diff --git a/data/nextstrain/MPXV/ancestral/image.png b/data/nextstrain/MPXV/ancestral/image.png new file mode 100644 index 000000000..2483c2193 Binary files /dev/null and b/data/nextstrain/MPXV/ancestral/image.png differ diff --git a/data/nextstrain/MPXV/ancestral/pathogen.json b/data/nextstrain/MPXV/ancestral/pathogen.json index 0ce33154a..3d0ebd4e5 100644 --- a/data/nextstrain/MPXV/ancestral/pathogen.json +++ b/data/nextstrain/MPXV/ancestral/pathogen.json @@ -17,6 +17,10 @@ "valueFriendly": "Reconstructed ancestral MPXV" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/ebola/image.png b/data/nextstrain/ebola/image.png new file mode 100644 index 000000000..b98de40c6 Binary files /dev/null and b/data/nextstrain/ebola/image.png differ diff --git a/data/nextstrain/ebola/pathogen.json b/data/nextstrain/ebola/pathogen.json index 9e136776d..d02cb149e 100644 --- a/data/nextstrain/ebola/pathogen.json +++ b/data/nextstrain/ebola/pathogen.json @@ -9,6 +9,10 @@ "valueFriendly": "UNKNOWN" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/enterovirus/d68/image.jpg b/data/nextstrain/enterovirus/d68/image.jpg new file mode 100644 index 000000000..4e4843f46 Binary files /dev/null and b/data/nextstrain/enterovirus/d68/image.jpg differ diff --git a/data/nextstrain/enterovirus/d68/pathogen.json b/data/nextstrain/enterovirus/d68/pathogen.json index 16397ebce..05a717d6c 100644 --- a/data/nextstrain/enterovirus/d68/pathogen.json +++ b/data/nextstrain/enterovirus/d68/pathogen.json @@ -9,6 +9,10 @@ "valueFriendly": "UNKNOWN" } }, + "image": { + "path": "image.jpg", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/flu_h1n1pdm_ha/CY121680/image.png b/data/nextstrain/flu_h1n1pdm_ha/CY121680/image.png new file mode 100644 index 000000000..3d262a4eb Binary files /dev/null and b/data/nextstrain/flu_h1n1pdm_ha/CY121680/image.png differ diff --git a/data/nextstrain/flu_h1n1pdm_ha/CY121680/pathogen.json b/data/nextstrain/flu_h1n1pdm_ha/CY121680/pathogen.json index 33c70a3d6..98eeadb0d 100644 --- a/data/nextstrain/flu_h1n1pdm_ha/CY121680/pathogen.json +++ b/data/nextstrain/flu_h1n1pdm_ha/CY121680/pathogen.json @@ -34,6 +34,10 @@ "valueFriendly": "A/California/07/2009" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/flu_h1n1pdm_ha/MW626062/image.png b/data/nextstrain/flu_h1n1pdm_ha/MW626062/image.png new file mode 100644 index 000000000..3d262a4eb Binary files /dev/null and b/data/nextstrain/flu_h1n1pdm_ha/MW626062/image.png differ diff --git a/data/nextstrain/flu_h1n1pdm_ha/MW626062/pathogen.json b/data/nextstrain/flu_h1n1pdm_ha/MW626062/pathogen.json index 5864a73a0..76c63ce3a 100644 --- a/data/nextstrain/flu_h1n1pdm_ha/MW626062/pathogen.json +++ b/data/nextstrain/flu_h1n1pdm_ha/MW626062/pathogen.json @@ -34,6 +34,10 @@ "valueFriendly": "A/Wisconsin/588/2019" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/flu_h1n1pdm_na/MW626056/image.png b/data/nextstrain/flu_h1n1pdm_na/MW626056/image.png new file mode 100644 index 000000000..3d262a4eb Binary files /dev/null and b/data/nextstrain/flu_h1n1pdm_na/MW626056/image.png differ diff --git a/data/nextstrain/flu_h1n1pdm_na/MW626056/pathogen.json b/data/nextstrain/flu_h1n1pdm_na/MW626056/pathogen.json index 238c3633d..f61a44f76 100644 --- a/data/nextstrain/flu_h1n1pdm_na/MW626056/pathogen.json +++ b/data/nextstrain/flu_h1n1pdm_na/MW626056/pathogen.json @@ -31,6 +31,10 @@ "valueFriendly": "A/Wisconsin/588/2019" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/flu_h3n2_ha/CY163680/image.png b/data/nextstrain/flu_h3n2_ha/CY163680/image.png new file mode 100644 index 000000000..8a629b620 Binary files /dev/null and b/data/nextstrain/flu_h3n2_ha/CY163680/image.png differ diff --git a/data/nextstrain/flu_h3n2_ha/CY163680/pathogen.json b/data/nextstrain/flu_h3n2_ha/CY163680/pathogen.json index 3bfd304d4..5372c8a61 100644 --- a/data/nextstrain/flu_h3n2_ha/CY163680/pathogen.json +++ b/data/nextstrain/flu_h3n2_ha/CY163680/pathogen.json @@ -34,6 +34,10 @@ "valueFriendly": "A/Wisconsin/67/2005" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/flu_h3n2_ha/EPI1857216/image.png b/data/nextstrain/flu_h3n2_ha/EPI1857216/image.png new file mode 100644 index 000000000..8a629b620 Binary files /dev/null and b/data/nextstrain/flu_h3n2_ha/EPI1857216/image.png differ diff --git a/data/nextstrain/flu_h3n2_ha/EPI1857216/pathogen.json b/data/nextstrain/flu_h3n2_ha/EPI1857216/pathogen.json index 46bdd6767..d1cbcd762 100644 --- a/data/nextstrain/flu_h3n2_ha/EPI1857216/pathogen.json +++ b/data/nextstrain/flu_h3n2_ha/EPI1857216/pathogen.json @@ -34,6 +34,10 @@ "valueFriendly": "A/Darwin/6/2021" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/flu_h3n2_na/EPI1857215/image.png b/data/nextstrain/flu_h3n2_na/EPI1857215/image.png new file mode 100644 index 000000000..8a629b620 Binary files /dev/null and b/data/nextstrain/flu_h3n2_na/EPI1857215/image.png differ diff --git a/data/nextstrain/flu_h3n2_na/EPI1857215/pathogen.json b/data/nextstrain/flu_h3n2_na/EPI1857215/pathogen.json index cbb7973c0..27cf40529 100644 --- a/data/nextstrain/flu_h3n2_na/EPI1857215/pathogen.json +++ b/data/nextstrain/flu_h3n2_na/EPI1857215/pathogen.json @@ -31,6 +31,10 @@ "valueFriendly": "A/Darwin/6/2021" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/hMPXV/NC_063383.1/image.png b/data/nextstrain/hMPXV/NC_063383.1/image.png new file mode 100644 index 000000000..2483c2193 Binary files /dev/null and b/data/nextstrain/hMPXV/NC_063383.1/image.png differ diff --git a/data/nextstrain/hMPXV/NC_063383.1/pathogen.json b/data/nextstrain/hMPXV/NC_063383.1/pathogen.json index 499016eaa..52291cd55 100644 --- a/data/nextstrain/hMPXV/NC_063383.1/pathogen.json +++ b/data/nextstrain/hMPXV/NC_063383.1/pathogen.json @@ -17,6 +17,10 @@ "valueFriendly": "MPXV-M5312_HM12_Rivers" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/hMPXV_B1/pseudo_ON563414/image.png b/data/nextstrain/hMPXV_B1/pseudo_ON563414/image.png new file mode 100644 index 000000000..2483c2193 Binary files /dev/null and b/data/nextstrain/hMPXV_B1/pseudo_ON563414/image.png differ diff --git a/data/nextstrain/hMPXV_B1/pseudo_ON563414/pathogen.json b/data/nextstrain/hMPXV_B1/pseudo_ON563414/pathogen.json index 76d798555..28c3a3413 100644 --- a/data/nextstrain/hMPXV_B1/pseudo_ON563414/pathogen.json +++ b/data/nextstrain/hMPXV_B1/pseudo_ON563414/pathogen.json @@ -17,6 +17,10 @@ "valueFriendly": "MPXV_USA_2022_MA001 in NC_063383 coordinates" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/rsv_a/EPI_ISL_412866/image.png b/data/nextstrain/rsv_a/EPI_ISL_412866/image.png new file mode 100644 index 000000000..7e48cc5a7 Binary files /dev/null and b/data/nextstrain/rsv_a/EPI_ISL_412866/image.png differ diff --git a/data/nextstrain/rsv_a/EPI_ISL_412866/pathogen.json b/data/nextstrain/rsv_a/EPI_ISL_412866/pathogen.json index 6ea63242c..7b24c9f10 100644 --- a/data/nextstrain/rsv_a/EPI_ISL_412866/pathogen.json +++ b/data/nextstrain/rsv_a/EPI_ISL_412866/pathogen.json @@ -19,6 +19,10 @@ "valueFriendly": "hRSV/A/England/397/2017" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/rsv_b/EPI_ISL_1653999/image.png b/data/nextstrain/rsv_b/EPI_ISL_1653999/image.png new file mode 100644 index 000000000..7e48cc5a7 Binary files /dev/null and b/data/nextstrain/rsv_b/EPI_ISL_1653999/image.png differ diff --git a/data/nextstrain/rsv_b/EPI_ISL_1653999/pathogen.json b/data/nextstrain/rsv_b/EPI_ISL_1653999/pathogen.json index 7fe152eb4..d93f7c095 100644 --- a/data/nextstrain/rsv_b/EPI_ISL_1653999/pathogen.json +++ b/data/nextstrain/rsv_b/EPI_ISL_1653999/pathogen.json @@ -19,6 +19,10 @@ "valueFriendly": "hRSV/B/Australia/VIC-RCH056/2019 " } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data/nextstrain/sars-cov-2-21L/BA.2/image.png b/data/nextstrain/sars-cov-2-21L/BA.2/image.png new file mode 100644 index 000000000..6dce9328a Binary files /dev/null and b/data/nextstrain/sars-cov-2-21L/BA.2/image.png differ diff --git a/data/nextstrain/sars-cov-2-21L/BA.2/pathogen.json b/data/nextstrain/sars-cov-2-21L/BA.2/pathogen.json index fc9391401..41b812d85 100644 --- a/data/nextstrain/sars-cov-2-21L/BA.2/pathogen.json +++ b/data/nextstrain/sars-cov-2-21L/BA.2/pathogen.json @@ -20,6 +20,10 @@ "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "defaultGene": "S", "deprecated": false, "enabled": true, diff --git a/data/nextstrain/sars-cov-2/MN908947/image.png b/data/nextstrain/sars-cov-2/MN908947/image.png new file mode 100644 index 000000000..6dce9328a Binary files /dev/null and b/data/nextstrain/sars-cov-2/MN908947/image.png differ diff --git a/data/nextstrain/sars-cov-2/MN908947/pathogen.json b/data/nextstrain/sars-cov-2/MN908947/pathogen.json index 645caabdf..4b7066f7a 100644 --- a/data/nextstrain/sars-cov-2/MN908947/pathogen.json +++ b/data/nextstrain/sars-cov-2/MN908947/pathogen.json @@ -20,6 +20,10 @@ "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "defaultGene": "S", "deprecated": false, "enabled": true, diff --git a/data/nextstrain/zika/image.png b/data/nextstrain/zika/image.png new file mode 100644 index 000000000..24f7173c1 Binary files /dev/null and b/data/nextstrain/zika/image.png differ diff --git a/data/nextstrain/zika/pathogen.json b/data/nextstrain/zika/pathogen.json index 6b70713a7..15f2fe137 100644 --- a/data/nextstrain/zika/pathogen.json +++ b/data/nextstrain/zika/pathogen.json @@ -13,6 +13,10 @@ "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "deprecated": false, "experimental": true, "files": { diff --git a/data_output/index.json b/data_output/index.json index 3c29ac35c..10fa17cb6 100644 --- a/data_output/index.json +++ b/data_output/index.json @@ -40,6 +40,10 @@ "valueFriendly": "Wuhan-Hu-1/2019" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -95,6 +99,10 @@ "valueFriendly": "BA.2" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -151,6 +159,10 @@ "valueFriendly": "Reconstructed ancestral MPXV" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -202,6 +214,10 @@ "valueFriendly": "MPXV-M5312_HM12_Rivers" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -254,6 +270,10 @@ "valueFriendly": "MPXV_USA_2022_MA001 in NC_063383 coordinates" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -309,6 +329,10 @@ "valueFriendly": "hRSV/A/England/397/2017" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -359,6 +383,10 @@ "valueFriendly": "hRSV/B/Australia/VIC-RCH056/2019 " } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -409,6 +437,10 @@ "valueFriendly": "A/California/07/2009" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -462,6 +494,10 @@ "valueFriendly": "A/Wisconsin/588/2019" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -515,6 +551,10 @@ "valueFriendly": "A/Wisconsin/588/2019" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -568,6 +608,10 @@ "valueFriendly": "A/Wisconsin/67/2005" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -621,6 +665,10 @@ "valueFriendly": "A/Darwin/6/2021" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -675,6 +723,10 @@ "valueFriendly": "A/Darwin/6/2021" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -1431,6 +1483,10 @@ "valueFriendly": "UNKNOWN" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -1472,6 +1528,10 @@ "valueFriendly": "UNKNOWN" } }, + "image": { + "path": "image.jpg", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", @@ -2695,6 +2755,10 @@ "valueFriendly": "UNKNOWN" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "files": { "changelog": "CHANGELOG.md", "examples": "sequences.fasta", diff --git a/data_output/nextstrain/MPXV/ancestral/unreleased/image.png b/data_output/nextstrain/MPXV/ancestral/unreleased/image.png new file mode 100644 index 000000000..2483c2193 Binary files /dev/null and b/data_output/nextstrain/MPXV/ancestral/unreleased/image.png differ diff --git a/data_output/nextstrain/MPXV/ancestral/unreleased/pathogen.json b/data_output/nextstrain/MPXV/ancestral/unreleased/pathogen.json index 0ce33154a..3d0ebd4e5 100644 --- a/data_output/nextstrain/MPXV/ancestral/unreleased/pathogen.json +++ b/data_output/nextstrain/MPXV/ancestral/unreleased/pathogen.json @@ -17,6 +17,10 @@ "valueFriendly": "Reconstructed ancestral MPXV" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/ebola/unreleased/image.png b/data_output/nextstrain/ebola/unreleased/image.png new file mode 100644 index 000000000..b98de40c6 Binary files /dev/null and b/data_output/nextstrain/ebola/unreleased/image.png differ diff --git a/data_output/nextstrain/ebola/unreleased/pathogen.json b/data_output/nextstrain/ebola/unreleased/pathogen.json index 9e136776d..d02cb149e 100644 --- a/data_output/nextstrain/ebola/unreleased/pathogen.json +++ b/data_output/nextstrain/ebola/unreleased/pathogen.json @@ -9,6 +9,10 @@ "valueFriendly": "UNKNOWN" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/enterovirus/d68/unreleased/image.jpg b/data_output/nextstrain/enterovirus/d68/unreleased/image.jpg new file mode 100644 index 000000000..4e4843f46 Binary files /dev/null and b/data_output/nextstrain/enterovirus/d68/unreleased/image.jpg differ diff --git a/data_output/nextstrain/enterovirus/d68/unreleased/pathogen.json b/data_output/nextstrain/enterovirus/d68/unreleased/pathogen.json index 16397ebce..05a717d6c 100644 --- a/data_output/nextstrain/enterovirus/d68/unreleased/pathogen.json +++ b/data_output/nextstrain/enterovirus/d68/unreleased/pathogen.json @@ -9,6 +9,10 @@ "valueFriendly": "UNKNOWN" } }, + "image": { + "path": "image.jpg", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/flu_h1n1pdm_ha/CY121680/unreleased/image.png b/data_output/nextstrain/flu_h1n1pdm_ha/CY121680/unreleased/image.png new file mode 100644 index 000000000..3d262a4eb Binary files /dev/null and b/data_output/nextstrain/flu_h1n1pdm_ha/CY121680/unreleased/image.png differ diff --git a/data_output/nextstrain/flu_h1n1pdm_ha/CY121680/unreleased/pathogen.json b/data_output/nextstrain/flu_h1n1pdm_ha/CY121680/unreleased/pathogen.json index 33c70a3d6..98eeadb0d 100644 --- a/data_output/nextstrain/flu_h1n1pdm_ha/CY121680/unreleased/pathogen.json +++ b/data_output/nextstrain/flu_h1n1pdm_ha/CY121680/unreleased/pathogen.json @@ -34,6 +34,10 @@ "valueFriendly": "A/California/07/2009" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/flu_h1n1pdm_ha/MW626062/unreleased/image.png b/data_output/nextstrain/flu_h1n1pdm_ha/MW626062/unreleased/image.png new file mode 100644 index 000000000..3d262a4eb Binary files /dev/null and b/data_output/nextstrain/flu_h1n1pdm_ha/MW626062/unreleased/image.png differ diff --git a/data_output/nextstrain/flu_h1n1pdm_ha/MW626062/unreleased/pathogen.json b/data_output/nextstrain/flu_h1n1pdm_ha/MW626062/unreleased/pathogen.json index 5864a73a0..76c63ce3a 100644 --- a/data_output/nextstrain/flu_h1n1pdm_ha/MW626062/unreleased/pathogen.json +++ b/data_output/nextstrain/flu_h1n1pdm_ha/MW626062/unreleased/pathogen.json @@ -34,6 +34,10 @@ "valueFriendly": "A/Wisconsin/588/2019" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/flu_h1n1pdm_na/MW626056/unreleased/image.png b/data_output/nextstrain/flu_h1n1pdm_na/MW626056/unreleased/image.png new file mode 100644 index 000000000..3d262a4eb Binary files /dev/null and b/data_output/nextstrain/flu_h1n1pdm_na/MW626056/unreleased/image.png differ diff --git a/data_output/nextstrain/flu_h1n1pdm_na/MW626056/unreleased/pathogen.json b/data_output/nextstrain/flu_h1n1pdm_na/MW626056/unreleased/pathogen.json index 238c3633d..f61a44f76 100644 --- a/data_output/nextstrain/flu_h1n1pdm_na/MW626056/unreleased/pathogen.json +++ b/data_output/nextstrain/flu_h1n1pdm_na/MW626056/unreleased/pathogen.json @@ -31,6 +31,10 @@ "valueFriendly": "A/Wisconsin/588/2019" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/flu_h3n2_ha/CY163680/unreleased/image.png b/data_output/nextstrain/flu_h3n2_ha/CY163680/unreleased/image.png new file mode 100644 index 000000000..8a629b620 Binary files /dev/null and b/data_output/nextstrain/flu_h3n2_ha/CY163680/unreleased/image.png differ diff --git a/data_output/nextstrain/flu_h3n2_ha/CY163680/unreleased/pathogen.json b/data_output/nextstrain/flu_h3n2_ha/CY163680/unreleased/pathogen.json index 3bfd304d4..5372c8a61 100644 --- a/data_output/nextstrain/flu_h3n2_ha/CY163680/unreleased/pathogen.json +++ b/data_output/nextstrain/flu_h3n2_ha/CY163680/unreleased/pathogen.json @@ -34,6 +34,10 @@ "valueFriendly": "A/Wisconsin/67/2005" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/flu_h3n2_ha/EPI1857216/unreleased/image.png b/data_output/nextstrain/flu_h3n2_ha/EPI1857216/unreleased/image.png new file mode 100644 index 000000000..8a629b620 Binary files /dev/null and b/data_output/nextstrain/flu_h3n2_ha/EPI1857216/unreleased/image.png differ diff --git a/data_output/nextstrain/flu_h3n2_ha/EPI1857216/unreleased/pathogen.json b/data_output/nextstrain/flu_h3n2_ha/EPI1857216/unreleased/pathogen.json index 46bdd6767..d1cbcd762 100644 --- a/data_output/nextstrain/flu_h3n2_ha/EPI1857216/unreleased/pathogen.json +++ b/data_output/nextstrain/flu_h3n2_ha/EPI1857216/unreleased/pathogen.json @@ -34,6 +34,10 @@ "valueFriendly": "A/Darwin/6/2021" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/flu_h3n2_na/EPI1857215/unreleased/image.png b/data_output/nextstrain/flu_h3n2_na/EPI1857215/unreleased/image.png new file mode 100644 index 000000000..8a629b620 Binary files /dev/null and b/data_output/nextstrain/flu_h3n2_na/EPI1857215/unreleased/image.png differ diff --git a/data_output/nextstrain/flu_h3n2_na/EPI1857215/unreleased/pathogen.json b/data_output/nextstrain/flu_h3n2_na/EPI1857215/unreleased/pathogen.json index cbb7973c0..27cf40529 100644 --- a/data_output/nextstrain/flu_h3n2_na/EPI1857215/unreleased/pathogen.json +++ b/data_output/nextstrain/flu_h3n2_na/EPI1857215/unreleased/pathogen.json @@ -31,6 +31,10 @@ "valueFriendly": "A/Darwin/6/2021" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/hMPXV/NC_063383.1/unreleased/image.png b/data_output/nextstrain/hMPXV/NC_063383.1/unreleased/image.png new file mode 100644 index 000000000..2483c2193 Binary files /dev/null and b/data_output/nextstrain/hMPXV/NC_063383.1/unreleased/image.png differ diff --git a/data_output/nextstrain/hMPXV/NC_063383.1/unreleased/pathogen.json b/data_output/nextstrain/hMPXV/NC_063383.1/unreleased/pathogen.json index 499016eaa..52291cd55 100644 --- a/data_output/nextstrain/hMPXV/NC_063383.1/unreleased/pathogen.json +++ b/data_output/nextstrain/hMPXV/NC_063383.1/unreleased/pathogen.json @@ -17,6 +17,10 @@ "valueFriendly": "MPXV-M5312_HM12_Rivers" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/hMPXV_B1/pseudo_ON563414/unreleased/image.png b/data_output/nextstrain/hMPXV_B1/pseudo_ON563414/unreleased/image.png new file mode 100644 index 000000000..2483c2193 Binary files /dev/null and b/data_output/nextstrain/hMPXV_B1/pseudo_ON563414/unreleased/image.png differ diff --git a/data_output/nextstrain/hMPXV_B1/pseudo_ON563414/unreleased/pathogen.json b/data_output/nextstrain/hMPXV_B1/pseudo_ON563414/unreleased/pathogen.json index 76d798555..28c3a3413 100644 --- a/data_output/nextstrain/hMPXV_B1/pseudo_ON563414/unreleased/pathogen.json +++ b/data_output/nextstrain/hMPXV_B1/pseudo_ON563414/unreleased/pathogen.json @@ -17,6 +17,10 @@ "valueFriendly": "MPXV_USA_2022_MA001 in NC_063383 coordinates" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/rsv_a/EPI_ISL_412866/unreleased/image.png b/data_output/nextstrain/rsv_a/EPI_ISL_412866/unreleased/image.png new file mode 100644 index 000000000..7e48cc5a7 Binary files /dev/null and b/data_output/nextstrain/rsv_a/EPI_ISL_412866/unreleased/image.png differ diff --git a/data_output/nextstrain/rsv_a/EPI_ISL_412866/unreleased/pathogen.json b/data_output/nextstrain/rsv_a/EPI_ISL_412866/unreleased/pathogen.json index 6ea63242c..7b24c9f10 100644 --- a/data_output/nextstrain/rsv_a/EPI_ISL_412866/unreleased/pathogen.json +++ b/data_output/nextstrain/rsv_a/EPI_ISL_412866/unreleased/pathogen.json @@ -19,6 +19,10 @@ "valueFriendly": "hRSV/A/England/397/2017" } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/rsv_b/EPI_ISL_1653999/unreleased/image.png b/data_output/nextstrain/rsv_b/EPI_ISL_1653999/unreleased/image.png new file mode 100644 index 000000000..7e48cc5a7 Binary files /dev/null and b/data_output/nextstrain/rsv_b/EPI_ISL_1653999/unreleased/image.png differ diff --git a/data_output/nextstrain/rsv_b/EPI_ISL_1653999/unreleased/pathogen.json b/data_output/nextstrain/rsv_b/EPI_ISL_1653999/unreleased/pathogen.json index 7fe152eb4..d93f7c095 100644 --- a/data_output/nextstrain/rsv_b/EPI_ISL_1653999/unreleased/pathogen.json +++ b/data_output/nextstrain/rsv_b/EPI_ISL_1653999/unreleased/pathogen.json @@ -19,6 +19,10 @@ "valueFriendly": "hRSV/B/Australia/VIC-RCH056/2019 " } }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/sars-cov-2-21L/BA.2/unreleased/image.png b/data_output/nextstrain/sars-cov-2-21L/BA.2/unreleased/image.png new file mode 100644 index 000000000..6dce9328a Binary files /dev/null and b/data_output/nextstrain/sars-cov-2-21L/BA.2/unreleased/image.png differ diff --git a/data_output/nextstrain/sars-cov-2-21L/BA.2/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2-21L/BA.2/unreleased/pathogen.json index fc9391401..41b812d85 100644 --- a/data_output/nextstrain/sars-cov-2-21L/BA.2/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2-21L/BA.2/unreleased/pathogen.json @@ -20,6 +20,10 @@ "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "defaultGene": "S", "deprecated": false, "enabled": true, diff --git a/data_output/nextstrain/sars-cov-2/MN908947/unreleased/image.png b/data_output/nextstrain/sars-cov-2/MN908947/unreleased/image.png new file mode 100644 index 000000000..6dce9328a Binary files /dev/null and b/data_output/nextstrain/sars-cov-2/MN908947/unreleased/image.png differ diff --git a/data_output/nextstrain/sars-cov-2/MN908947/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/MN908947/unreleased/pathogen.json index 645caabdf..4b7066f7a 100644 --- a/data_output/nextstrain/sars-cov-2/MN908947/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/MN908947/unreleased/pathogen.json @@ -20,6 +20,10 @@ "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "defaultGene": "S", "deprecated": false, "enabled": true, diff --git a/data_output/nextstrain/zika/unreleased/image.png b/data_output/nextstrain/zika/unreleased/image.png new file mode 100644 index 000000000..24f7173c1 Binary files /dev/null and b/data_output/nextstrain/zika/unreleased/image.png differ diff --git a/data_output/nextstrain/zika/unreleased/pathogen.json b/data_output/nextstrain/zika/unreleased/pathogen.json index 6b70713a7..15f2fe137 100644 --- a/data_output/nextstrain/zika/unreleased/pathogen.json +++ b/data_output/nextstrain/zika/unreleased/pathogen.json @@ -13,6 +13,10 @@ "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" }, + "image": { + "path": "image.png", + "source": "nextstrain.org" + }, "deprecated": false, "experimental": true, "files": { diff --git a/scripts/rebuild_v3 b/scripts/rebuild_v3 index 274fb5c5e..893118358 100755 --- a/scripts/rebuild_v3 +++ b/scripts/rebuild_v3 @@ -7,7 +7,7 @@ import argparse import json from copy import deepcopy from os import getcwd -from os.path import dirname, realpath, join, relpath, isfile +from os.path import dirname, realpath, join, relpath, isfile, exists from lib.changelog import changelog_prepare from lib.container import dict_get, dict_get_required, dict_set, unique, find_index_by, first, format_list, \ @@ -74,6 +74,7 @@ def index_one_dataset(args, pathogen_json_path: str, updated_at: str): "enabled": False if dict_get(pathogen_json, ["enabled"]) == False else True, "experimental": True if dict_get(pathogen_json, ["experimental"]) == True else False, "attributes": dict_get_required(pathogen_json, ["attributes"]), + "image": dict_get(pathogen_json, ["image"]), "files": dict_get_required(pathogen_json, ["files"]), "capabilities": get_dataset_capabilities(pathogen_json, dataset_dir), }) @@ -391,6 +392,12 @@ def create_dataset_package(args, dataset, pathogen_json, tag, dataset_dir): else: copy(inpath, outpath) + image_path = dict_get(pathogen_json, ["image", "path"]) + if image_path: + copy(join(dataset_dir, image_path), join(out_dir, image_path)) + elif any([exists(join(dataset_dir, f"image.{ext}")) for ext in ["png", "jpg", "gif", "svg"]]): + l.warning(f"In dataset {path}: Image file found, but pathogen.json does not have a correponding entry") + zip_basename = join(out_dir, "dataset") make_zip(dataset_dir, zip_basename)