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Merge branch 'main' of github.com:togoid/togoid-config into main
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@sh-ikeda
sh-ikeda committed Dec 17, 2024
2 parents d284d99 + 237a96d commit 8161fc8
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2 changes: 1 addition & 1 deletion log/config-summary.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ hgnc-ncbigene nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00073 Gene NC
hgnc-omim_gene nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00154 Gene OMIM gene http://identifiers.org/mim/ tio:TIO_000001 is nearly equivalent to is nearly equivalent to tio:TIO_000001 is nearly equivalent to is nearly equivalent to Bimonthly "awk -F \"\\t\" 'FNR>=2&&$32{gsub(\"\\\"\",\"\",$32); split($32,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-pubmed nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00179 Literature PubMed http://rdf.ncbi.nlm.nih.gov/pubmed/ tio:TIO_000032 has reference has reference tio:TIO_000033 is reference of is reference of Bimonthly "awk -F \"\\t\" 'FNR>=2&&$27{gsub(\"\\\"\",\"\",$27); split($27,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-refseq_genomic nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00187 Gene RefSeq genomic http://identifiers.org/refseq/ tio:TIO_000001 is nearly equivalent to is nearly equivalent to tio:TIO_000001 is nearly equivalent to is nearly equivalent to Bimonthly "awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^NG_/)print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-refseq_rna nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00187 Transcript RefSeq RNA http://identifiers.org/refseq/ tio:TIO_000035 gene is transcribed to transcript is transcribed to tio:TIO_000034 transcript is transcribed from gene is transcribed from Bimonthly "awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^[NX][MR]_/)print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-refseq_rna nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00187 Transcript RefSeq RNA http://identifiers.org/refseq/ tio:TIO_000035 gene is transcribed to transcript is transcribed to tio:TIO_000034 transcript is transcribed from gene is transcribed from Bimonthly "awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^[NX][MR]_/)print substr($1,6) \"\\t\" gensub(/\\.$/,\"\",\"g\",a[k])}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-rgd nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00188 Gene RGD http://identifiers.org/rgd/ tio:TIO_000017 sequence is orthologous to sequence is orthologous to tio:TIO_000017 sequence is orthologous to sequence is orthologous to Bimonthly "awk -F \"\\t\" 'FNR>=2&&$29{gsub(\"\\\"\",\"\",$29); split($29,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hgnc-uniprot nbdc01774 Gene HGNC http://identifiers.org/hgnc/ nbdc00221 Protein UniProt http://purl.uniprot.org/uniprot/ tio:TIO_000025 gene has protein as product has gene product tio:TIO_000024 protein is product of gene is product of gene Bimonthly "awk -F \"\\t\" 'FNR>=2&&$26{gsub(\"\\\"\",\"\",$26); split($26,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
hmdb-chebi nbdc00909 Compound HMDB http://identifiers.org/hmdb/ nbdc00027 Compound ChEBI compound http://purl.obolibrary.org/obo/CHEBI_ tio:TIO_000001 is nearly equivalent to is nearly equivalent to tio:TIO_000001 is nearly equivalent to is nearly equivalent to Triennial "awk -F \"\\t\" '$2==\"chebi_id\"{print $1 \"\\t\" $3}' $TOGOID_ROOT/input/hmdb/hmdb_metabolites.tsv"
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105 changes: 61 additions & 44 deletions log/error.log
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@@ -1,13 +1,72 @@
Error: download_file(input/glytoucan, https://glycosmos.org/download/glycosmos_ggdbs_pubmed.csv): Command failed with status (8): [wget --quiet --recursive --no-parent --no-...]
Error: check_remote_file_time(input/homologene/homologene.data, https://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current/homologene.data): no time information in ""
Error: Remote file is empty
# Error: output/tsv/affy_probeset-ncbigene.tsv new file size per old 248 / 314378 = 0.000788859271323057 < 0.5
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML <html><head>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML <title>503 Service Unavailable</title>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML </head><body>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML <h1>Service Unavailable</h1>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML <p>The server is temporarily unable to service your
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to be malformed request due to maintenance downtime or capacity
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML problems. Please try again later.</p>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML </body></html>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML <html><head>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML <title>503 Service Unavailable</title>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML </head><body>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML <h1>Service Unavailable</h1>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML <p>The server is temporarily unable to service your
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to be malformed request due to maintenance downtime or capacity
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML problems. Please try again later.</p>
# Error: output/tsv/affy_probeset-ncbigene.tsv seems to contain HTML </body></html>
# Error: output/tsv/assembly_insdc-bioproject.tsv new file size per old 0 / 58955319 = 0.0 < 0.5
# Error: Failed to create output/tsv/assembly_insdc-bioproject.tsv or created file was empty
# Error: output/tsv/assembly_insdc-biosample.tsv new file size per old 0 / 60555966 = 0.0 < 0.5
# Error: Failed to create output/tsv/assembly_insdc-biosample.tsv or created file was empty
# Error: output/tsv/assembly_insdc-insdc_master.tsv new file size per old 0 / 63716447 = 0.0 < 0.5
# Error: Failed to create output/tsv/assembly_insdc-insdc_master.tsv or created file was empty
# Error: output/tsv/bioproject-biosample.tsv new file size per old 0 / 63710867 = 0.0 < 0.5
# Error: Failed to create output/tsv/bioproject-biosample.tsv or created file was empty
# Error: output/tsv/bioproject_umbrella-bioproject.tsv new file size per old 0 / 2475955 = 0.0 < 0.5
# Error: Failed to create output/tsv/bioproject_umbrella-bioproject.tsv or created file was 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: output/tsv/ensembl_gene-ensembl_protein.tsv new file size per old 0 / 493740466 = 0.0 < 0.5
# Error: Failed to create output/tsv/ensembl_gene-ensembl_protein.tsv or created file was empty
# Error: output/tsv/ensembl_gene-ensembl_transcript.tsv new file size per old 0 / 606499011 = 0.0 < 0.5
# Error: Failed to create output/tsv/ensembl_gene-ensembl_transcript.tsv or created file was empty
# Error: output/tsv/ensembl_gene-ncbigene.tsv new file size per old 0 / 425488063 = 0.0 < 0.5
# Error: Failed to create output/tsv/ensembl_gene-ncbigene.tsv or created file was empty
# Error: output/tsv/ensembl_gene-uniprot.tsv new file size per old 0 / 159598297 = 0.0 < 0.5
# Error: Failed to create output/tsv/ensembl_gene-uniprot.tsv or created file was empty
# Error: output/tsv/ensembl_protein-ensembl_transcript.tsv new file size per old 0 / 493651516 = 0.0 < 0.5
# Error: Failed to create output/tsv/ensembl_protein-ensembl_transcript.tsv or created file was empty
# Error: output/tsv/ensembl_transcript-go.tsv new file size per old 0 / 1491765002 = 0.0 < 0.5
# Error: Failed to create output/tsv/ensembl_transcript-go.tsv or created file was empty
# Error: output/tsv/ensembl_transcript-refseq_rna.tsv new file size per old 0 / 1283309099 = 0.0 < 0.5
# Error: Failed to create output/tsv/ensembl_transcript-refseq_rna.tsv or created file was empty
# Error: output/tsv/gea-bioproject.tsv new file size per old 0 / 3032 = 0.0 < 0.5
# Error: Failed to create output/tsv/gea-bioproject.tsv or created file was empty
# Error: output/tsv/gea-biosample.tsv new file size per old 0 / 121104 = 0.0 < 0.5
# Error: Failed to create output/tsv/gea-biosample.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: 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/glytoucan-doid.tsv new file size per old 0 / 4376 = 0.0 < 0.5
# Error: Failed to create output/tsv/glytoucan-doid.tsv or created file was empty
# Error: output/tsv/hgnc-ccds.tsv new file size per old 252491 / 544502 = 0.46370995882476096 < 0.5
# Error: output/tsv/insdc-bioproject.tsv new file size per old 0 / 1191557755 = 0.0 < 0.5
# Error: Failed to create output/tsv/insdc-bioproject.tsv or created file was empty
# Error: output/tsv/insdc-biosample.tsv new file size per old 0 / 4269980335 = 0.0 < 0.5
# Error: Failed to create output/tsv/insdc-biosample.tsv or created file was empty
# Error: output/tsv/insdc_master-bioproject.tsv new file size per old 0 / 41801168 = 0.0 < 0.5
# Error: Failed to create output/tsv/insdc_master-bioproject.tsv or created file was empty
# Error: output/tsv/insdc_master-biosample.tsv new file size per old 0 / 43765492 = 0.0 < 0.5
# Error: Failed to create output/tsv/insdc_master-biosample.tsv or created file was empty
# Error: output/tsv/jga_study-jga_dataset.tsv new file size per old 0 / 4378 = 0.0 < 0.5
# Error: Failed to create output/tsv/jga_study-jga_dataset.tsv or created file was empty
# Error: output/tsv/jga_study-nbdc_human_db.tsv new file size per old 0 / 5795 = 0.0 < 0.5
# Error: Failed to create output/tsv/jga_study-nbdc_human_db.tsv or created file was empty
# Error: output/tsv/jga_study-pubmed.tsv new file size per old 0 / 2597 = 0.0 < 0.5
# Error: Failed to create output/tsv/jga_study-pubmed.tsv or created file was empty
# 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>403 Forbidden</title>
Expand Down Expand Up @@ -63,46 +122,4 @@ Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/pa
# Error: Failed to create output/tsv/mondo-omim_phenotype.tsv or created file was empty
# Error: output/tsv/mondo-orphanet_phenotype.tsv new file size per old 0 / 146923 = 0.0 < 0.5
# Error: Failed to create output/tsv/mondo-orphanet_phenotype.tsv or created file was empty
# Error: output/tsv/ncit_disease-ncit_tissue.tsv new file size per old 291 / 385314 = 0.0007552282034911786 < 0.5
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <html><head>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <title>408 Request Timeout</title>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML </head><body>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <h1>Request Timeout</h1>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <p>Server timeout waiting for the HTTP request from the client.</p>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <p>Additionally a 502 Bad Gateway
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML error was encountered while trying to use an ErrorDocument to handle the request.</p>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML </body></html>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <html><head>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <title>408 Request Timeout</title>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML </head><body>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <h1>Request Timeout</h1>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <p>Server timeout waiting for the HTTP request from the client.</p>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML <p>Additionally a 502 Bad Gateway
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML error was encountered while trying to use an ErrorDocument to handle the request.</p>
# Error: output/tsv/ncit_disease-ncit_tissue.tsv seems to contain HTML </body></html>
# Error: output/tsv/togovar-ensembl_transcript.tsv new file size per old 0 / 8069270901 = 0.0 < 0.5
# Error: Failed to create output/tsv/togovar-ensembl_transcript.tsv or created file was empty
# Error: output/tsv/togovar-ncbigene.tsv new file size per old 0 / 1097267175 = 0.0 < 0.5
# Error: Failed to create output/tsv/togovar-ncbigene.tsv or created file was empty
# Error: output/tsv/togovar-pubmed.tsv new file size per old 0 / 14408635 = 0.0 < 0.5
# Error: Failed to create output/tsv/togovar-pubmed.tsv or created file was empty
# Error: output/tsv/togovar-refseq_rna.tsv new file size per old 0 / 4180808277 = 0.0 < 0.5
# Error: Failed to create output/tsv/togovar-refseq_rna.tsv or created file was empty
# Error: output/tsv/uberon-ncit_tissue.tsv new file size per old 288 / 38722 = 0.007437632353700738 < 0.5
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML <html><head>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML <title>502 Proxy Error</title>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML </head><body>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML <h1>Proxy Error</h1>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML <p>The proxy server received an invalid
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML response from an upstream server.<br />
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server could not handle the request<p>Reason: <strong>Error reading from remote server</strong></p></p>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML </body></html>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML <html><head>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML <title>502 Proxy Error</title>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML </head><body>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML <h1>Proxy Error</h1>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML <p>The proxy server received an invalid
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML response from an upstream server.<br />
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML The proxy server could not handle the request<p>Reason: <strong>Error reading from remote server</strong></p></p>
# Error: output/tsv/uberon-ncit_tissue.tsv seems to contain HTML </body></html>
# Error: output/tsv/wikipathways-uniprot.tsv new file size per old 60240 / 470542 = 0.12802257821830995 < 0.5
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