Mercurial > repos > yating-l > jbrowsearchivecreator
diff util/index/DatabaseIndex.py @ 14:3f9971a91096 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
author | yating-l |
---|---|
date | Wed, 20 Jun 2018 17:24:45 -0400 |
parents | 237707a6b74d |
children |
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--- a/util/index/DatabaseIndex.py Tue Jun 19 17:59:51 2018 -0400 +++ b/util/index/DatabaseIndex.py Wed Jun 20 17:24:45 2018 -0400 @@ -7,38 +7,33 @@ def __init__(self, database, **args): self.database = database self.seqType=args.get("seqType") - self.useIframe=args.get("useIframe") - self.iframeHeight=args.get("iframeHeight") - self.iframeWidth=args.get("iframeWidth") + def setExtLink(self): - return self.setDatabaseLink(self.database, self.seqType, self.useIframe, self.iframeHeight, self.iframeWidth) + return self.setDatabaseLink(self.database, self.seqType) - def setDatabaseLink(self, database, seqType=None, useIframe=None, iframeHeight=None, iframeWidth=None): + def setDatabaseLink(self, database, seqType=None): database_settings = collections.OrderedDict() + database_settings.update({"label": "View feature details in the database", + "action": "iframeDialog", + "iconClass": "dijitIconDatabase", + "title": "feature {name}"}) + if "NCBI" in database: if not seqType: - database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$" + database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term={name}" elif seqType == 2: - database_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$" + database_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/{name}" elif seqType == 1: - database_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$" + database_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/{name}" else: raise Exception("Sequence Type {0} is not valid, should be either protein (seqType==2) or nucleotide (seqType==1). Stopping the application".format(seqType)) elif "UniProt" in database: - database_settings["url"] = "http://www.uniprot.org/uniprot/$$" + database_settings["url"] = "http://www.uniprot.org/uniprot/{name}" elif "FlyBase" in database: - database_settings["url"] = "http://flybase.org/reports/$$" + database_settings["url"] = "http://flybase.org/reports/{name}" else: - database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$" - database_settings["urlLabel"] = database + " Details:" - if useIframe or useIframe is None: - database_settings["iframeUrl"] = database_settings["url"] - if not iframeHeight: - iframeHeight = "600" - if not iframeWidth: - iframeWidth = "800" - database_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth) + database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term={name}" return database_settings