Merge pull request #279 from togoid/main

release 2024-12-05
togoid · Dec 5, 2024 · a60d98f · a60d98f
2 parents 7f62a4f + 8f602e0
commit a60d98f
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diff --git a/Dockerfile b/Dockerfile
@@ -6,7 +6,7 @@ RUN apt-get update -y && apt-get install -y \
       libjson-perl=4.04000-1 \
       libany-uri-escape-perl=0.01-3 \
       libwww-perl=6.61-1 \
-      curl=7.81.0-1ubuntu1.18 \
+      curl=7.81.0-1ubuntu1.19 \
       wget=1.21.2-2ubuntu1 \
       gawk=1:5.1.0-1build3 \
       python3=3.10.6-1~22.04.1 \

diff --git a/docs/help.md b/docs/help.md
@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-11-26
+Datasets last updated: 2024-12-05
 
 ## About
 - [TogoID](https://togoid.dbcls.jp/) is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an [ontology](https://togoid.dbcls.jp/ontology) that defines the semantics of the dataset relations.
@@ -10,7 +10,7 @@ Datasets last updated: 2024-11-26
 ## Video tutorial
 - [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
 
-## Statistics (as of 2024-11-26)
+## Statistics (as of 2024-12-05)
 - Number of target datasets 
     - 105 (from 73 databases)
 - For details on the target DBs and ID examples, please refer to the "DATASETS" tab. 

diff --git a/docs/help_ja.md b/docs/help_ja.md
@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-11-26
+Datasets last updated: 2024-12-05
 
 ## About
 - [TogoID](https://togoid.dbcls.jp/) は、直感的なインターフェースにより生命科学系データベース(DB)間のつながりを探索的に確認しながらID変換を行うことができるウェブアプリケーションです。同一の実体を指すID間の変換だけでなく、関連する別のカテゴリーのIDへの変換も可能です。また、直接リンクされていないDBのID間でも、他のDBを経由した変換を探索することができます。
@@ -10,7 +10,7 @@ Datasets last updated: 2024-11-26
 ## 動画マニュアル
 - [TogoIDを使って生命科学系データベースのさまざまなIDを探索的に変換する](https://youtu.be/gXnvm6Fn4R8)
 
-## 統計 (2024-11-26)
+## 統計 (2024-12-05)
 - 対象データセット数 
     - 105 (73 のデータベースに由来)
 - 対象DBの詳細やID例については、"DATASETS" タブ からご覧いただけます。 

diff --git a/docs/news.md b/docs/news.md
@@ -1,3 +1,6 @@
+# 2024-12-05
+- Weekly update has been completed.
+
 # 2024-11-26
 - Weekly update has been completed.
 

diff --git a/log/error.log b/log/error.log
@@ -3,61 +3,49 @@ Error: check_remote_file_time(input/homologene/homologene.data, https://ftp.ncbi
 Error: Remote file is empty
 # Error: output/tsv/chembl_target-ensembl_gene.tsv new file size per old 0 / 61845 = 0.0 < 0.5
 # Error: Failed to create output/tsv/chembl_target-ensembl_gene.tsv or created file was empty
-Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/partialmatch?wurcs=WURCS%3D2.0%2F4%2C11%2C10%2F%5Ba2122h-1b_1-5%5D%5Ba2112h-1b_1-5%5D%5Ba2122h-1b_1-5_2%2ANCC%2F3%3DO%5D%5Ba1221m-1a_1-5%5D%2F1-2-3-2-3-2-3-4-2-3-2%2Fa4-b1_b3-c1_c4-d1_d3-e1_e4-f1_f3-g1_g3-h1_g4-i1_i3-j1_j4-k1&rootnode=true G64227KZ
+Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/partialmatch?wurcs=WURCS%3D2.0%2F4%2C10%2C9%2F%5Ba2122h-1b_1-5%5D%5Ba2112h-1b_1-5%5D%5BAad21122h-2a_2-6_5%2ANCC%2F3%3DO%5D%5Ba2112h-1b_1-5_2%2ANCC%2F3%3DO%5D%2F1-2-3-3-3-4-2-3-3-3%2Fa4-b1_b3-c2_b4-f1_c8-d2_d8-e2_f3-g1_f6-j2_g3-h2_h8-i2&rootnode=true G14091MR
 # Error: output/tsv/glycomotif-glytoucan.tsv new file size per old 0 / 2804382 = 0.0 < 0.5
 # Error: Failed to create output/tsv/glycomotif-glytoucan.tsv or created file was empty
 # Error: output/tsv/glytoucan-doid.tsv new file size per old 1538 / 4376 = 0.35146252285191953 < 0.5
 # Error: output/tsv/hgnc-ccds.tsv new file size per old 252491 / 544502 = 0.46370995882476096 < 0.5
-# Error: output/tsv/lipidmaps-chebi.tsv new file size per old 248 / 253350 = 0.0009788829682257747 < 0.5
+# Error: output/tsv/lipidmaps-chebi.tsv new file size per old 148 / 253350 = 0.000584172093941188 < 0.5
 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <html><head>
-# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <title>503 Service Unavailable</title>
+# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <title>403 Forbidden</title>
 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML </head><body>
-# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <h1>Service Unavailable</h1>
-# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <p>The server is temporarily unable to service your
-# Error: output/tsv/lipidmaps-chebi.tsv seems to be malformed request due to maintenance downtime or capacity
-# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML problems. Please try again later.</p>
+# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <h1>Forbidden</h1>
+# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <p>You don't have permission to access this resource.</p>
 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML </body></html>
 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <html><head>
-# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <title>503 Service Unavailable</title>
+# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <title>403 Forbidden</title>
 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML </head><body>
-# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <h1>Service Unavailable</h1>
-# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <p>The server is temporarily unable to service your
-# Error: output/tsv/lipidmaps-chebi.tsv seems to be malformed request due to maintenance downtime or capacity
-# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML problems. Please try again later.</p>
+# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <h1>Forbidden</h1>
+# Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <p>You don't have permission to access this resource.</p>
 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML </body></html>
-# Error: output/tsv/lipidmaps-inchi_key.tsv new file size per old 248 / 1976727 = 0.0001254599142926666 < 0.5
+# Error: output/tsv/lipidmaps-inchi_key.tsv new file size per old 148 / 1976727 = 7.487123917465588e-05 < 0.5
 # Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <html><head>
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <title>503 Service Unavailable</title>
+# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <title>403 Forbidden</title>
 # Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML </head><body>
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <h1>Service Unavailable</h1>
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <p>The server is temporarily unable to service your
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to be malformed request due to maintenance downtime or capacity
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML problems. Please try again later.</p>
+# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <h1>Forbidden</h1>
+# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <p>You don't have permission to access this resource.</p>
 # Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML </body></html>
 # Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <html><head>
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <title>503 Service Unavailable</title>
+# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <title>403 Forbidden</title>
 # Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML </head><body>
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <h1>Service Unavailable</h1>
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <p>The server is temporarily unable to service your
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to be malformed request due to maintenance downtime or capacity
-# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML problems. Please try again later.</p>
+# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <h1>Forbidden</h1>
+# Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML <p>You don't have permission to access this resource.</p>
 # Error: output/tsv/lipidmaps-inchi_key.tsv seems to contain HTML </body></html>
-# Error: output/tsv/lipidmaps-swisslipids.tsv new file size per old 248 / 284047 = 0.0008730949455547849 < 0.5
+# Error: output/tsv/lipidmaps-swisslipids.tsv new file size per old 148 / 284047 = 0.0005210405320246297 < 0.5
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <html><head>
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <title>503 Service Unavailable</title>
+# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <title>403 Forbidden</title>
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML </head><body>
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <h1>Service Unavailable</h1>
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <p>The server is temporarily unable to service your
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to be malformed request due to maintenance downtime or capacity
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML problems. Please try again later.</p>
+# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <h1>Forbidden</h1>
+# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <p>You don't have permission to access this resource.</p>
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML </body></html>
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <html><head>
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <title>503 Service Unavailable</title>
+# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <title>403 Forbidden</title>
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML </head><body>
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <h1>Service Unavailable</h1>
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <p>The server is temporarily unable to service your
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to be malformed request due to maintenance downtime or capacity
-# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML problems. Please try again later.</p>
+# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <h1>Forbidden</h1>
+# Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML <p>You don't have permission to access this resource.</p>
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML </body></html>
 # Error: output/tsv/mbgd_gene-uniprot.tsv new file size per old 0 / 4017692184 = 0.0 < 0.5
 # Error: Failed to create output/tsv/mbgd_gene-uniprot.tsv or created file was empty