geneontology / paint

This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
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issue with NOTES in 2.17 #20

Closed krchristie closed 8 years ago

krchristie commented 8 years ago

Hi Suzi,

While 2.17 definitely does save the notes, I noticed a different issue with the notes in 2.17.

If I had a family open that had text in the NOTES area (e.g. PTHR12858), and then I open another family using the "New" option, the NOTES field is not cleared and the text from the previous family remains present for the new family.

-Karen

P.S. Having updated my svn repository so that it reflects all of the recent file changes, I was working on committing the families I've done this week and I noticed something odd I wanted to mention it since it seems weird. If it's a bug and you want a separate GitHub issue, I'll be happy to open one.

PTHR13405 is a family for which I wanted to commit updated annotations. After saving from Paint-2.17 (which I needed to use to get the correct behaviour with respect to propagations and an experimental NOT annotation), I checked my svn status and three files are showing a M flag (the .exp, .gaf, and .txt) files which is fine. However, 2.17 also wrote a .attr file, which was not recognized by the SVN repository. I also noticed that my newly curated families which were saved by Paint 2.14 do NOT have .attr files. Since the .attr files were removed from the repository by the rollback and 2.14 did not write .attr files, it seems odd to me that 2.17 IS writing a .attr file. So I wanted to mention this.

selewis commented 8 years ago

Fixed.

Grab v2.18

Don't worry about the .attr files for two reasons 1. it grabs them dynamically from PANTHER (they're only for offline use) and even then it tries both the .tab and .attr files as these have the same content, so either works. p.s. offline is not working right now, but no one has noticed, so it's low priority.

I'll update the repository to hold just the .attr version.

-S

On Fri, Apr 29, 2016 at 4:33 PM, Karen R Christie notifications@github.com wrote:

Hi Suzi,

While 2.17 definitely does save the notes, I noticed a different issue with the notes in 2.17.

If I had a family open that had text in the NOTES area (e.g. PTHR12858), and then I open another family using the "New" option, the NOTES field is not cleared and the text from the previous family remains present for the new family.

-Karen

P.S. Having updated my svn repository so that it reflects all of the recent file changes, I was working on committing the families I've done this week and I noticed something odd I wanted to mention it since it seems weird. If it's a bug and you want a separate GitHub issue, I'll be happy to open one.

PTHR13405 is a family for which I wanted to commit updated annotations. After saving from Paint-2.17 (which I needed to use to get the correct behaviour with respect to propagations and an experimental NOT annotation), I checked my svn status and three files are showing a M flag (the .exp, .gaf, and .txt) files which is fine. However, 2.17 also wrote a .attr file, which was not recognized by the SVN repository. I also noticed that my newly curated families which were saved by Paint 2.14 do NOT have .attr files. Since the .attr files were removed from the repository by the rollback and 2.14 did not write .attr files, it seems odd to me that 2.17 IS writing a .attr file. So I wanted to mention this.

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/geneontology/paint/issues/20

selewis commented 8 years ago

All are suffixed .attr now.

On Sat, Apr 30, 2016 at 7:29 PM, Suzanna Lewis selewis@lbl.gov wrote:

Fixed.

Grab v2.18

Don't worry about the .attr files for two reasons 1. it grabs them dynamically from PANTHER (they're only for offline use) and even then it tries both the .tab and .attr files as these have the same content, so either works. p.s. offline is not working right now, but no one has noticed, so it's low priority.

I'll update the repository to hold just the .attr version.

-S

On Fri, Apr 29, 2016 at 4:33 PM, Karen R Christie < notifications@github.com> wrote:

Hi Suzi,

While 2.17 definitely does save the notes, I noticed a different issue with the notes in 2.17.

If I had a family open that had text in the NOTES area (e.g. PTHR12858), and then I open another family using the "New" option, the NOTES field is not cleared and the text from the previous family remains present for the new family.

-Karen

P.S. Having updated my svn repository so that it reflects all of the recent file changes, I was working on committing the families I've done this week and I noticed something odd I wanted to mention it since it seems weird. If it's a bug and you want a separate GitHub issue, I'll be happy to open one.

PTHR13405 is a family for which I wanted to commit updated annotations. After saving from Paint-2.17 (which I needed to use to get the correct behaviour with respect to propagations and an experimental NOT annotation), I checked my svn status and three files are showing a M flag (the .exp, .gaf, and .txt) files which is fine. However, 2.17 also wrote a .attr file, which was not recognized by the SVN repository. I also noticed that my newly curated families which were saved by Paint 2.14 do NOT have .attr files. Since the .attr files were removed from the repository by the rollback and 2.14 did not write .attr files, it seems odd to me that 2.17 IS writing a .attr file. So I wanted to mention this.

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/geneontology/paint/issues/20

krchristie commented 8 years ago

Thanks Suzi, for the fix as well as clarification on the .attr files.

v2.18 looks good to me too on this issue.