1. KEGGREST
  2. NAMESPACE
Browse code

use POST to fetch color maps

jvolkening authored on 23/11/2020 05:35:37
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NAMESPACE
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@@ -1,6 +1,6 @@
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 importFrom(utils, download.file, head)
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-importFrom(httr, GET, http_status, content, stop_for_status)
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+importFrom(httr, GET, POST, http_status, content, stop_for_status)
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 importFrom(png, readPNG, writePNG)
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 importFrom(Biostrings, readAAStringSet, readDNAStringSet,
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     DNAStringSet, AAStringSet)
Browse code

keggConv supports more than 100 identifiers

- iterate when more than 100 ids provided
- seems to be a (empirically determined) limit on KEGG's part
- closes #1

Martin Morgan authored on 10/02/2018 12:13:28
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NAMESPACE
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@@ -1,4 +1,5 @@
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+importFrom(utils, download.file, head)
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 importFrom(httr, GET, http_status, content, stop_for_status)
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 importFrom(png, readPNG, writePNG)
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 importFrom(Biostrings, readAAStringSet, readDNAStringSet,
Browse code

Fix issue reported by Martin: use httr::stop_for_status(response) instead of parsing response, which may change over time.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@112198 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 06/01/2016 00:13:20
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NAMESPACE
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@@ -1,8 +1,9 @@
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-importFrom(httr, GET, http_status, content)
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+importFrom(httr, GET, http_status, content, stop_for_status)
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 importFrom(png, readPNG, writePNG)
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 importFrom(Biostrings, readAAStringSet, readDNAStringSet,
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     DNAStringSet, AAStringSet)
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+import(methods)
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 export(
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     keggInfo,
Browse code

improving flat file parsing, step 2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72494 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/01/2013 00:05:28
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NAMESPACE
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@@ -1,7 +1,8 @@
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 importFrom(httr, GET, http_status, content)
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 importFrom(png, readPNG, writePNG)
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-importFrom(Biostrings, readAAStringSet)
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+importFrom(Biostrings, readAAStringSet, readDNAStringSet,
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+    DNAStringSet, AAStringSet)
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 export(
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     keggInfo,
Browse code

keggGet with aaseq or ntseq option now returns an AAStringSet object

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72220 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/01/2013 19:59:12
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NAMESPACE
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@@ -1,6 +1,7 @@
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 importFrom(httr, GET, http_status, content)
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 importFrom(png, readPNG, writePNG)
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+importFrom(Biostrings, readAAStringSet)
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 export(
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     keggInfo,
Browse code

Extensive rewrite, deciding to expose all functionality in KEGG REST API, rather than trying to create a drop-in replacement for KEGGSOAP which is not widely used (and much of its functionality did not make the transition to REST). Passes check with --no-tests, because tests have not been rewritten yet. Also still need to add a vignette.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72211 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/01/2013 00:44:55
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NAMESPACE
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@@ -1,39 +1,16 @@
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 importFrom(httr, GET, http_status, content)
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+importFrom(png, readPNG, writePNG)
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+
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+export(
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+    keggInfo,
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+    keggList,
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+    listDatabases,
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+    keggFind,
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+    keggGet,
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+    keggConv,
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+    keggLink,
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+    mark.pathway.by.objects,
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+    color.pathway.by.objects
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+)
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-export(color.pathway.by.objects,
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-       get.best.best.neighbors.by.gene,
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-       getBestNeighbors,
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-       get.best.neighbors.by.gene,
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-       get.compounds.by.pathway,
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-       get.enzymes.by.pathway,
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-       get.genes.by.motifs,
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-       get.genes.by.organism,
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-       get.genes.by.pathway,
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-       get.motifs.by.gene,
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-       get.paralogs.by.gene,
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-       get.pathways.by.compounds,
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-       get.pathways.by.enzymes,
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-       get.pathways.by.genes,
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-       get.pathways.by.reactions,
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-       get.reactions.by.pathway,
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-       list.databases,
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-       list.organisms,
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-       list.pathways,
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-       mark.pathway.by.objects,
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-       search.compounds.by.name,
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-       search.glycans.by.name,
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-       search.compounds.by.composition,
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-       search.glycans.by.composition,
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-       search.glycans.by.mass,
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-       search.compounds.by.mass,
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-       search.compounds.by.subcomp,
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-       search.glycans.by.kcam,
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-       bget,
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-       bconv,
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-       get.ko.by.gene,
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-       get.ko.by.ko.class,
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-       get.genes.by.ko.class,
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-       get.genes.by.ko,
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-       get.kos.by.pathway,
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-       get.pathways.by.kos)
Browse code

cleanup, add questions for KEGG

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72159 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 23/12/2012 21:52:40
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NAMESPACE
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@@ -1,8 +1,6 @@
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 importFrom(httr, GET, http_status, content)
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-importFrom(methods, slot, slotNames)
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-
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 export(color.pathway.by.objects,
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        get.best.best.neighbors.by.gene,
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        getBestNeighbors,
Browse code

implemented mark.pathway.by.objects()/color.pathway.by.objects(), general cleanup

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72155 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 23/12/2012 20:25:19
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NAMESPACE
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@@ -1,4 +1,8 @@
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+importFrom(httr, GET, http_status, content)
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+
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+importFrom(methods, slot, slotNames)
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+
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 export(color.pathway.by.objects,
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        get.best.best.neighbors.by.gene,
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        getBestNeighbors,
Browse code

initial checkin, only one function works (get.genes.by.pathway())

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72144 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 22/12/2012 02:17:15
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NAMESPACE
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new file mode 100644
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+
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+export(color.pathway.by.objects,
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+       get.best.best.neighbors.by.gene,
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+       getBestNeighbors,
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+       get.best.neighbors.by.gene,
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+       get.compounds.by.pathway,
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+       get.enzymes.by.pathway,
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+       get.genes.by.motifs,
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+       get.genes.by.organism,
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+       get.genes.by.pathway,
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+       get.motifs.by.gene,
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+       get.paralogs.by.gene,
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+       get.pathways.by.compounds,
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+       get.pathways.by.enzymes,
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+       get.pathways.by.genes,
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+       get.pathways.by.reactions,
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+       get.reactions.by.pathway,
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+       list.databases,
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+       list.organisms,
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+       list.pathways,
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+       mark.pathway.by.objects,
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+       search.compounds.by.name,
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+       search.glycans.by.name,
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+       search.compounds.by.composition,
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+       search.glycans.by.composition,
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+       search.glycans.by.mass,
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+       search.compounds.by.mass,
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+       search.compounds.by.subcomp,
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+       search.glycans.by.kcam,
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+       bget,
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+       bconv,
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+       get.ko.by.gene,
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+       get.ko.by.ko.class,
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+       get.genes.by.ko.class,
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+       get.genes.by.ko,
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+       get.kos.by.pathway,
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+       get.pathways.by.kos)