genbank-fetch-ids.py
index 1962daa..e9e7315 100755
--- a/workflows/pull-data/genbank/genbank-fetch-ids.py
+++ b/workflows/pull-data/genbank/genbank-fetch-ids.py
@@ -6,28 +6,19 @@
 #
 # See also directory .guix-run and README.md
 
-BATCH_SIZE=5000
-
 import argparse
-import json
-import os
-import requests
 import sys
-import xml.etree.ElementTree as ET
-from datetime import date, datetime
-from dateutil.parser import parse
+
+from Bio import Entrez
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--max', type=int, help='Max queries', required=False)
 parser.add_argument('--skip', type=str, help='File with ids to skip, 1 id per line', required=False)
 args = parser.parse_args()
 
-from Bio import Entrez
-Entrez.email = 'another_email@gmail.com' # FIXME
-
-# min_acceptable_collection_date = datetime(2019, 12, 1)
+BATCH_SIZE = 5000
 
-today_date = date.today().strftime("%Y.%m.%d")
+Entrez.email = 'another_email@gmail.com'  # FIXME
 
 skip = set()
 if args.skip:
@@ -36,10 +27,11 @@ if args.skip:
         for line in content:
             skip.add(line.strip())
 
-print(f"Skip size is {len(skip)}",file=sys.stderr)
+print(f"Skip size is {len(skip)}", file=sys.stderr)
 
 # Try to search several strings
 TERMS = ['SARS-CoV-2', 'SARS-CoV2', 'SARS CoV2', 'SARSCoV2', 'txid2697049[Organism]']
+
 # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq) starting with
 PREFIX = ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']
 
@@ -47,22 +39,27 @@ ids = set()
 for term in TERMS:
     num_read = BATCH_SIZE
     retstart = 0
+
     while num_read == BATCH_SIZE:
         record = Entrez.read(
-            Entrez.esearch(db='nuccore', term=term, idtype='acc',
-                           retstart=retstart, retmax=BATCH_SIZE)
+            Entrez.esearch(db='nuccore', term=term, idtype='acc', retstart=retstart, retmax=BATCH_SIZE)
         )
+
         idlist = record['IdList']
         new_ids = set(idlist)
         num_read = len(new_ids)
-        print(num_read,":",idlist[0],file=sys.stderr)
         retstart += num_read
-        new_ids.difference_update(skip) # remove skip ids
+
+        print(num_read, ":", idlist[0], file=sys.stderr)
+
+        new_ids.difference_update(skip)  # remove skip ids
         new_ids = set([id for id in new_ids if id[:2] not in PREFIX])
-        ids.update(new_ids)             # add to total set
-        print(f"Term: {term} --> #{len(new_ids)} new IDs ---> Total unique IDs #{len(ids)})",file=sys.stderr)
+        ids.update(new_ids)  # add to total set
+
+        print(f"Term: {term} --> #{len(new_ids)} new IDs ---> Total unique IDs #{len(ids)}", file=sys.stderr)
+
         if args.max and len(ids) > args.max:
-            print(f"Stopping past #{args.max} items",file=sys.stderr)
+            print(f"Stopping past #{args.max} items", file=sys.stderr)
             break
 
 for id in ids:
diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py
index 85d615c..026c03f 100644
--- a/workflows/pull-data/genbank/genbank.py
+++ b/workflows/pull-data/genbank/genbank.py
@@ -111,7 +111,8 @@ def get_metadata(id, gbseq):
         # print(n,file=sys.stderr)
         if n != 'Unpublished':
             institute,address = n.split(',',1)
-            submitter.submitter_name = institute.split(') ')[1]
+            if ")" in institute:
+                submitter.submitter_name = institute.split(')')[1]
             submitter.submitter_address = address.strip()
     except AttributeError:
         pass
diff --git a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
index 9414864..1a8035d 100755
--- a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
+++ b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
@@ -33,43 +33,47 @@ states = {}
 
 for xmlfn in args.files:
     print(f"--- Reading {xmlfn}")
-    with gzip.open(xmlfn, 'r') as f:
-        xml = f.read().decode()
-        tree = ET.fromstring(xml)
-        for gb in tree.findall('./GBSeq'):
-            valid = None
-            error = None
-            meta = {}
-            id = gb.find("GBSeq_locus").text
-            basename = dir+"/"+id
-            print(f"    parsing {id}")
-            try:
-                valid,meta = genbank.get_metadata(id,gb)
-                if valid:
-                    # --- write JSON
-                    jsonfn = basename + ".json"
-                    with open(jsonfn, 'w') as outfile:
-                        print(f"    writing {jsonfn}")
-                        json.dump(meta, outfile, indent=4)
-                    # --- write FASTA
-                    fa = basename+".fa"
-                    seq = genbank.get_sequence(id,gb)
-                    print(f"    writing {fa}")
-                    with open(fa,"w") as f2:
-                        f2.write(f"> {id}\n")
-                        f2.write(seq)
-                    # print(seq)
-            except genbank.GBError as e:
-                error = f"{e} for {id}"
-                print(error,file=sys.stderr)
-                valid = False
-            state = {}
-            state['valid'] = valid
-            if error:
-                state['error'] = error
-            if meta['warnings']:
-                state['warnings'] = meta['warnings']
-            states[id] = state
+    try:
+        with gzip.open(xmlfn, 'r') as f:
+            xml = f.read().decode()
+    except Exception:
+        with open(xmlfn, 'r') as f:
+            xml = f.read()
+    tree = ET.fromstring(xml)
+    for gb in tree.findall('./GBSeq'):
+        valid = None
+        error = None
+        meta = {}
+        id = gb.find("GBSeq_locus").text
+        basename = dir+"/"+id
+        print(f"    parsing {id}")
+        try:
+            valid,meta = genbank.get_metadata(id,gb)
+            if valid:
+                # --- write JSON
+                jsonfn = basename + ".json"
+                with open(jsonfn, 'w') as outfile:
+                    print(f"    writing {jsonfn}")
+                    json.dump(meta, outfile, indent=4)
+                # --- write FASTA
+                fa = basename+".fa"
+                seq = genbank.get_sequence(id,gb)
+                print(f"    writing {fa}")
+                with open(fa,"w") as f2:
+                    f2.write(f"> {id}\n")
+                    f2.write(seq)
+                # print(seq)
+        except genbank.GBError as e:
+            error = f"{e} for {id}"
+            print(error,file=sys.stderr)
+            valid = False
+        state = {}
+        state['valid'] = valid
+        if error:
+            state['error'] = error
+        if meta['warnings']:
+            state['warnings'] = meta['warnings']
+        states[id] = state
 
 statefn = dir + '/state.json'
 with open(statefn, 'w') as outfile:
diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/update-from-genbank.py
index dca5563..95f5a93 100755
--- a/workflows/pull-data/genbank/update-from-genbank.py
+++ b/workflows/pull-data/genbank/update-from-genbank.py
@@ -14,22 +14,21 @@ import sys
 from utils import chunks
 
 from Bio import Entrez
-Entrez.email = 'another_email@gmail.com' # FIXME
 
-BATCH=100
+Entrez.email = 'another_email@gmail.com'  # FIXME
+
+BATCH = 100
 
 parser = argparse.ArgumentParser()
-parser.add_argument('--max', type=int, help='Max queries', required=False)
 parser.add_argument('--ids', type=str, help='File with ids to fetch, 1 id per line', required=True)
 parser.add_argument('--out', type=str, help='Directory to write to', required=True)
+parser.add_argument('--max', type=int, help='Max queries', required=False)
 
 args = parser.parse_args()
 
 ids = set()
 with open(args.ids) as f:
-    content = f.readlines()
-    for line in content:
-        ids.add(line.strip())
+    ids.update([line.strip() for line in f])
 
 dir = args.out
 if not os.path.exists(dir):
@@ -37,12 +36,14 @@ if not os.path.exists(dir):
 
 request_num = BATCH
 if args.max:
-  request_num = min(BATCH,args.max)
+    request_num = min(BATCH, args.max)
+
+for num_chunk, ids_chunk in enumerate(chunks(list(ids), request_num)):
+    xmlfn = os.path.join(dir, f"metadata_{num_chunk}.xml.gz")
+    print(f"Fetching {xmlfn} ({num_chunk * request_num})", file=sys.stderr)
 
-for i, idsx in enumerate(chunks(list(ids), request_num)):
-    xmlfn = os.path.join(dir, f"metadata_{i}.xml.gz")
-    print(f"Fetching {xmlfn} ({i*request_num})",file=sys.stderr)
     with gzip.open(xmlfn, 'w') as f:
-        f.write((Entrez.efetch(db='nuccore', id=idsx, retmode='xml').read()).encode())
-    if args.max and i*request_num >= args.max:
+        f.write(Entrez.efetch(db='nuccore', id=ids_chunk, retmode='xml').read().encode())
+
+    if args.max and num_chunk * request_num >= args.max:
         break
diff --git a/workflows/pull-data/genbank/utils.py b/workflows/pull-data/genbank/utils.py
index 3efc67a..96920a5 100644
--- a/workflows/pull-data/genbank/utils.py
+++ b/workflows/pull-data/genbank/utils.py
@@ -1,5 +1,6 @@
 import os
 
+
 def is_integer(string_to_check):
     try:
         int(string_to_check)
@@ -7,19 +8,26 @@ def is_integer(string_to_check):
     except ValueError:
         return False
 
+
 def chunks(lst, n):
     for i in range(0, len(lst), n):
         yield lst[i:i + n]
 
+
 def check_and_get_ontology_dictionaries(dir_ontology_dictionaries):
-    # Check duplicated entry looking at all dictionaries
+    """
+    Check duplicated entry by looking in all dictionaries
+    """
+
     field_to_term_to_uri_dict = {}
 
-    path_dict_xxx_csv_list = [os.path.join(dir_ontology_dictionaries, name_xxx_csv) for name_xxx_csv in
-                              os.listdir(dir_ontology_dictionaries) if name_xxx_csv.endswith('.csv')]
+    path_dict_xxx_csv_list = [
+        os.path.join(dir_ontology_dictionaries, name_xxx_csv) for name_xxx_csv in
+        os.listdir(dir_ontology_dictionaries) if name_xxx_csv.endswith('.csv')
+    ]
 
     for path_dict_xxx_csv in path_dict_xxx_csv_list:
-        print('Read {}'.format(path_dict_xxx_csv))
+        print(f'Read {path_dict_xxx_csv}')
 
         with open(path_dict_xxx_csv) as f:
             for line in f:
@@ -31,7 +39,7 @@ def check_and_get_ontology_dictionaries(dir_ontology_dictionaries):
                 term = term.strip('"')
 
                 if term in field_to_term_to_uri_dict:
-                    print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term))
+                    print(f'Warning: in the dictionaries there are more entries for the same term ({term}).')
                     continue
 
                 field_to_term_to_uri_dict[term] = uri
@@ -54,9 +62,9 @@ def check_and_get_ontology_dictionaries(dir_ontology_dictionaries):
                 term = term.strip('"')
 
                 if term in field_to_term_to_uri_dict[field]:
-                    print('Warning: in the {} dictionary there are more entries for the same term ({}).'.format(field, term))
+                    print(f'Warning: in the {field} dictionary there are more entries for the same term ({term}).')
                     continue
 
                 field_to_term_to_uri_dict[field][term] = uri
 
-    return field_to_term_to_uri_dict
\ No newline at end of file
+    return field_to_term_to_uri_dict
diff --git a/workflows/tools/pubseq-fetch-data.py b/workflows/tools/pubseq-fetch-data.py
new file mode 100755
index 0000000..ef4edde
--- /dev/null
+++ b/workflows/tools/pubseq-fetch-data.py
@@ -0,0 +1,55 @@
+#!/usr/bin/env python3
+
+import argparse
+import json
+import os
+import requests
+import sys
+import time
+
+parser = argparse.ArgumentParser(description="""
+
+Fetch metadata (JSON) from PubSeq and optionally the FASTA files.  IDs
+can be passed in on the command line or in a file.
+
+""")
+parser.add_argument('--fasta', action='store_true', help='Also fetch FASTA records')
+parser.add_argument('--out', type=str, help='Directory to write to',
+required=True)
+parser.add_argument('--ids', type=str, help='File with ids', required=False)
+parser.add_argument('id', nargs='*', help='id(s)')
+args = parser.parse_args()
+
+dir = args.out
+if not os.path.exists(dir):
+    raise Exception(f"Directory {dir} does not exist")
+
+ids = args.id
+if (len(ids)==0):
+    print(f"Reading {args.ids}")
+    with open(args.ids) as f:
+        ids = [ l.strip() for l in f.readlines() ]
+
+for id in ids:
+    print(id)
+    jsonfn = dir+"/"+id+".json"
+    if not os.path.exists(jsonfn):
+        count = 0
+        r = requests.get(f"http://covid19.genenetwork.org/api/sample/{id}.json")
+        while not r:
+            count += 1
+            if count>10: raise Exception(f"Can not find record for {id}")
+            time.sleep(15)
+            r = requests.get(f"http://covid19.genenetwork.org/api/sample/{id}.json")
+        m_url = r.json()[0]['metadata']
+        mr = requests.get(m_url)
+        with open(dir+"/"+id+".json","w") as outf:
+            outf.write(mr.text)
+        if args.fasta:
+            fastafn = dir+"/"+id+".fa"
+            if os.path.exists(fastafn): continue
+            fa_url = r.json()[0]['fasta']
+            fr = requests.get(fa_url)
+            with open(fastafn,"w") as outf:
+                outf.write(fr.text)
+
diff --git a/workflows/tools/sparql-fetch-ids b/workflows/tools/pubseq-fetch-ids
index 19b2d82..f5920ec 100755
--- a/workflows/tools/sparql-fetch-ids
+++ b/workflows/tools/pubseq-fetch-ids
@@ -2,7 +2,7 @@
 #
 # Use a SPARQL query to fetch all IDs in the PubSeq database
 #
-#   sparql-fetch-ids > pubseq_ids.txt
+#   pubseq-fetch-ids > pubseq_ids.txt
 #
 # Note: requires Ruby 3.x. Older Ruby gives a syntax error