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From: Michael P. <mic...@ho...> - 2001-01-26 01:52:57
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Jason and Jiaye, I tried to download a control bundle on my new installation, but = db2xml.pl failed because it couldn't find CanonicalSequenceFeature.pm. I don't see it or anything in = Genex/CanonicalSequenceFeature in the install tree. I no longer find this table in the database either. = What's up?=20 Regards, Michael Pear |
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From: <ja...@op...> - 2001-01-26 02:54:57
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"Michael Pear" <mic...@ho...> writes: > I tried to download a control bundle on my new installation, but > db2xml.pl failed because it couldn't find > CanonicalSequenceFeature.pm. I don't see it or anything in > Genex/CanonicalSequenceFeature in the install tree. I no longer find > this table in the database either. What's up? This was in the Release Notes for DB v0.8.1, but for some reason, I didn't include it in the Server install notes: From the release notes: * All tables related to Canonical Sequence Features were removed (CanonicalSequenceFeature, CSF_ExternalDBLink, UserCanonicalLink, RelatedCSF) * the two CSF related columns in UserSequenceFeature were removed (putative_csf_fk, nonunique_flag) And it looks like *I* didn't debug things enough :-( CSF was supposed to go away a month ago, it has always been an unsupported feature, and since it was never really broken, it never made it high enough on my priority to remove. I did it last release. Todd and/or Lonny. Will the CT break without CSF in the control bundle? Should I just output a blank CSF section for now? Mea culpa, mea culpa, jas. |
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From: Michael P. <mic...@ho...> - 2001-01-26 03:44:09
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I missed the Release Notes for the DB...I see them on sourceforge now. I did a quick check by doing an rgrep on the install tree and there are still a lot of references to CanonicalSequenceFeature in xml2db.pl as well, so even if the curation tool can handle it, having nothing there may break submission using xml2db.pl Regards, Michael Pear ----- Original Message ----- From: "Jason E. Stewart" <ja...@op...> To: "Michael Pear" <mic...@ho...> Cc: "Jason E. Stewart" <ja...@op...>; "Jiaye Zhou" <ze...@in...>; <gen...@li...> Sent: Thursday, January 25, 2001 6:56 PM Subject: [GeneX-dev] Re: CanonicalSequenceFeature is missing... > "Michael Pear" <mic...@ho...> writes: > > > I tried to download a control bundle on my new installation, but > > db2xml.pl failed because it couldn't find > > CanonicalSequenceFeature.pm. I don't see it or anything in > > Genex/CanonicalSequenceFeature in the install tree. I no longer find > > this table in the database either. What's up? > > This was in the Release Notes for DB v0.8.1, but for some reason, I > didn't include it in the Server install notes: > > From the release notes: > > * All tables related to Canonical Sequence Features were removed > (CanonicalSequenceFeature, CSF_ExternalDBLink, UserCanonicalLink, > RelatedCSF) > * the two CSF related columns in UserSequenceFeature were removed > (putative_csf_fk, nonunique_flag) > > And it looks like *I* didn't debug things enough :-( > > CSF was supposed to go away a month ago, it has always been an > unsupported feature, and since it was never really broken, it never > made it high enough on my priority to remove. I did it last release. > > Todd and/or Lonny. Will the CT break without CSF in the control > bundle? Should I just output a blank CSF section for now? > > Mea culpa, mea culpa, > jas. > > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: <ja...@op...> - 2001-01-26 05:15:35
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"Michael Pear" <mic...@ho...> writes: > I missed the Release Notes for the DB...I see them on sourceforge > now. Not your fault, since the changes were in the Genex.pm API, I should have indicated it there. I have just started using release notes for the Server, though, so I'm just learning how I should do it. > I did a quick check by doing an rgrep on the install tree and there > are still a lot of references to CanonicalSequenceFeature in xml2db.pl > as well, so even if the curation tool can handle it, having nothing there > may break submission using xml2db.pl Yes, Jiaye just found this out yesterday when he and I worked on the XML API. He will have that fixed in a day or two. I have removed the references to CSF in db2xml, and it prints out, but I've found a rather troubling bug in the USF_ExternalDBLink class that looks like another nasty linking table bug (did I mention that linking tables give me gas??). I'm working to crack that one right now. The good news is, as soon as I fix this, you will only need to update your Genex.pm installation. As a stand-alone perl module, it uses your already installed Config.pm to configure and install itself, so the upgrade should be easy. I hope to post it later tonight to sourceforge. Your a great help, Michael, and a good sport, jas. |
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From: Jiaye Z. <ze...@in...> - 2001-01-26 05:48:59
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Hi Michael, Actually, I don't think this will break the xml2db code. It will just ignore the missing top level xml elements which are CannonicalSequenceFeature. In fact, I believe that I have tested the code against files that are missing CSF, but that would be a while ago and I haven't done any development on the CSF end. I have known of the decision on not supporting CSF, but since the Curation Tool has been outputing CSF, I never removed the code that handled it. Perhaps this is a good time for me to clean that part of the code up. Jiaye Quoting Michael Pear <mic...@ho...>: > I missed the Release Notes for the DB...I see them on sourceforge > now. > > I did a quick check by doing an rgrep on the install tree and there > are still a lot of references to CanonicalSequenceFeature in xml2db.pl > as well, so even if the curation tool can handle it, having nothing > there > may break submission using xml2db.pl > > Regards, > > Michael Pear > > ----- Original Message ----- > From: "Jason E. Stewart" <ja...@op...> > To: "Michael Pear" <mic...@ho...> > Cc: "Jason E. Stewart" <ja...@op...>; "Jiaye Zhou" > <ze...@in...>; > <gen...@li...> > Sent: Thursday, January 25, 2001 6:56 PM > Subject: [GeneX-dev] Re: CanonicalSequenceFeature is missing... > > > > "Michael Pear" <mic...@ho...> writes: > > > > > I tried to download a control bundle on my new installation, but > > > db2xml.pl failed because it couldn't find > > > CanonicalSequenceFeature.pm. I don't see it or anything in > > > Genex/CanonicalSequenceFeature in the install tree. I no longer find > > > this table in the database either. What's up? > > > > This was in the Release Notes for DB v0.8.1, but for some reason, I > > didn't include it in the Server install notes: > > > > From the release notes: > > > > * All tables related to Canonical Sequence Features were removed > > (CanonicalSequenceFeature, CSF_ExternalDBLink, UserCanonicalLink, > > RelatedCSF) > > * the two CSF related columns in UserSequenceFeature were removed > > (putative_csf_fk, nonunique_flag) > > > > And it looks like *I* didn't debug things enough :-( > > > > CSF was supposed to go away a month ago, it has always been an > > unsupported feature, and since it was never really broken, it never > > made it high enough on my priority to remove. I did it last release. > > > > Todd and/or Lonny. Will the CT break without CSF in the control > > bundle? Should I just output a blank CSF section for now? > > > > Mea culpa, mea culpa, > > jas. > > > > > > > > _______________________________________________ > > Genex-dev mailing list > > Gen...@li... > > http://lists.sourceforge.net/lists/listinfo/genex-dev > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev > |
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From: Michael P. <mic...@ho...> - 2001-01-26 14:00:38
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You might want to look at the code with the idea of ignoring any CSF section that comes in an XML file... If I resubmit one of my existing experiment sets from last week, if nothing is there to handle it, will it fail if you remove all mention of it? Will it fail if I use the current version? In the long-term, you'll need to consider compatibility from release to release, so this might be a sample preparation of how to handle the situation. My guess is as the most downstream module, you should only be changing this after everyone else, with the only immediate action to ignore any tags associated with CSF as they no longer have meaning to the db. This probably includes a possible reference from USF. Regards, Michael Pear ----- Original Message ----- From: "Jiaye Zhou" <ze...@in...> To: <gen...@li...>; "Michael Pear" <mic...@ho...> Sent: Thursday, January 25, 2001 8:01 PM Subject: Re: [GeneX-dev] Re: CanonicalSequenceFeature is missing... > > Hi Michael, > > Actually, I don't think this will break the xml2db code. It will just ignore > the missing top level xml elements which are CannonicalSequenceFeature. In fact, > I believe that I have tested the code against files that are missing CSF, but > that would be a while ago and I haven't done any development on the CSF end. > I have known of the decision on not supporting CSF, but since the Curation > Tool has been outputing CSF, I never removed the code that handled it. Perhaps > this is a good time for me to clean that part of the code up. > > Jiaye > > Quoting Michael Pear <mic...@ho...>: > > > I missed the Release Notes for the DB...I see them on sourceforge > > now. > > > > I did a quick check by doing an rgrep on the install tree and there > > are still a lot of references to CanonicalSequenceFeature in xml2db.pl > > as well, so even if the curation tool can handle it, having nothing > > there > > may break submission using xml2db.pl > > > > Regards, > > > > Michael Pear > > > > ----- Original Message ----- > > From: "Jason E. Stewart" <ja...@op...> > > To: "Michael Pear" <mic...@ho...> > > Cc: "Jason E. Stewart" <ja...@op...>; "Jiaye Zhou" > > <ze...@in...>; > > <gen...@li...> > > Sent: Thursday, January 25, 2001 6:56 PM > > Subject: [GeneX-dev] Re: CanonicalSequenceFeature is missing... > > > > > > > "Michael Pear" <mic...@ho...> writes: > > > > > > > I tried to download a control bundle on my new installation, but > > > > db2xml.pl failed because it couldn't find > > > > CanonicalSequenceFeature.pm. I don't see it or anything in > > > > Genex/CanonicalSequenceFeature in the install tree. I no longer find > > > > this table in the database either. What's up? > > > > > > This was in the Release Notes for DB v0.8.1, but for some reason, I > > > didn't include it in the Server install notes: > > > > > > From the release notes: > > > > > > * All tables related to Canonical Sequence Features were removed > > > (CanonicalSequenceFeature, CSF_ExternalDBLink, UserCanonicalLink, > > > RelatedCSF) > > > * the two CSF related columns in UserSequenceFeature were removed > > > (putative_csf_fk, nonunique_flag) > > > > > > And it looks like *I* didn't debug things enough :-( > > > > > > CSF was supposed to go away a month ago, it has always been an > > > unsupported feature, and since it was never really broken, it never > > > made it high enough on my priority to remove. I did it last release. > > > > > > Todd and/or Lonny. Will the CT break without CSF in the control > > > bundle? Should I just output a blank CSF section for now? > > > > > > Mea culpa, mea culpa, > > > jas. > > > > > > > > > > > > _______________________________________________ > > > Genex-dev mailing list > > > Gen...@li... > > > http://lists.sourceforge.net/lists/listinfo/genex-dev > > > > > > _______________________________________________ > > Genex-dev mailing list > > Gen...@li... > > http://lists.sourceforge.net/lists/listinfo/genex-dev > > |
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From: Todd P. <tf...@nc...> - 2001-01-26 14:49:30
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Curation tool won't barf if the files aren't referenced in the GeneXML external file list. ----- Original Message ----- From: "Michael Pear" <mic...@ho...> To: "Jiaye Zhou" <ze...@in...> Cc: <gen...@li...> Sent: Friday, January 26, 2001 7:03 AM Subject: Re: [GeneX-dev] Re: CanonicalSequenceFeature is missing... > You might want to look at the code with the idea > of ignoring any CSF section that comes in an XML file... > If I resubmit one of my existing experiment sets from last > week, if nothing is there to handle it, will it fail if you remove all > mention of it? Will it fail if I use the current version? In the long-term, > you'll need to consider compatibility from release to release, so this > might be a sample preparation of how to handle the situation. > > My guess is as the most downstream module, you should only be > changing this after everyone else, with the only immediate action > to ignore any tags associated with CSF as they no longer have meaning > to the db. This probably includes a possible reference from USF. > > Regards, > > Michael Pear > > ----- Original Message ----- > From: "Jiaye Zhou" <ze...@in...> > To: <gen...@li...>; "Michael Pear" <mic...@ho...> > Sent: Thursday, January 25, 2001 8:01 PM > Subject: Re: [GeneX-dev] Re: CanonicalSequenceFeature is missing... > > > > > > Hi Michael, > > > > Actually, I don't think this will break the xml2db code. It will just ignore > > the missing top level xml elements which are CannonicalSequenceFeature. In fact, > > I believe that I have tested the code against files that are missing CSF, but > > that would be a while ago and I haven't done any development on the CSF end. > > I have known of the decision on not supporting CSF, but since the Curation > > Tool has been outputing CSF, I never removed the code that handled it. Perhaps > > this is a good time for me to clean that part of the code up. > > > > Jiaye > > > > Quoting Michael Pear <mic...@ho...>: > > > > > I missed the Release Notes for the DB...I see them on sourceforge > > > now. > > > > > > I did a quick check by doing an rgrep on the install tree and there > > > are still a lot of references to CanonicalSequenceFeature in xml2db.pl > > > as well, so even if the curation tool can handle it, having nothing > > > there > > > may break submission using xml2db.pl > > > > > > Regards, > > > > > > Michael Pear > > > > > > ----- Original Message ----- > > > From: "Jason E. Stewart" <ja...@op...> > > > To: "Michael Pear" <mic...@ho...> > > > Cc: "Jason E. Stewart" <ja...@op...>; "Jiaye Zhou" > > > <ze...@in...>; > > > <gen...@li...> > > > Sent: Thursday, January 25, 2001 6:56 PM > > > Subject: [GeneX-dev] Re: CanonicalSequenceFeature is missing... > > > > > > > > > > "Michael Pear" <mic...@ho...> writes: > > > > > > > > > I tried to download a control bundle on my new installation, but > > > > > db2xml.pl failed because it couldn't find > > > > > CanonicalSequenceFeature.pm. I don't see it or anything in > > > > > Genex/CanonicalSequenceFeature in the install tree. I no longer find > > > > > this table in the database either. What's up? > > > > > > > > This was in the Release Notes for DB v0.8.1, but for some reason, I > > > > didn't include it in the Server install notes: > > > > > > > > From the release notes: > > > > > > > > * All tables related to Canonical Sequence Features were removed > > > > (CanonicalSequenceFeature, CSF_ExternalDBLink, UserCanonicalLink, > > > > RelatedCSF) > > > > * the two CSF related columns in UserSequenceFeature were removed > > > > (putative_csf_fk, nonunique_flag) > > > > > > > > And it looks like *I* didn't debug things enough :-( > > > > > > > > CSF was supposed to go away a month ago, it has always been an > > > > unsupported feature, and since it was never really broken, it never > > > > made it high enough on my priority to remove. I did it last release. > > > > > > > > Todd and/or Lonny. Will the CT break without CSF in the control > > > > bundle? Should I just output a blank CSF section for now? > > > > > > > > Mea culpa, mea culpa, > > > > jas. > > > > > > > > > > > > > > > > _______________________________________________ > > > > Genex-dev mailing list > > > > Gen...@li... > > > > http://lists.sourceforge.net/lists/listinfo/genex-dev > > > > > > > > > _______________________________________________ > > > Genex-dev mailing list > > > Gen...@li... > > > http://lists.sourceforge.net/lists/listinfo/genex-dev > > > > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev > |
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