User:A-Kondo
From FANTOM5_SSTAR
All activities in SSTAR
What:Updates of Sample IDs provided by DDBJ
The target platform:Resource Browser
When:31/July/2014.
How:Run java code
akondo.data.operation.wiki.update.AccessionNumberUpdate.java
What:Updates of Sample IDs provided by DDBJ
The target platform:SSTAR
When:1/August/2014.
How:Run java code
akondo.data.operation.wiki.update.AccessionNumberUpdate.java
What:Fix link on the AccessionId
The target platform:SSTAR
When:4/August/2014.
How:We copy the template(DRAccessionNumber) from RB to SSTAR.
Because the accessionId is linked wrong URL.
As a result, the some accessionId linked to right URL, but some accessionIds remain wrong.
We copy the f5samples template from RB to SSTAR. then the URL linked to DDBJ is fixed.
We found other problems:
1. Why the “LibraryIDs” template is not exist on SSTAR.
2. How to create new Templete on the Media Wiki.
What:Updates of the Timecourse collaborator's name. Replace to name and email link.
The target platform:Resource Browser
When:18/August/2014.
How:Run java code
akondo.data.operation.wiki.update.CollaboratorsEmailUpdate.java
Total time: 2:49.503s
Finished at: Mon Aug 18 14:56:04 JST 2014
Final Memory: 7M/177M
What:Create templete
The target platform:ResourceBrowser
When:12/Sepember/2014.
How:copy the template code of CL to new templates below:
BFO, CHEBI, EFO, GO, IAO, OBI, UO
What:Updates of Ontology pages by javacode using obo file.
The target platform:ResourceBrowser
When:12/Sepember/2014.
How:Run java code akondo.data.operation.ontology.OntologyFix3.java
What:Check Ontology pages.
The target platform:ResourceBrowser
When:16/Sepember/2014.
How:Ontology pages looks good. About the pages that has no ID, we will wait Kasukasa-san or Kawaji-san decide that remove or update the pages before we delete them. The pages are below:
Disposition
MaterialEntity
NCBITaxon
NCBITaxon_10088
NCBITaxon_2759
ProcessualEntity
Role
SpecificallyDependentContinu
What:Update Timecourse Pages(Human)
The target platform:ResourceBrowser
When:16/Sepember/2014.
How: running java class
akondo.data.operation.wiki.update.SPTimeCourseUpdate
Copy the "TimeCourse" template source code. And create new template "Time_Course".
Paste the source code to "Time_Course" and save it.
The difference of the "Time_Course" and the "TimeCourse" is just name.
Copy each human and mouse Timecourse page's source code. And save 2 copies to text-file on server.
Remove all the Timecourse pages from Resource browser.
Create new Timecourse pages using the saved text-file on the server.
To create human TC pages, enter the URL for new Timecourse page like: https://fantom5-collaboration.gsc.riken.jp/resource_browser/TimeCourse:XXXXXX Click the "edit" link and paste the source code from the human text-file you saved on server. Before click the save button, update the template name to "Time_Course".
Repeat the new TC page creation for All the human and mouse.
update pagename on excel file.
Copy the discription colomn and paste to pagename column. Imad-san update the pagename to replace "-" to other words.
Run the java code.
Running time is about 90minutes.
What:Change tamplate to show all samples and TC as default.
The target platform:ResourceBrowser
When:28/October/2014.
How:update timecourse template manually.
iDisplayLenght: 10 → -1 aLenghtMenu: [[15, -1], [15, "All"]] → [[-1], ["All"]]
human and mouse use same template.
And the sample template was changed as same as Timecourse template.
What:Update Timecourse pagename.
The target platform:ResourceBrowser
When:29/October/2014.
How:Using java class akondo.data.operation.wiki.update.SPTimeCourseUpdate
For the clearity, we devided the new_timecourse.tsv to the new_timecourse_human.tsv and new_timecourse_mouse.tsv .
We run the program twice for each file, the human and the mouse.
We found the bug on the program that is the "edittoken" has not been taken.
it is requred for the function movepage(), so that we fix the program and re-run it.
The TC list page's reflesh is required to rebuild the list for updated data.
iPS Timecourse should start with the little "i", but It was started with large letter "I".
probably, the small letter is not acceptable on the sematic wiki.
So that we added "Human_" before the iPS Timecourse name.
What:Adjust the column width in the list of Timecourse to show Timecourse name in a single line.
The target platform:ResourceBrowser
When:30/October/2014.
How:update the template of human timecourse list page.
What:Add Overview, Sample description, Quality control to Saos osteosarcoma page.it is sample preview. description date is copied from wiki.
The target platform:ResourceBrowser
When:12/November/2014.
How:Add properties TCOverview, TCSample_description and TCQuality_control to Template:TimeCourse. And add property values to the Saos osteosarcoma page. The description datas are copies from fantom wiki.
What:Phase2 data update from metadata.
The target platform:ResourceBrowser
When:27,28/November/2014.
How:We created new java code for updating sample.
akondo.data.operation.wiki.update.SampleMetadataUpdateforMouse akondo.data.operation.wiki.update.SampleMetadataUpdateforHuman
These code updates using text file Human_sample_metadata.txt mouse_sample_metadata.txt
we have to remove double quotes from these text file. because double quotes on wiki code caused corruption of wiki format.
we started running the code for Human from 27th 4pm to 11pm. The program finished normally. next day we start running the code for Mouse from 28th 9:30am to 11:30pm.
The code running finished normally. We delete one sample below manually.
10005-101B1
At the meeting on afternoon, we found that some samples were not updated correctly.
12250-129H9 12251-129I1 12254-129I4 12255-129I5 12256-129I6
The reason of that was 5 samples on the list on webdav were overlaped. we fix the 5 samples list, and updated them again.
What:Phase2 data update (manual update) Because quality control samples do not appear in the sample list.
The target platform:ResourceBrowser
When:1/December/2014.
How:update 3 samples on browser.
10101-102D2 10101-102D3 10101-102D4
update properties:
sample_categories : tissues → control species : blank → Mouse (Mus musculus)
What:Try combine the files together.
The target platform:
DRA000991.txt
DRA001026.txt
DRA001027.txt
DRA001028.txt
DRA001101.txt
DRA002216.txt
DRA002711.txt
DRA002747.txt
DRA002748.txt
When:1/December/2014.
What:Library_id update
The target platform:ResourceBrowser
When:2/December/2014.
How:copy the "library_id" property's value from sstar to RB. 10101-102D2, 10101-102D3, 10101-102D4, 3139-67G5
What:accession number update
The target platform:ResourceBrowser
When:2/December/2014. from 2 pm to 10:30 pm
How:java code (akondo.data.operation.wiki.update.AccessionNumberUpdate.java) read from text file(/Users/a-kondo/development/fantom5/sample_update/all_dra00.txt). put the "accession_numbers" into param to update accession number.
Result: Some sample has no Accession numbers table in its page. I guess they have no DRA_sample_Accession property before this update. We have to update again with two properties (DRA_sample_Accession, accession_numbers) updating.
What:Timecourse Description update.
The target platform:ResourceBrowser
When:9/December/2014.
How:edit wiki page manually.
- Adipocyte differentiation
What:Timecourse Description update.
The target platform:ResourceBrowser
When:10/December/2014.
How:edit wiki page manually.
- All Human Timecourses.
What:Timecourse Description update.
The target platform:ResourceBrowser
When:11/December/2014.
How:edit wiki page manually.
- All mouse Timecourses.
- Expend Overview box by default.
memo
{{#ask:[[Category:FF Samples]][[timecourse::{{PAGENAME}}]] |?# |?Category |?Name |?Time |?Donor |format=broadtable |offset=0 |limit=20 |mainlabel= |class=sortable wikitable smwtable }}
The line that has duplicated library ID can be remove.
Update two library_ids to the same value.
What:Add 2columns(time, donor) to the sample list on the Timecourse page.
The target platform:ResourceBrowser
When:08-09/January/2015.
How:
- Defined Time and Donor property by Special Pages.
- Edited F5samples template to add set#time and set#donor statement.
- Edited Timecourse template
- add time and donor into the query result.
- add headers=plain parameter to remove link from table header.
- define aoColumnDefs on datatable(javascript) to remove sort function from donor column.
- Run java code.
- Rebuild the timecourse page(save page).
What:Add new properties and update Timecourse name.
The target platform:ResourceBrowser
When:2-3/February/2015.
How:java code
- TCAddProperties.java
- TCNameUpdateUrgent
First, Add properties and update Timecourse lists.
Second, Update timecourse name.(I forget it and update later.)
api.php could be not accessible (forbidden). Takeda-san found that resolve.conf on f5-webapp3 was updated.
He don't know why.
What:fix folder name of JASPER logo file
The target platform:ResourceBrowser
When:5/March/2015.
How:manualy
Target page: Browse_Transcription_Factors_hg19, Template:JASPAR motif
seqlogos -> seqlogo
What:Update TC pages
The target platform:ResourceBrowser
When:5/March/2015.
How:akondo.data.operation.wiki.update.SPTimecourseUpdateUrgent
What:Templeate F5sample update
The target platform:Test(f5-webapp2)
When:9/March/2015.
How:manual
I added additional updating to the "timecourse" propterty on F5sample template.
Property "Timecourse" (as page type) with input value "{{{timecourse}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.
Because the timecourse PAGENAME had been changed in the past update. For example
Old page name: TimeCourse:BMM_TB_activation_IL4 Current page name BMM_TB_activation_IL4
What:Epifactor update
The target platform:f5-webapp3.gsc.riken.jp
When:24/june/2015.
How:Java code
What:update page for PHASE2 CAGE Peak.
The target platform:f5-webapp2.gsc.riken.jp
When:23/july/2015.
How:Java code
For adding the new namespace, the Localsettings.php updated. added the line below: $wgExtraNamespaces[3026] = "FFCP_PHASE2"; $wgExtraNamespaces[3027] = "FFCP_PHASE2_talk"; $smwgNamespacesWithSemanticLinks[3026] = true;
Query for count EntrezGene
174802
Short meeting memo(13 Aug 2014)
Serkan-san, Imad-san, Kasukawa-san, A.Kondo
1. LibraryIds template is not exists for SSTAR.
Serkan-san has created the "LibraryIds" template for Resource Browser before his vacation.
But has not created for the SSTAR.
He created the template for SSTAR but it did not work well.
Because "library_id_phase_based" is not exist on SSTAR.
And currently it is not necessary to create "LibraryIds" template for SSTAR.
2. How to create the new template.
To create the new template, open other template and modify the template neme on URL to new template name.
fantom5-collaboration.gsc.riken.jp/resource_browser/Template:new_template_name
You will see the messages that mean the template is not exists.
Click "create" on menu.
The new template will create.
3. Other memo
The Additional Information table on Resource Browser is different from SSTAR.
The "External link for information" in Additional Information table has been added by Serkan-san
that is the latest update for SSTAR. Alistair san requested it.
"External link for information" will be able to be added to Resource browser by copying the template.
The Resource Broswer has more informations than SSTAR,
because the Resource browser is evolving constantly.
And SSTAR's update has been frozen.
Resource Browser should be updated carefully by comparing the both resource.
There are the items that is old and not required.
Meeting memo(14 Aug 2014)
Attendee: Serkan-san, A.Kondo
The discussion is about what is the current request for the phase2.
We have to get the list that includes only phase2 data.
because we have to find the data which should be redirected to phase1 page.
Meeting memo(21 Aug 2014)
Attendee: Imad-san,A.Kondo
Imad-san showed me how to find missing samples.The result is
- 5 samples for human missing in RB
- 513 samples for mm missing in RB.
We will ask Serkan-san tomorrow about the question below:
1. Which class is suitable to update samples using missing samples list(ID & Name).
2. How to create the Timecourse page.
A.Kondo will check the Java class one by one.
Meeting memo(8 Sep 2014)
The OntologyFix3.java is the class for update ontology of SSTAR.
This class requires Onology list and sample id lists.
We already have ontology list but we do not have sample id list.
We need to find how to create the phase2 sampleid list (CL.txt、DOID.txt、FFontology.txt、UBERON.txt).
These are probabry made automatically by java class.
source check after meeting(9/10)
OntologyFix3.java is update the value of "is_a", "derives_from", "part_of", "develops_from", "union_of", "disjoint_from"
in the ff-phase2-140729.obo.
In this class, the CL.txt or DOID.txt or other several files are read but it not used.
1.Time-course names
2. Time-course samples ----SampleID, LibraryID
3. FF Ontology file ---- ff-phase2-140729.obo
1. Time-course → Zenbu (done)
2. Time-course → Sample
3. Sample → FFontology
Future query memo(12 Nov 2014)
query test and query result for phase 2 release:
smb://Ascot/lsdm/Resource Browser/Data/phase_2_sample_release
Meeting memo(13 Jan 2015)
data check after last week updating.
- 12642-134G5 was skipped as header (→ update again soon.)
- 5 samples missing on BMM TB infection IL13.(→investigate the problem.)
- BMM TB infection nonstimulated has no overview.
- MSC osteocytes has no overview.
Short meeting memo(13 Apr 2015)
- EntresGene template have been already updated. We have to update each page by java code.
- The java code will be ready in this week. And we will test on the test server then we will update real data.
Short meeting memo(26 Aug 2015)
- Co-expression cluster page."Number of FFCP members" is sorted by the alphabetical sort.This should be sorted by Numeric sort.
- Create Query of Ontology list for each sample.not urgent.
Short meeting memo(25 Dec 2015)
- In the future, new features for SSTAR should be added.
- Add pages for Chicken genome.
- Link to directory
- Accession number(?)
- f5-webapp2/f5-webapp3 are old and hardware support will expired. We have to migrate these servers to f5-serv.
- The new server will be available after YBIC power maintenance (6th Feb 2016).
- Version up MediaWiki and Semantic mediawiki. We proberbry are able to use update script in wiki directory.
- We have to setup the new server before 1st Apr.