Merge pull request #9 from nextstrain/fix-incorrect-dataset-urls

Fix unintentional defining of multiple datasets
nextstrain · Jun 24, 2020 · 6a56b0b · 6a56b0b
2 parents 88b2aad + b189b94
commit 6a56b0b
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diff --git a/identify_multiple_datasets.sh b/identify_multiple_datasets.sh
@@ -0,0 +1,21 @@
+
+curl http://localhost:4000 &>/dev/null
+auspice_exit_code=$?
+if [[ ! $auspice_exit_code -eq "0" ]]; then
+  echo "It doesn't appear that an auspice server is running on port 4000!"
+  echo "Please start auspice and point it at this directory for narratives, e.g."
+  echo "    auspice view --datasetDir ."
+  exit 2;
+fi
+
+for fn in *.md; do
+  prefix=$( echo ${fn} | tr '_' '/' | sed -e 's/\.md//' )
+  lod=$( curl http://localhost:4000/charon/getNarrative?prefix=${prefix} 2>/dev/null | jq 'map(.dataset) | unique ' )
+  n=$( echo $lod | jq ' length ' )
+  if [ ! ${n} = "" ] && [ ! "$n" -eq "1" ]; then
+    echo "Narrative: ${fn} defines ${n} different datasets.";
+    echo ${lod};
+    echo;
+    # code $fn;
+  fi
+done
diff --git a/ncov_sit-rep_2020-01-23.md b/ncov_sit-rep_2020-01-23.md
@@ -189,7 +189,7 @@ These three samples are [known to come from a single family](https://twitter.com
 The fourth sample does not seem to be related to the other three, or to any other of the available sequences.
 Its genome has one mutation not seen in any other genome.
 
-# [Potential within-family transmission 2](https://nextstrain.org/ncov?d=tree&f_city=Zhuhai)
+# [Potential within-family transmission 2](https://nextstrain.org/ncov/2020-01-23?d=tree&f_city=Zhuhai)
 
 Similarly, there are two genetically-identical isolates from Zhuhai (Southeastern China, Guangdong Province) which form a cluster, sharing one unique mutation seen in no other isolate.
 

diff --git a/ncov_sit-rep_2020-01-25.md b/ncov_sit-rep_2020-01-25.md
@@ -176,7 +176,7 @@ The observation of such strong clustering of human infections can be explained b
 
 At the moment, most mutations that can be observed are singletons – they are unique to individual genomes. Only the sequences that form the two clusters from Guangdong and the sequence form the USA share mutations – we will explore these in later slides.
 
-# [Within-family transmission 1](https://nextstrain.org/2020-01-25/ncov?m=div&d=tree&f_location=Zhuhai)
+# [Within-family transmission 1](https://nextstrain.org/ncov/2020-01-25?m=div&d=tree&f_location=Zhuhai)
 
 There are two genetically-identical isolates from Zhuhai (Southeastern China, Guangdong Province) which form a cluster, sharing one unique mutation seen in no other isolate (you can hover your mouse over the branches to see which mutations are present).
 

diff --git a/ncov_sit-rep_2020-01-30.md b/ncov_sit-rep_2020-01-30.md
@@ -8,7 +8,7 @@ dataset: "https://nextstrain.org/ncov/2020-01-30?d=map"
 abstract: "This report uses publicly shared novel coronavirus (nCoV) genomic data from GISAID and Genbank to estimate rates and patterns of viral epidemic spread. We plan to issue updated situation reports as new data is produced and shared. This website is optimized for display on desktop browsers."
 ---
 
-# [Executive summary](https://nextstrain.org/ncov/2020-01-30/2020-01-30)
+# [Executive summary](https://nextstrain.org/ncov/2020-01-30)
 
 ```auspiceMainDisplayMarkdown
 ## Executive summary

diff --git a/ncov_sit-rep_2020-03-13.md b/ncov_sit-rep_2020-03-13.md
@@ -77,7 +77,7 @@ In this week's updates, we report:
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [COVID-19 Resources](https://nextstrain.org/ncov/2020-03-05)
+# [COVID-19 Resources](https://nextstrain.org/ncov/2020-03-13)
 We've prepared some resources that are worth reading to familiarize yourself with COVID-19 and the virus that causes it, SARS-CoV-2.
 This information will make interpreting the data we present in this narrative easier; if you aren't familiar with phylogenetic trees, we encourage you to check out the ['How to Read Phylogenies' narrative](https://nextstrain.org/narratives/trees-background/) and come back when you're ready.
 
@@ -216,7 +216,7 @@ Social distancing -- that is, decreasing the number of people you encounter each
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [FAQs & Misconceptions](https://nextstrain.org/ncov/2020-03-05)
+# [FAQs & Misconceptions](https://nextstrain.org/ncov/2020-03-13)
 
 #### We know that a lot of people have questions about COVID-19.
 
@@ -259,7 +259,7 @@ In an effort to try and explain why these views are incorrect, scientists have a
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [Scientific credit](https://nextstrain.org/ncov/2020-03-05?d=map&c=author)
+# [Scientific credit](https://nextstrain.org/ncov/2020-03-13?d=map&c=author)
 
 We would like to acknowledge the amazing and timely work done by all scientists involved in this outbreak, and particularly those working in China.
 Only through the rapid sharing of genomic data and metadata are analyses such as these possible.
@@ -400,7 +400,7 @@ We are grateful for the data gathered by these originating labs:
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [Detailed scientific credit](https://nextstrain.org/ncov/2020-03-05?d=map&c=author)
+# [Detailed scientific credit](https://nextstrain.org/ncov/2020-03-13?d=map&c=author)
 
 These data were shared via [GISAID](https://gisaid.org).
 We gratefully acknowledge their contributions.

diff --git a/ncov_sit-rep_2020-03-27.md b/ncov_sit-rep_2020-03-27.md
@@ -237,7 +237,7 @@ Sequencing efforts are ramping up, and we will report back as the situation beco
 
 <!-- ##### slide break ##### -->
 <!-- This is left-side text 13-->
-# [Export of COVID-19 from Iran](https://nextstrain.org/ncov?c=division_exposure&label=clade:A3&m=div&d=tree,map&f_division_exposure=Iran)
+# [Export of COVID-19 from Iran](https://nextstrain.org/ncov/2020-03-27?c=division_exposure&label=clade:A3&m=div&d=tree,map&f_division_exposure=Iran)
 <!-- There is no right side text -->
 
 We do not yet have viral genomes from Iran.

diff --git a/ncov_sit-rep_2020-04-03.md b/ncov_sit-rep_2020-04-03.md
@@ -76,7 +76,7 @@ We applaud the groups working to generate additional data for these regions. As
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text 2-->
-# [COVID-19 Resources](https://nextstrain.org/ncov/2020-03-27)
+# [COVID-19 Resources](https://nextstrain.org/ncov/2020-04-03)
 We've prepared some resources that are worth reading to familiarize yourself with COVID-19 and the virus that causes it, SARS-CoV-2, also known as hCov-19.
 This information will make interpreting the data we present in this narrative easier.
 <br><br>
@@ -245,7 +245,7 @@ Interestingly, most of the surrounding sequences (faded tips) are from the U.S.,
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 15-->
-# [What you can do](https://nextstrain.org/ncov/2020-03-27?c=country&d=map&p=full)
+# [What you can do](https://nextstrain.org/ncov/2020-04-03?c=country&d=map&p=full)
 #### ...as an individual
 * Practice strict social distancing.
 * Even if you are not vulnerable, practice social distancing to protect others.
@@ -614,7 +614,7 @@ We are grateful for the data gathered by these originating labs:
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [Detailed scientific credit](https://nextstrain.org/ncov/2020-03-05?d=map&c=author)
+# [Detailed scientific credit](https://nextstrain.org/ncov/2020-04-03?d=map&c=author)
 
 These data were shared via [GISAID](https://gisaid.org).
 We gratefully acknowledge their contributions.

diff --git a/ncov_sit-rep_2020-04-10.md b/ncov_sit-rep_2020-04-10.md
@@ -80,7 +80,7 @@ We've prepared some resources that will make interpreting the data we present in
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text 3-->
-# [A note on sampling](https://nextstrain.org/ncov/global/2020-04-10?c=country&r=country&d=map&p=grid&legend=closed)
+# [A note on sampling](https://nextstrain.org/ncov/global/2020-04-09?c=country&r=country&d=map&p=grid&legend=closed)
 We currently have sequences from samples taken in 57 countries across 6 continents. This is an incredible achievement -- sequencing an unknown, large RNA virus in the midst of a pandemic is difficult, and is only possible through the incredible work and timely sharing of data by scientists and physicians around the world.
 <br><br>
 While this data enables us to infer many useful characteristics of the outbreak and track its spread in real time, it's important to emphasize that our conclusions are limited by the available data.
@@ -176,7 +176,7 @@ This resoundingly demonstrates that this pandemic is a global fight; we all must
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 12-->
-# [Takeaway](https://nextstrain.org/ncov/2020-03-27?c=country&d=map&p=full)
+# [Takeaway](https://nextstrain.org/ncov/global/2020-04-09?c=country&d=map&p=full)
 
 Regional and national outbreaks are and will be deeply intertwined.
 <br><br>
@@ -212,7 +212,7 @@ This pandemic is a global fight; we all must help control this virus everywhere
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [Scientific credit](https://nextstrain.org/ncov/2020-04-10?d=map&c=author)
+# [Scientific credit](https://nextstrain.org/ncov/global/2020-04-09?d=map&c=author)
 
 We would like to acknowledge the amazing and timely work done by all scientists involved in this outbreak, and particularly those working in China.
 Only through the rapid sharing of genomic data and metadata are analyses such as these possible.
@@ -630,7 +630,7 @@ We are grateful for the data gathered by these originating labs:
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [Detailed scientific credit](https://nextstrain.org/ncov/2020-03-05?d=map&c=author)
+# [Detailed scientific credit](https://nextstrain.org/ncov/global/2020-04-09?d=map&c=author)
 
 These data were shared via [GISAID](https://gisaid.org).
 We gratefully acknowledge their contributions.

diff --git a/ncov_sit-rep_2020-04-17.md b/ncov_sit-rep_2020-04-17.md
@@ -151,7 +151,7 @@ There have also been several introductions to the Rocky Mountain West. Zooming i
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 10-->
-# [What you can do](https://nextstrain.org/ncov/north-america/2020-03-27?c=country&d=map&p=full)
+# [What you can do](https://nextstrain.org/ncov/north-america/2020-04-17?c=country&d=map&p=full)
 #### ...as an individual
 * Practice strict social distancing, especially if you are in a vulnerable group.
 * Wear a mask in public.
@@ -680,7 +680,7 @@ We are grateful for the data gathered by these originating labs:
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [Detailed scientific credit](https://nextstrain.org/ncov/north-america/2020-03-05?d=map&c=author)
+# [Detailed scientific credit](https://nextstrain.org/ncov/north-america/2020-04-17?d=map&c=author)
 
 These data were shared via [GISAID](https://gisaid.org).
 We gratefully acknowledge their contributions.

diff --git a/ncov_sit-rep_2020-04-24.md b/ncov_sit-rep_2020-04-24.md
@@ -183,7 +183,7 @@ This is evidence for many separate introductions, largely from Europe, to many n
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 11-->
-# [What you can do](https://nextstrain.org/ncov/2020-03-27?c=country&d=map&p=full)
+# [What you can do](https://nextstrain.org/ncov/africa/2020-04-24?c=country&d=map&p=full)
 #### ...as an individual
 * Practice strict social distancing, especially if you are in a vulnerable group.
 * Remember that even if you are not super vulnerable, many people around you are; follow these practices to protect others.
@@ -225,7 +225,7 @@ This is evidence for many separate introductions, largely from Europe, to many n
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text 12-->
-# [Scientific credit](https://nextstrain.org/ncov/2020-04-24?d=map&c=author)
+# [Scientific credit](https://nextstrain.org/ncov/africa/2020-04-24?d=map&c=author)
 
 We would like to acknowledge the amazing and timely work done by all scientists involved in this outbreak.
 Only through the rapid sharing of genomic data and metadata are analyses such as these possible.

diff --git a/ncov_sit-rep_2020-05-01.md b/ncov_sit-rep_2020-05-01.md
@@ -93,7 +93,7 @@ For example, the map shows many samples from Iceland, the U.K., and the Netherla
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 4-->
-# [Many introductions to Russia](https://nextstrain.org/ncov/europe/2020-04-29?c=division&d=tree,map&f_country=Russia&p=full&r=division)
+# [Many introductions to Russia](https://nextstrain.org/ncov/europe/2020-05-01?c=division&d=tree,map&f_country=Russia&p=full&r=division)
 
 Highlighting samples from Russia, we see that they are scattered both geographically (across Russia) and genomically (across the tree).
 <br><br>
@@ -105,7 +105,7 @@ While there are a few samples towards the bottom of the tree that are most close
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 5-->
-# [Heterogeneous outbreak in Moscow](https://nextstrain.org/ncov/europe/2020-04-29?c=division&d=tree&f_country=Russia&f_division=Moscow&label=clade:A2&p=full&r=division&m=div)
+# [Heterogeneous outbreak in Moscow](https://nextstrain.org/ncov/europe/2020-05-01?c=division&d=tree&f_country=Russia&f_division=Moscow&label=clade:A2&p=full&r=division&m=div)
 
 An example of frequent importation can be seen by zooming in on samples from Moscow.
 <br><br>
@@ -116,7 +116,7 @@ Given the number of confirmed cases in Moscow, it's likely that at least some of
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 6-->
-# [Large outbreak cluster in St. Petersburg, sparked in early March](https://nextstrain.org/ncov/europe/2020-04-29?c=division&d=tree&f_country=Russia&f_division=Saint-Petersburg&f_region=Europe&label=clade:A2&p=full&r=division)
+# [Large outbreak cluster in St. Petersburg, sparked in early March](https://nextstrain.org/ncov/europe/2020-05-01?c=division&d=tree&f_country=Russia&f_division=Saint-Petersburg&f_region=Europe&label=clade:A2&p=full&r=division)
 
 We can look at St. Petersburg as a counterexample.
 <br><br>
@@ -128,7 +128,7 @@ This pattern is consistent with one of these introductions to St. Petersburg tak
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 7-->
-# [Five local transmission chains in the Czech Republic](https://nextstrain.org/ncov/europe/2020-04-29?d=tree,map&f_country=Czech%20Republic&m=div&p=full)
+# [Five local transmission chains in the Czech Republic](https://nextstrain.org/ncov/europe/2020-05-01?d=tree,map&f_country=Czech%20Republic&m=div&p=full)
 
 The data from the Czech Republic show a mix of these two patterns.
 <br><br>
@@ -140,7 +140,7 @@ From this, we can say that there were at least 7 introductions to the Czech Repu
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 8-->
-# [Extensive mixing of cases across Turkey](https://nextstrain.org/ncov/europe/2020-04-29?c=country_exposure&d=tree,map&f_country=Turkey&label=clade:A2&p=full&r=division)
+# [Extensive mixing of cases across Turkey](https://nextstrain.org/ncov/europe/2020-05-01?c=country_exposure&d=tree,map&f_country=Turkey&label=clade:A2&p=full&r=division)
 
 In the middle of the tree, we see a string of cases sampled from many different provinces around Turkey.
 Some of these cases have reported travel history to Saudi Arabia, with subsequent closely related cases in Turkey.
@@ -157,7 +157,7 @@ We may also speculate that a large gathering could explain these observations, a
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text 9-->
-# [At least 11 introductions to Poland](https://nextstrain.org/ncov/europe/2020-04-29?d=tree,map&f_country=Poland&p=full&legend=closed)
+# [At least 11 introductions to Poland](https://nextstrain.org/ncov/europe/2020-05-01?d=tree,map&f_country=Poland&p=full&legend=closed)
 
 We have 15 sequences from Poland on Nextstrain. Of these 15, at least 11 of them represent separate introductions from elsewhere in the world.
 As in Moscow, given the number of reported cases, we might expect that several of these introductions have seeded local transmission chains in Poland, but we can't yet see this in the genomic data.
@@ -166,7 +166,7 @@ As in Moscow, given the number of reported cases, we might expect that several o
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 10-->
-# [Early samples from Hungary, Latvia, Slovakia and Slovenia](https://nextstrain.org/ncov/europe/2020-04-29?d=tree,map&f_country=Hungary,Latvia,Slovakia,Slovenia&f_region=Europe&p=full&legend=closed)
+# [Early samples from Hungary, Latvia, Slovakia and Slovenia](https://nextstrain.org/ncov/europe/2020-05-01?d=tree,map&f_country=Hungary,Latvia,Slovakia,Slovenia&f_region=Europe&p=full&legend=closed)
 
 In March, 20 sequences were submitted from Hungary, Latvia, Slovakia, and Slovenia.
 While we don't yet have enough data from these countries to draw firm conclusions, we applaud these early efforts and will continue to monitor the incoming data.
@@ -175,7 +175,7 @@ While we don't yet have enough data from these countries to draw firm conclusion
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 11-->
-# [What you can do](https://nextstrain.org/ncov/2020-03-27?c=country&d=map&p=full)
+# [What you can do](https://nextstrain.org/ncov/europe/2020-05-01?c=country&d=map&p=full)
 #### ...as an individual
 * Practice strict social distancing, especially if you are in a vulnerable group.
 * Remember that even if you are not super vulnerable, many people around you are; follow these practices to protect others.
@@ -218,7 +218,7 @@ While we don't yet have enough data from these countries to draw firm conclusion
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text 12-->
-# [Scientific credit](https://nextstrain.org/ncov/2020-05-01?d=map&c=author)
+# [Scientific credit](https://nextstrain.org/ncov/europe/2020-05-01?d=map&c=author)
 
 We would like to acknowledge the amazing and timely work done by all scientists involved in this outbreak.
 Only through the rapid sharing of genomic data and metadata are analyses such as these possible.

diff --git a/ncov_sit-rep_2020-05-08.md b/ncov_sit-rep_2020-05-08.md
@@ -31,7 +31,7 @@ abstract: "This weekly report uses publicly shared genomic data to track the spr
 <!-- numbers can be tagged ilke this: 161</tag> - this is just for us to help find them to update! Just leave in the </tag> bit. -->
 
 <!-- This is left-side text 1-->
-# [Table of Contents](https://nextstrain.org/ncov/2020-05-08?d=tree,map&p=grid)
+# [Table of Contents](https://nextstrain.org/ncov/asia/2020-05-08?d=tree,map&p=grid)
 
 * [Background resources](https://nextstrain.org/narratives/ncov/sit-rep/2020-05-08?n=2).     
 * [About this data](https://nextstrain.org/narratives/ncov/sit-rep/2020-05-08?n=3).  
@@ -135,7 +135,7 @@ The consistency of this pattern is strong evidence that the virus frequently cro
 
 <!-- ############ SLIDE BREAK ############# -->
 <!-- This is left-side text 13-->
-# [What you can do](https://nextstrain.org/ncov/2020-05-08?c=country&d=map&p=full)
+# [What you can do](https://nextstrain.org/ncov/asia/2020-05-08?c=country&d=map&p=full)
 #### ...as an individual
 * Practice strict social distancing, especially if you are in a vulnerable group.
 * Remember that even if you are not super vulnerable, many people around you are; follow these practices to protect others.
@@ -172,7 +172,7 @@ The consistency of this pattern is strong evidence that the virus frequently cro
 <!-- ############ SLIDE BREAK ############# -->
 
 <!-- This is left-side text -->
-# [Scientific credit](https://nextstrain.org/ncov/2020-05-06?d=map&c=author)
+# [Scientific credit](https://nextstrain.org/ncov/asia/2020-05-08?d=map&c=author)
 
 We would like to acknowledge the amazing and timely work done by all scientists involved in this outbreak.
 Only through the rapid sharing of genomic data and metadata are analyses such as these possible.