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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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bug with saving notes file #17

Closed krchristie closed 8 years ago

krchristie commented 8 years ago

Hi,

I am working with PAINT 2.0-beta14 (instead of beta1.14). I noticed today that when I save, this version is not saving my changes to the manual portion of the notes.

I am working on PTHR12858, which is a family I had worked on and saved previously (but not committed the files to SVN). Today, I opened my existing files into PAINT, made component annotation propagations (there were none in this aspect previously), and edited the NOTES section of the Evidence tab. Then I saved (allowing the suggested default to save PTHR12858.gaf in the directory from which I had opened the files).

To confirm my save, I often read the notes file (via command line more), so I noticed that the # NOTES section was unchanged from what had been there originally. However, the "# cellular_component" section of the .txt file was fine; the new annotations were present.

Listing of files AFTER saving (I do not have ls command from before saving)

bash-3.2$ ls -al
total 3920
drwxr-xr-x    13 krc  JAX\Domain Users     442 Apr 25 10:57 .
drwxr-xr-x  2889 krc  JAX\Domain Users   98226 Mar 10 11:44 ..
-rw-r--r--     1 krc  JAX\Domain Users   33458 Apr 28  2015 PTHR12858.attr
-rw-r--r--     1 krc  JAX\Domain Users    8490 Apr 25 10:59 PTHR12858.exp
-rw-r--r--     1 krc  JAX\Domain Users  178028 Apr 25 10:59 PTHR12858.gaf
-rw-r--r--     1 krc  JAX\Domain Users  923879 Apr 25 10:59 PTHR12858.mia
-rw-r--r--     1 krc  JAX\Domain Users  762796 Apr 28  2015 PTHR12858.msa
-rw-r--r--     1 krc  JAX\Domain Users     454 Apr 28  2015 PTHR12858.paint
-rw-r--r--     1 krc  JAX\Domain Users      18 Apr 28  2015 PTHR12858.sfan
-rw-r--r--     1 krc  JAX\Domain Users   38423 Apr 25 10:59 PTHR12858.tab
-rw-r--r--     1 krc  JAX\Domain Users   16609 Apr 25 10:59 PTHR12858.tree
-rw-r--r--     1 krc  JAX\Domain Users    2140 Apr 25 10:59 PTHR12858.txt
-rw-r--r--     1 krc  JAX\Domain Users    8820 Apr 25 10:59 PTHR12858.wts

text of .txt file after saving:

bash-3.2$ more PTHR12858.txt 
# HISTORY
25 Apr 2016: Saved by krc using Paint 2.0-beta14

# molecular_function
20150428: root_PTN000304594 has function U3 snoRNA binding (GO:0034511) 
20150428: root_PTN000304594 has function GTP binding (GO:0005525) 
20150428: root_PTN000304594 has function GTPase activity (GO:0003924) 

# cellular_component
20160425: Eukaryota_PTN000304671 is found in preribosome, small subunit precursor (GO:0030688) 
20160425: Eukaryota_PTN000304595 is found in 90S preribosome (GO:0030686) 

# biological_process
20150428: root_PTN000304594 participates in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462) 
20150428: root_PTN000304594 participates in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000479) 

# WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED

# NOTES
This family contains two proteins that are both involved in rRNA processing within the precursor of the ribosome to produce the mature SSU rRNA. Although the family has a duplication node at the top, this is probably OK as according to the UniProt pages for S. cerevisiae BMS1 and TSR1, both proteins are in the Bms1-like GTPase family within the TRAFAC class translation factor GTPase superfamily.
*** - still waiting for CC annotation for preribosome to propagate

# REFERENCE
Annotation inferences using phylogenetic trees
The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).

This is the text that is present in the PAINT NOTES window after editing, but which did not get saved:

This family contains two proteins that are both involved in rRNA processing within the precursor of the ribosome to produce the mature SSU rRNA. Although the family has a duplication node at the top, this is probably OK as according to the UniProt pages for S. cerevisiae BMS1 and TSR1, both proteins are in the Bms1-like GTPase family within the TRAFAC class translation factor GTPase superfamily. Note though that BMS1 is included in two reviews of the Small Subunit (SSU) processome which is an early complex involved in processing the primary ribosomal transcript into ribosomal subunits and which specifically affects formation of the small subunit. TSR1, on the other hand, is not included in either of these reviews, though experimental data in S. cerevisiae has identified it is being part of the "preribosome, small subunit precursor".

- Phipps et al. 2011. The small subunit processome in ribosome biogenesis—progress and prospects (PMID:21318072)

- Feng et al. 2013. Origin and Evolution of the Eukaryotic SSU Processome Revealed by a Comprehensive Genomic Analysis and Implications for the Origin of the Nucleolus (PMID:24214024)
krchristie commented 8 years ago

and here is the console output from the Terminal window, the whole thing from launching PAINT to saving

bash-3.2$ ./launchPAINT.sh 
2016-04-25 09:21:05,167 INFO  (PaintYaml:45) Trying config found at: config/preferences.yaml
2016-04-25 09:21:05,215 INFO  (PaintYaml:50) Using config found at: config/preferences.yaml
2016-04-25 09:21:05,330 INFO  (PaintStartupTask:203) Loading Paint version 2.0-beta14
2016-04-25 09:21:07,343 INFO  (class:571) View #4, Garbage0, is a garbage view--destroying
2016-04-25 09:29:54,858 INFO  (LoginUtil:404) Logging in to Panther URL:  http://paintcuration.usc.edu
2016-04-25 09:29:57.863 java[7048:2556888] Unable to simultaneously satisfy constraints:
(
    "",
    "",
    "",
    "",
    ""
)
Will attempt to recover by breaking constraint 

Set the NSUserDefault NSConstraintBasedLayoutVisualizeMutuallyExclusiveConstraints to YES to have -[NSWindow visualizeConstraints:] automatically called when this happens.  And/or, break on objc_exception_throw to catch this in the debugger.
2016-04-25 09:30:23.634 java[7048:2556888] *** WARNING: Method userSpaceScaleFactor in class NSWindow is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. 
2016-04-25 09:31:55,735 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl
2016-04-25 09:44:31,367 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl
2016-04-25 09:44:31,722 INFO  (Reasoner:117) ELK reasoner was created
2016-04-25 09:44:37,516 INFO  (LoggingStageExecutor:70) Loading of Axioms started
2016-04-25 09:44:37,530 INFO  (AbstractReasonerStage:161) Loading of Axioms using 8 workers
2016-04-25 09:44:38,150 WARN  (ChangeIndexingProcessor:66) ELK does not support InverseObjectProperties. Axiom ignored:
InverseObjectProperties( )
2016-04-25 09:44:42,097 INFO  (LoggingStageExecutor:103) Loading of Axioms took 4568 ms
2016-04-25 09:44:42,097 INFO  (LoggingStageExecutor:70) Property Saturation Initialization started
2016-04-25 09:44:42,098 INFO  (AbstractReasonerStage:161) Property Saturation Initialization using 8 workers
2016-04-25 09:44:42,099 INFO  (LoggingStageExecutor:103) Property Saturation Initialization took 1 ms
2016-04-25 09:44:42,099 INFO  (LoggingStageExecutor:70) Reflexive Property Computation started
2016-04-25 09:44:42,106 INFO  (AbstractReasonerStage:161) Reflexive Property Computation using 8 workers
2016-04-25 09:44:42,150 INFO  (LoggingStageExecutor:103) Reflexive Property Computation took 50 ms
2016-04-25 09:44:42,150 INFO  (LoggingStageExecutor:70) Object Property Hierarchy and Composition Computation started
2016-04-25 09:44:42,153 INFO  (AbstractReasonerStage:161) Object Property Hierarchy and Composition Computation using 8 workers
2016-04-25 09:44:42,158 INFO  (LoggingStageExecutor:103) Object Property Hierarchy and Composition Computation took 7 ms
2016-04-25 09:44:42,159 INFO  (LoggingStageExecutor:70) Context Initialization started
2016-04-25 09:44:42,159 INFO  (AbstractReasonerStage:161) Context Initialization using 8 workers
2016-04-25 09:44:42,161 INFO  (LoggingStageExecutor:103) Context Initialization took 2 ms
2016-04-25 09:44:42,161 INFO  (LoggingStageExecutor:70) Consistency Checking started
2016-04-25 09:44:42,167 INFO  (AbstractReasonerStage:161) Consistency Checking using 8 workers
2016-04-25 09:44:42,230 INFO  (LoggingStageExecutor:103) Consistency Checking took 68 ms
2016-04-25 09:44:42,230 INFO  (LoggingStageExecutor:70) Class Taxonomy Computation started
2016-04-25 09:44:42,239 INFO  (AbstractReasonerStage:161) Class Taxonomy Computation using 8 workers
2016-04-25 09:44:52,033 INFO  (LoggingStageExecutor:103) Class Taxonomy Computation took 9803 ms
2016-04-25 09:46:23,060 INFO  (DisplayTree:70) There are 295 nodes in the PTHR12858 tree
2016-04-25 09:47:37,822 INFO  (GafPropagator:197) building GAF document
2016-04-25 09:47:37,823 INFO  (GAFParser:299) Open stream as file
2016-04-25 10:57:55,369 INFO  (GafRecorder:81) Wrote updated paint GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR12858/PTHR12858.gaf
2016-04-25 10:57:55,372 INFO  (GafRecorder:121) Wrote experimental evidence GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR12858/PTHR12858.exp
2016-04-25 10:58:17,115 INFO  (GafRecorder:81) Wrote updated paint GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR12858/PTHR12858.gaf
2016-04-25 10:58:17,116 INFO  (GafRecorder:121) Wrote experimental evidence GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR12858/PTHR12858.exp
2016-04-25 10:59:11,337 INFO  (GafRecorder:81) Wrote updated paint GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR12858/PTHR12858.gaf
2016-04-25 10:59:11,339 INFO  (GafRecorder:121) Wrote experimental evidence GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR12858/PTHR12858.exp
selewis commented 8 years ago

Karen, have you committed these files? Preferably the 'before' version. Need this specific case to duplicate the problem (and hence fix it)

krchristie commented 8 years ago

I had not committed the before files. Thus, when I saved from Paing2.0-beta14, I overwrote my originals.

However, you could recreate the important part of the file by using the file that exists after saving since the "NOTES" portion still IS the original version of the text. My original file also would have had no component annotations. So, this file below (same as what's in first comment in this ticket) has the original text of the free text #NOTES section. The new text is also included in the original comment.

# HISTORY
25 Apr 2016: Saved by krc using Paint 2.0-beta14
# molecular_function
20150428: root_PTN000304594 has function U3 snoRNA binding (GO:0034511) 
20150428: root_PTN000304594 has function GTP binding (GO:0005525) 
20150428: root_PTN000304594 has function GTPase activity (GO:0003924) 
# cellular_component
20160425: Eukaryota_PTN000304671 is found in preribosome, small subunit precursor (GO:0030688) 
20160425: Eukaryota_PTN000304595 is found in 90S preribosome (GO:0030686) 
# biological_process
20150428: root_PTN000304594 participates in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462) 
20150428: root_PTN000304594 participates in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000479) 
# WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED
# NOTES
This family contains two proteins that are both involved in rRNA processing within the precursor of the ribosome to produce the mature SSU rRNA. Although the family has a duplication node at the top, this is probably OK as according to the UniProt pages for S. cerevisiae BMS1 and TSR1, both proteins are in the Bms1-like GTPase family within the TRAFAC class translation factor GTPase superfamily.
*** - still waiting for CC annotation for preribosome to propagate
# REFERENCE
Annotation inferences using phylogenetic trees
The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).
krchristie commented 8 years ago

Alternatively, here are a couple familes that I commited to SVN last year with Paint-1.14 that have notes files.

PTHR32465 PTHR31148

selewis commented 8 years ago

Odd thing though is that I just ran an update and I don't see this family at all. One of the versions should be there.

Did you commit it to go/gene-associations/submission/paint/ ??

On Tue, Apr 26, 2016 at 4:53 PM, Karen R Christie notifications@github.com wrote:

Alternatively, here are a couple familes that I commited last year with Paint-1.14 that have notes files.

PTHR32465 PTHR31148

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/geneontology/paint/issues/17#issuecomment-214923512

krchristie commented 8 years ago

You shouldn't see it. I haven't committed it.

selewis commented 8 years ago

Ah that's fine then.

No trouble duplicating, quite odd. code-rot

On Tue, Apr 26, 2016 at 4:58 PM, Karen R Christie notifications@github.com wrote:

You shouldn't see it. I haven't committed it.

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/geneontology/paint/issues/17#issuecomment-214924321

selewis commented 8 years ago

This was quite a serious bug. Think I've nailed it (hope so). Look at PAINT v2.16

krchristie commented 8 years ago

Looks good to me. Tested once with 2.16 and again with a different family with 2.17.

Thanks!