From 6e6afb4b6be3f2f2c1b8b56d85d8c2089f709d26 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Fri, 17 Jul 2020 17:59:16 -0400
Subject: Comment out some broken links for now

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 bh20simplewebuploader/templates/resource.html |  6 +++---
 scripts/cleanup.py                            | 23 +++++++++++++++++++++--
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html
index 91b6c20..9a905c2 100644
--- a/bh20simplewebuploader/templates/resource.html
+++ b/bh20simplewebuploader/templates/resource.html
@@ -6,13 +6,13 @@
       {% 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><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 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="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>
diff --git a/scripts/cleanup.py b/scripts/cleanup.py
index 78f34c8..6919305 100644
--- a/scripts/cleanup.py
+++ b/scripts/cleanup.py
@@ -1,7 +1,13 @@
 import arvados
 import arvados.util
+import arvados.keep
+import ruamel.yaml
 
 api = arvados.api()
+keepclient = arvados.keep.KeepClient(api_client=api)
+
+UPLOADER_PROJECT = 'lugli-j7d0g-n5clictpuvwk8aa'
+VALIDATED_PROJECT = 'lugli-j7d0g-5ct8p1i1wrgyjvp'
 
 delete_patterns = [
     "%missing%`collection_location`%",
@@ -21,7 +27,7 @@ revalidate_patterns = [
 
 for p in delete_patterns:
     c = arvados.util.list_all(api.collections().list, filters=[
-        ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"],
+        ["owner_uuid", "=", UPLOADER_PROJECT],
         ["properties.errors", "like", p]])
     for i in c:
         print("trashing %s %s" % (i["uuid"], i["properties"].get("sequence_label")))
@@ -29,7 +35,7 @@ for p in delete_patterns:
 
 for p in revalidate_patterns:
     c = arvados.util.list_all(api.collections().list, filters=[
-        ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"],
+        ["owner_uuid", "=", UPLOADER_PROJECT],
         ["properties.errors", "like", p]])
     for i in c:
         print("clearing status %s %s" % (i["uuid"], i["properties"].get("sequence_label")))
@@ -39,3 +45,16 @@ for p in revalidate_patterns:
         if "errors" in pr:
             del pr["errors"]
         api.collections().update(uuid=i["uuid"], body={"properties": pr}).execute()
+
+c = arvados.util.list_all(api.collections().list, filters=[
+    ["owner_uuid", "=", VALIDATED_PROJECT],
+    ["properties.sequence_label", "exists", False]])
+for i in c:
+    col = arvados.collection.Collection(i["uuid"], api_client=api, keep_client=keepclient)
+    with col.open("metadata.yaml") as md:
+        metadata_content = ruamel.yaml.round_trip_load(md)
+    colprop = col.get_properties()
+    colprop["sequence_label"] = metadata_content["sample"]["sample_id"]
+
+    print("fixing sequence label %s %s" % (i["uuid"], colprop.get("sequence_label")))
+    api.collections().update(uuid=i["uuid"], body={"properties": colprop}).execute()
-- 
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