lower memory request to 1G #52
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Currently if we configure openshift to run two pods for the website new deployments fail due to memory quotas. This change will allow us to run two pods and gracefully deploy new changes. Based on openshift Memory metrics we are using ~ 1040 MiB. This is just the requested amount and the app is allowed to utilize more than this.
dleehr
approved these changes
Feb 3, 2020
3 tasks
johnbradley
pushed a commit
to Duke-GCB/ddh
that referenced
this pull request
Jan 21, 2021
point ddh.com repo to ddh.com image
matthewhirschey
added a commit
that referenced
this pull request
Jan 29, 2021
commit b974b16beb18d8f2778ea965d2650f72095cb4ec
Merge: a3c1467 c3b6396
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Fri Jan 29 10:07:17 2021 -0500
Merge pull request #58 from matthewhirschey/org-reorg
Reorganize the organization of the app
commit c3b6396c13dbed8c2aff52a540fd73e598f71a7b
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Jan 29 10:03:46 2021 -0500
fix tests for app_params.R
commit c38bb04f7baf8bc5e9f5f12dba62feb9859715ac
Merge: 74e1597 3e78f10
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Jan 29 09:57:41 2021 -0500
git merge master
Merge branch 'org-reorg' of https://github.com/matthewhirschey/ddh.com into org-reorg
# Conflicts:
# code/app.R
commit 74e1597de369271a720b3543c5e4240b990540e2
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Jan 29 09:56:30 2021 -0500
add app_params.R
trying to make John's life easier; and so tests can run without these set in app.R
commit 3e78f1066fd74319841d639ed5408783f4c7c60f
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Jan 28 16:50:15 2021 -0500
app.R global settings tests
Tests that private and app_data_dir are set to the appropriate
values for this repo.
commit 43384c7048f7a1eeb156627213d8a70f096b72d9
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Jan 28 16:18:38 2021 -0500
update slurm scripts to use generate_data_private.R
commit fc32a0e49efdddbbb636612518c6e74167f6a4f6
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Jan 27 12:51:22 2021 -0500
Update code/fun_reports.R
commit 141c027248711f4b8d10f62e2db8e52c39543418
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 26 16:26:40 2021 -0500
Set-up private report function
Private report function called in private page
commit f2c161b437d905e34b51470ac162e2c456436638
Merge: 18bfcea 28ce9e1
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 26 13:28:07 2021 -0500
Merge branch 'org-reorg' of https://github.com/matthewhirschey/ddh.com into org-reorg
commit 18bfcea70e69aa59295182c9d2e4d6bd920e1b9a
Merge: 010092b 83b44a9
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 26 13:26:29 2021 -0500
Merge branch 'org-reorg' of https://github.com/matthewhirschey/ddh.com into org-reorg
commit 28ce9e19437fb97ce9a4c99c836fc6dcc8550ab5
Merge: 010092b 83b44a9
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 26 13:26:29 2021 -0500
Merge branch 'org-reorg' of https://github.com/matthewhirschey/ddh.com into org-reorg
commit 010092b48f7b00b6faab276e5d199ef4894f8d45
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 26 13:26:21 2021 -0500
new expdep plot
This new plot type compares expression vs. dependency, and is a good test case to build a report that can hold back a plot in private.
commit e3abcad235cc3478e7f3c8dcb78c42c8e5aaa3e5
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Jan 25 10:18:52 2021 -0500
Add report_gene_private file
Will need two files for report generation: both public and private, which call some functions (public) or all functions (private)
commit a3c1467291755ce0315d80dee875670f10305316
Merge: 372f7de b7e75a9
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Jan 25 10:09:46 2021 -0500
Merge pull request #57 from matthewhirschey/backup-postgres-db
Add cron job to backup the database
commit b7e75a9a394da65ee6e4f785a044fad9b80847ee
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Jan 25 09:51:10 2021 -0500
remove backup job yaml
commit 22d143cb07c92aaa8f6b8943f13f392719e0c4ac
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Jan 25 09:48:00 2021 -0500
backup auth db every month
Adds openshift cron job template for backing up the database to DDS.
To create run
```
oc create -f BackupAuthDBCronJob.yaml
```
You can see cronjobs from the command line like so:
```
oc get cronjob
```
commit a7918df86b64cf955d4002f03b0fd22772fadf60
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Jan 22 15:25:17 2021 -0500
adds template to backup auth database
File: openshift/BackupAuthDB.yaml
Backs up database to a DukeDS project named
ddh-com-backups.
commit 83b44a91d71d5bdbeebb37000ed2e69ca88ed9bb
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Jan 22 08:47:57 2021 -0500
fix upload-data.sh wrong variable name
commit b6237c6ffc0188fd3d19ce23eeea8ce30d3493ff
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Jan 22 08:38:50 2021 -0500
slurm: abstract out docker image and DDS project name
Based on conversation: https://3.basecamp.com/4316284/buckets/14415887/messages/3391363907
commit 90d93b8f1aaee3d9a4d776b5d9eae3b860e0180f
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 15:26:19 2021 -0500
ignore tempNetwork_files
commit 7f8ce714609858e55ed681fbfe6b8905f3a8d7c0
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 15:25:18 2021 -0500
housekeeping
commit 7eaf581c6a9d8612bd8586b8dbf6d2a9c0646375
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 15:24:53 2021 -0500
update public pages
commit 3af81afede327ee2c3c148fdb352565c95e9172a
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 15:24:20 2021 -0500
add some fonts
commit 686b4aa19d9c5c8f4076e1a72d39f6665d43081a
Merge: 856ace1 372f7de
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 14:52:21 2021 -0500
merge master
not too messy, this time.
Merge branch 'master' into org-reorg
# Conflicts:
# code/generate_drug_data_private.R
commit 856ace16e6c8bf13859612ae7e605b3a7eb80c63
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 14:48:48 2021 -0500
Adding 20Q4 and some test data
commit ca0209bcf46cbcbf810f2a415a732ac868932da4
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 13:50:05 2021 -0500
split drug_data.R
Made common generate_drug_data_names.R and made a private generate_drug_data_private.R to keep data generation secret for now.
commit 07614e506a84d397c4c7e43b9fe7f912620fde31
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 13:36:47 2021 -0500
minor text changes to shiny_text.R
commit a2cf8e6d0c18c33a56c94a320f1e98b7afb078e2
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 09:32:29 2021 -0500
Rename public v. private
Renamed pages from empty to private, from public to empty, and set the Boolean from public to private. This is going to overwrite the history for the pages, given that some are now the same name, but different file. Moving forward, you need to set private to either TRUE or FALSE. Also added a place holder for data that if private == TRUE, then {add these data}.
commit 87f078a4c6b7735d3b07402e75346b90f282121e
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 20 09:00:38 2021 -0500
update text
removed some redundant text in the labels
commit 372f7de176d3a4d001dabea9bf868e3920274352
Merge: 38b0a28 9c49c69
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Thu Jan 14 20:25:30 2021 -0500
Merge pull request #56 from matthewhirschey/20Q4
remove focus() from steps 3 & 4
commit 9c49c6929024cc08a67c131ab2a9d30e0db46c7c
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Jan 14 20:23:15 2021 -0500
remove focus() from steps 3 & 4
commit 38b0a28c2d487999e3eb56e1ab50d5f1012093af
Merge: 27e82de 0e80402
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Thu Jan 14 10:46:17 2021 -0500
Merge pull request #55 from matthewhirschey/20Q4
update drug_data for 20Q4
commit 0e8040256891cd34c2a9a3a179d54fb70ec04895
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Jan 14 10:44:59 2021 -0500
update drug_data for 20Q4
Needed to get unique ids after webchem returned multiple, also needed to update some variables after an update to corrr (on my end) renamed rowname to term, so tried to use index in most cases, plus a few renames.
commit 27e82dea7b2a37a0288825b584cb5b88df0ffb3d
Merge: 6f78011 913e41c
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Wed Jan 13 10:08:36 2021 -0500
Merge pull request #54 from matthewhirschey/20Q4
20 q4
commit 913e41c7cb85db2771540caa8d04254d12277c5c
Merge: e1884bc 0d0c141
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 13 09:58:01 2021 -0500
merge master
Merge branch 'master' into 20Q4
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
commit e1884bccdabefa5c3e9908190ac77eb4f2db3479
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 13 09:57:04 2021 -0500
remove stretch()
stretch() was looking for 'term' but couldn't find it, so threw an error. To fix, I used a more explicit pivot_longer. Also was explicit about packages for functions.
commit c068774f8aa33fde0068501226d76d709c344300
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 12 16:40:41 2021 -0500
Add x-axis label to make_correlation()
commit e282ba4ba60f07219e1dd9208916f8d437b22764
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 12 14:56:22 2021 -0500
Add make_correlations to report
commit 6f78011389091c91d49d258bf3325fe5616a0f2b
Merge: 6300f48 e6e27b6
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Jan 12 14:10:02 2021 -0500
Merge pull request #53 from matthewhirschey/slurm-script-cleanup
Cleanup slurm scripts
commit e6e27b615300182e0dc5e93be23c45e1c0c08f89
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Jan 12 13:41:25 2021 -0500
use matthewhirschey/ddh.com for singularity image
commit 4311ac282ad3db023f41234aabb509814aeaddc1
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Jan 12 13:40:43 2021 -0500
remove unused slurm scripts
commit 6300f48c8b6ad34598cbbcbb1c12ff55e315fd42
Merge: 0d0c141 f012936
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Tue Jan 12 12:03:08 2021 -0500
Merge pull request #52 from matthewhirschey/20Q4
point ddh.com repo to ddh.com image
commit f012936f97565a9e0dbf00d6659f00e9d595dee6
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 12 12:02:42 2021 -0500
point ddh.com repo to ddh.com image
commit f607e367dd22256ca4a26ea328e23d54b720c95c
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 12 12:01:37 2021 -0500
remove ggploty from make_correlations
memory hog, so made it static; much better.
commit 8546154e6c73f7c089389659c0d55402e870e0c8
Merge: ba0ce63 0d0c141
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 12 11:00:00 2021 -0500
merge master
Merge branch 'master' into org-reorg
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
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# the commit.
commit ba0ce631983c24e5f255f4d4dcb5731b0420b29b
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 12 09:00:29 2021 -0500
build correlation plot
Added make_correlation(), new data set, test data set, and shiny fun() to wrap it. Problem is that it is slow and takes a ton of memory. Considering moving it to the report only.
commit 0d0c141a0bc816c6438ee2fbb50ebb3defc8e51a
Merge: 4e86ad9 2229b7e
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Jan 12 09:07:51 2021 +0100
Merge pull request #48 from matthewhirschey/data-viz-update
Fixes #22
commit 133012ad0a123eafe522cd45f24a9e4ca247903c
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Jan 11 15:40:28 2021 -0500
Adds id to ddhNavbarPage
This allows using updateNavbarPage to select an item in the navbar.
I set "geneNavBar" as the id for the gene_page nav bar.
This name is then used to observe the link_to_cellDependenciesPlotDash
click.
The code in navbarPageWithForm used by ddhNavbarPage is based
on shiny::navbarPage but allows us to add the search panel.
commit 893c1de34a4767c3ec7615a6a1727bca8f9db3dd
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Jan 11 14:49:47 2021 -0500
progress on dashboard links
added actionLink, and observeEvent
commit adb9c7b2a2ef8ce89d567dad1b44d79ca192425d
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Jan 11 13:40:30 2021 -0500
add gray to graph
commit 4e86ad9c8e6a0b197ea9575d1f2b85e8a9f753ac
Merge: 30bf92a f10142e
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Mon Jan 11 13:23:02 2021 -0500
Merge pull request #51 from matthewhirschey/20Q4
remove furrr library
commit f10142ef5ef017272b57a3078865a826872df41c
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Jan 11 13:22:28 2021 -0500
remove furrr library
Also remove commented out code after JB tested
commit 55317f78e7e795f5419f3556ae88b967788bf814
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Jan 11 13:20:11 2021 -0500
dashboard prep
Add values to tabPanels to call them, make first depdash plot, add shadow style to shiny_cards
commit 30bf92a103e72dcaddfcd804e2c7b77092a4e6a2
Merge: 21c0bb9 bc58149
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Mon Jan 11 09:04:50 2021 -0500
Merge pull request #47 from matthewhirschey/20Q4
20 q4 + webchem
commit bc58149312902458b2282a03d9460eba6d3a0ed5
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Jan 11 08:28:05 2021 -0500
use webchem instead of rpubchem
Switched to using webchem since rpubchem has been removed from
CRAN for a policy violation 2020-08-07. Not sure what the problem
was. webchem seems to be more resilient when fetching cids.
I didn't encounter any errors like I did for rpubchem.
The webchem version took 2 hours to fetch the cids.
generate_drug_data.R failed later in the processing due to
a lack of system resources(I think).
commit 2229b7efe9d06aafed0c22fcb287a63403d39741
Merge: 85a5ad0 21c0bb9
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Mon Jan 11 13:20:55 2021 +0100
Merge branch 'master' into data-viz-update
commit 85a5ad04021f7c485897a2c37ac93b1858367107
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sat Jan 9 17:04:45 2021 +0100
:art: fix aspect ratio of plots
* fixes aspect ratio of depbins in PDF report
- fixed height for single gene queries
- dynamic height for pathway and custom gene list queries
- maximum height for plots with 13 or more genes
* fixes aspect ratio of depbins in PDF report
- dynamic scaling for all queries which results in a nice aspect ratio also for single gene queries
* wider plot for graph to avoid overlapping in queries with many genes (encountered with Cholestorol query)
* higher sublineae plot to avoid overlapping y text labels (encountered with Cholestorol query)
commit 28ed719da95be19ada9275f98038ab91ef7a1e18
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Jan 8 15:59:03 2021 -0500
add test data to github repo
commit be7c47db4933ab8c4459c919894a5e4efd1c9375
Merge: ad5a899 d650c88
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Jan 8 15:58:15 2021 -0500
Merge branch 'org-reorg' of https://github.com/matthewhirschey/ddh.com into org-reorg
commit ad5a89932a699e7e62a75ba9c3343bff77d0469e
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Jan 8 15:57:02 2021 -0500
dashboard placeholder
commit d650c88f143376d341d322f39cf74f88889215b7
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Jan 8 15:57:02 2021 -0500
dashboard placeholder
commit 324b0865cc0abc57eead04808800b734370058a3
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Jan 8 15:48:23 2021 -0500
first pass at public v. private pages
commit cdc489678640c0c5e556a1592a7ebd4a2536a6b1
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Jan 7 21:23:47 2021 -0500
fix justification formatting
it was all about misplaced parentheses :[.....
fluidRows were not wrapped properly. Now they are.
commit 8d82227f80637f0542373c6a0ed5f3a52a2457d0
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Jan 7 16:33:41 2021 -0500
add CDK-R/rpubchem github library
commit d068ca4acfdb29dc0dd752f22461890a7101981c
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Jan 7 15:55:28 2021 -0500
stash 20Q3
commit b57e4f76489705179df6e0b3253431833be2bbcf
Merge: 3fcc3d7 21c0bb9
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Jan 7 15:54:44 2021 -0500
merge master
Merge branch 'master' into org-reorg
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
commit 3fcc3d7414e5f15565208a1ef7f788d6a5505975
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Jan 7 15:49:59 2021 -0500
re-org navbar
First pass at reorganizing nav bar. Adding place holders.
commit 6b7028139976b60d3887cacb6b1ff9b251541071
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Jan 7 13:45:32 2021 -0500
update drug data
Error on drug data generation prevented 20Q4 from finishing. This adds two libraries (one new -rpubchem (download from github), and one we've used previously -furrr).
commit 1d2a552c9825d3726175a9ac5a962bb58c5b1254
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Jan 7 11:31:05 2021 -0500
udpate graph on methods
udpate graph to vizNetwork, also needed to update rename variables because of change in default behavior of CorrR package
commit 21c0bb9c8272520b87ec0b427cd0477bfbf31b87
Merge: 385deca 58ce650
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Wed Jan 6 14:46:15 2021 -0500
Merge pull request #42 from matthewhirschey/network-graph-update
Network graph update; nice work @ben-neubert !!!
commit 385deca0ccd38e22a5185e699d34e7735f2d41c1
Merge: a8c17ec fac59d3
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Wed Jan 6 05:15:46 2021 -0500
Merge pull request #46 from matthewhirschey/20Q4
Change sleep from 0.15s to 0.5
commit fac59d3d0b2ae0912b3153c8b6784d9c0ab3c19d
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 6 05:12:45 2021 -0500
Change sleep from 0.15s to 0.5
Keep getting 503 error on step two of data generation, so change to add more sleep
commit c5a6b6f3e60de1ff213c73abb462d470c46ebf70
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Jan 6 05:08:33 2021 -0500
update twitter titles
commit 58ce650e17a72007e4681e6fcd7288f0ec67e164
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Tue Jan 5 18:32:28 2021 -0500
Modified methods to include a visNetwork graph instead of a ggraph version.
commit 2463657e368e14bc6b139ae57ad1f95b4439a96b
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Jan 5 16:32:42 2021 -0500
fix small plot font sizes
Adds fig_retina = 1 option to fix small fonts when running
within Docker. Fix based on:
https://cran.rstudio.com/web/packages/showtext/vignettes/introduction.html#working-with-r-markdown
I also removed latex_engine option since this option is for
PDF documents.
commit 8058be78fdb8b2d729c027fa03e619e3c9e8ad97
Merge: b9cda8e d4beb4c
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Jan 5 15:00:28 2021 -0500
Merge branch 'network-graph-update' of github.com:matthewhirschey/ddh.com into network-graph-update
commit b9cda8e13b342728a1026175a788ea086938bd1f
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Jan 5 15:00:00 2021 -0500
Revert "remove ggraph requirement"
This reverts commit 7e11c371e82a4f2e5c6b08675e2f3467ec152e49.
We are still using ggraph for now.
commit d4beb4c41252965921235c5b3290560593ceb9fe
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Tue Jan 5 13:57:41 2021 -0500
Added pagetitle to the html report.
commit a8c17ec925ad2404a59574a7d2d82ba90e7f35de
Merge: dffe987 cf911f4
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Tue Jan 5 13:43:06 2021 -0500
Merge pull request #45 from matthewhirschey/20Q4
20 q4
commit cf911f41c868505e3d0b083c78b828987d6ce778
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 5 13:35:33 2021 -0500
re-remove quarterly_release.R
commit 006cb695a83471ca43ffc9b6de87db25b7070c6d
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 5 13:34:03 2021 -0500
remove expression_join
Replaces expression_join with expression_names, and updates the fun make_tweet(). Need to talk with JB about line 75.
commit 0f1f919cd47184e39ed8bc622d75d14bd473164a
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Jan 5 11:16:00 2021 -0500
rename to create_methods.R
commit 28e53d30a401b34c1b350288e08f8f326da0c614
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Jan 5 09:45:36 2021 -0500
add htmltools Docker requirement
commit 7e11c371e82a4f2e5c6b08675e2f3467ec152e49
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Jan 5 08:53:22 2021 -0500
remove ggraph requirement
commit dcb836e1f05e788bbd3073f81ad7459c2324a88d
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Jan 4 21:21:10 2021 -0500
update methods for 20Q4
commit 18df7fe8461bd5faaf7153bcd114c48b9265ddb9
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Jan 4 21:20:59 2021 -0500
update generate_methods
Updated generate_methods.R so it can be run locally to prepare for a new quarterly release. Deleted old quarterly_release for redundancy with generate_methods.R and generate_data.R
commit 8bd4207598392bbcf7ce8c377c5a32a8dfaea070
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Mon Jan 4 18:24:50 2021 -0500
Switched generated report to HTML format. Removed ggraph from report and included visNetwork graph instead.
commit aa76ae2420bd44d8f5e0ba6c4ecfd539738e1197
Merge: a33bf67 cdbafed
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Sun Dec 20 16:09:30 2020 -0500
Merge branch 'network-graph-update' of https://github.com/matthewhirschey/ddh.com into network-graph-update
commit a33bf678b95b3b192456e6db76a9ee39dbbcee8a
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Sun Dec 20 16:09:15 2020 -0500
Fixed bug with href within node tooltips.
commit cdbafed4d5e5c18a55393fa71dea0c295310a2b3
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Dec 16 17:31:27 2020 -0500
base-shiny: remove networkD3 and add visNetwork
commit f8ed24f8943cf2d36797fcee2b7b100645a29409
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Wed Dec 16 13:05:16 2020 -0500
Removed visNetwork webshot implementation in DDH reports. Restored ggraph for report image generation.
commit a073b0f699b6d7b03bdcb4e52b48eaa22b7cac9c
Merge: da30e40 dffe987
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Tue Dec 15 17:55:50 2020 -0500
Merged with Master
Merge branch 'master' into network-graph-update
# Conflicts:
# code/fun_graphs.R
commit dffe9877ff5809a7d4a4758c306079fb22d2612f
Merge: 920d0fc 4de1d27
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Wed Dec 9 17:48:39 2020 +0100
Merge pull request #43 from matthewhirschey/data-viz-update
* adding new main colors for each class (genes, cells, drugs) plus color sets and palette functions for each
* some minor fixes such as fixing tooltip dotplot plotly, size legend symbols network, ...
commit 4de1d27c4c718dd908a8f66e5c8ecfef994967bf
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Wed Dec 9 14:40:22 2020 +0100
:lipstick: fix CVD issues
violet not magenta to avoid prblems with blueish colors for colorblind people
commit cbcdcc8de65443747d5bcb4de26331b989d10dd7
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Wed Dec 9 09:07:54 2020 +0100
:art: cells coded as purple, not blue
commit d794c0991c9437f5f6b5514e0ed00e4ffd75810b
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Dec 8 20:07:16 2020 +0100
:art: assign all main colors and palette functions in generate_colors.R
commit dfc8d376ea4b5084909a2026d53da23f79c2195c
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Dec 8 15:49:26 2020 +0100
:art: fix legend graph plot
commit 181fe7e7612bbdf4b7edcf27bff0a00c58db2bb0
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Dec 8 15:26:41 2020 +0100
:art: fix symbol size legend
commit cc25537c80e411f0d8b20a72646b1a4a6192b516
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Dec 8 15:26:23 2020 +0100
:lipstick: fix spacing sublineage plot text
commit 56bb17a48f221225963293935b44b7777a3efd81
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Dec 8 15:25:50 2020 +0100
:art: fix color assignment + T/F
commit 14db36b712c9f1e6061c23b4f2cb6ef86217b16e
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Dec 8 09:51:41 2020 +0100
:lipstick: fix sourcing color function
commit da30e40d39e734a69de2249513857dabc8ddb3e5
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Sat Dec 5 15:17:28 2020 -0500
Removed ggraph network in report. Added visNetwork HTML to the report zip.
commit 2450408adb6704e6e4087b1a9b3557a049c1d166
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Dec 4 09:08:34 2020 -0500
updating urls for 20Q4
Adding ability to run quarterly_release, after updating current_release, to make it easier to batch actions required to update code before generating data on server. Also cleaning up some comments
commit 91d0a7ac4a88aa29f1d7b753060a81b40cf5e50b
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Fri Dec 4 09:55:35 2020 +0100
:heavy_plus_sign: add function for color palette generation
commit 00b2695d90ac1505c19eb58a25755d7c4d03f28f
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Thu Dec 3 13:35:30 2020 -0500
Fixed issue with network legend being small in report using a premade legend image.
commit 39d213e7ccc62398d1cc7dcac7bc84238d880870
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Fri Nov 27 15:17:23 2020 -0500
Fixed zoom of graph when there is a disconnected query gene. Cleaned up the code.
commit f826f8e3517c7d43688fbde4889399f7d36c7499
Merge: 28d6147 920d0fc
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Nov 19 14:51:37 2020 -0500
merge master
Merge branch 'master' into network-graph-update
commit 920d0fc3f1768c3b39bc77d74638dd769bc7fa12
Merge: b1683f8 fc4be97
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Nov 17 13:15:33 2020 -0500
Merge pull request #41 from matthewhirschey/two-step-report-building
Two step report building
commit fc4be9702d8c47ee827315f881ae823ffc3d6ad9
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Nov 17 08:50:00 2020 -0500
Fix Error in ctx$invalidate
Rest of error message:
> Reactive context was created in one process and invalidated from another
This only occurred when running report generation in the background
failed with this error. The problem was setting report_zip_path.
I moved the call into the finally block.
commit 28d6147bde820f05d17ae754bf188c104ed21697
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Mon Nov 16 21:02:02 2020 -0500
Quick bug fix to ensure query gene is listed first on the legend
commit 9bef1c7045a94649de3722ac57f1b4c6b744e5b5
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Mon Nov 16 17:53:01 2020 -0500
Network graph update. Fixed bugs related to discussion with Matt. Implemented ability to download the network graph as an html. Implemented ability to include only positive or negative correlations in the network. Integrated visNetwork within report generation.
commit e71326e72c08116fe21b279150fb2cd63b8a5c38
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Nov 16 16:40:54 2020 -0500
tweak messages when building zip files
commit d45859b45bf91cba6d91bd5047a2ab38fa178fc3
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Nov 13 11:34:38 2020 -0500
make download button more noticeable
Based on suggestion from https://3.basecamp.com/4316284/buckets/14415887/todos/3165907023
commit b1683f83ecb03b58529fdb9417737d018f53deae
Merge: 887e3b5 737bfa2
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Nov 13 11:23:48 2020 -0500
Merge pull request #40 from matthewhirschey/fix-duplicate-search-results
fix duplicate genes in search
commit 307aedf3ab359968645824ade41e37767aec959c
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Nov 13 11:23:02 2020 -0500
cleanup zip directory when session ends
commit 737bfa209373c4e0a91586a11fa8cc13d2966907
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Nov 13 09:34:39 2020 -0500
add tests for ADSS example
Also removes un-necessary change.
commit 4685e8bd5d0ba2488db9b5ce840da04ab3ab6bed
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Nov 11 10:23:37 2020 -0500
two phase report generation
Updates to the "DOWNLOADS" tab:
Adds "Generate report" button that will create a zip file
containing the pdf report and images. When the report generation
completes the "Download report" button will be shown the
"Generate report" button is hidden.
commit 485551d09214bd46364e0341e83208ed59629257
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Nov 10 14:28:00 2020 -0500
deduplicate search rows using key after sorting
Adds sort_dedup_and_limit that sorts by rank descending, keeps distinct rows by
key and limits rows.
commit ba3e60370242fb62a2803528823b3be3ad509736
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Nov 10 11:25:05 2020 -0500
filter non-max ranked items from search results
commit 887e3b5b520c325b6ae2c78f692f85bd868c66c4
Merge: b925220 fb907f1
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Mon Nov 2 08:51:51 2020 +0100
Merge pull request #37 from matthewhirschey/data-viz-update
Data viz update
commit fb907f13b00d478b96b97354deb5e4dc6e547b80
Merge: 6574167 b925220
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Mon Nov 2 08:51:28 2020 +0100
Merge branch 'master' into data-viz-update
commit cefddb80b4a738c29ad1cbbbfd570d2dba00589f
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Fri Oct 30 17:49:43 2020 -0400
visNetwork implementation of the Network Graph
commit b92522057fa25466be4bc3e140f718434c7df368
Merge: 113f42d d2cb1ed
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Oct 28 12:54:23 2020 -0400
Merge pull request #39 from matthewhirschey/38-increase-probe-timeout
increase ddh-shiny-app probe timeout to 60 seconds
commit d2cb1ed7b89a9855e412f5714b2510701a3fb8e8
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Oct 28 09:43:44 2020 -0400
increase ddh-shiny-app probe timeout to 60 seconds
Also removes initialDelaySeconds for probes. Due
to how R is lazy and doesn't load data at startup
this was just wasted time.
commit 65741678212c9d2ec59cfb69eae014ebb6b1dfd4
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 18:46:06 2020 +0100
:lipstick: set to most recent data
commit 8bcab5c9a3b54eebd3fb61411f7b77a772b2c76b
Merge: 01e7464 bb09637
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 18:44:36 2020 +0100
Merge branch 'data-viz-update' of https://github.com/matthewhirschey/ddh.com into data-viz-update
commit 01e7464aae5dd9f65dc3860632a64066ddafc6b6
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 18:44:33 2020 +0100
:art: add custom font to cellanatogram
commit bb0963703b2aae33ad265cf19e3ef2189b4548e6
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sun Oct 25 13:37:20 2020 -0400
install Roboto Slab and Nunito Sans fonts
Adds code to download and install google fonts to base image.
commit e7b80391a6204307f21a884cc006f23a59f1ac56
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 13:59:55 2020 +0100
:bug: change data dir
commit e27a804e7137a9ca9ea13951e1e108bd9567196f
Merge: f788de2 113f42d
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 13:47:25 2020 +0100
Merge branch 'master' into data-viz-update
commit f788de29cdc84d8f8a79f85ab639c2e35efeafea
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 13:47:07 2020 +0100
:art: custom height for density plots depending on search type
commit 1c7ccc393eaa80a451fa9e4a50daf7930eff5be9
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 13:33:01 2020 +0100
:art: change to custom fonts via `showtext`
* works locally with fotns installed, to be tested on server
commit 13a0d278d5ac549040304e434407a0bfbaf71529
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 13:32:29 2020 +0100
:art: change fonts ü edge color network
commit 95bbde1edb318092229389804aa436a4fb4d1a53
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 13:32:05 2020 +0100
:heavy_plus_sign: update dependencies
commit 55fa36d90b3ab897a1954533d83d78a2e7401a4f
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 13:31:51 2020 +0100
:art: fix aspect ratios and fonts PNG + PDF
* added custom fonts for all PNG + PDF outputs
* fixes all fig sizes in PNG + PDF except distribution plot
* need of a sumamry var # of genes to sacale height for dependency plots
commit d5e23131fd6d65545c70b308c50c2d0ff0930f1e
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Sun Oct 25 13:08:53 2020 +0100
:heavy_plus_sign: change dependencies
* remove scico (not needed anymore for colors)
* add showtext for custom fonts (works at least for me locally on Win10 with fonts "Nunito Sans" and "Roboto SLab" installed)
commit 113f42d705db73e267da7f13364e90fe48abdac0
Merge: f1de11d 461472e
Author: Ben Neubert <38669590+ben-neubert@users.noreply.github.com>
Date: Fri Oct 23 17:15:56 2020 -0400
Merge pull request #36 from matthewhirschey/testDataUpdate
Modified test data to work with network graph
commit 6af040544f56db6b8163dd42a90b5dbe725a0d2f
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Fri Oct 23 14:28:51 2020 +0200
:art: fix aspect ratios of exported png's
This commit fixes the heights of the png files as mentioned in issue #22
* added different aspect ratios depending on chart saved
* added dpi setting
* added cairo device
Problems:
* somehow dynamic scaling for more than 1 gene not working
* currently no way to access number of genes in pathway to dynamically scale density plot for pathways -> information in data_values needed @johnbradley
* currently I see no way to include different aspect ratios in the pdf file -> maybe create pdf template that we render with fig.width and fig.height set in chunks? @johnbradley
commit 461472e3a76b8724885ad05c2dbdc5a1afcb2b3a
Author: Ben Neubert <bcn6fe@virginia.edu>
Date: Tue Oct 20 15:57:26 2020 -0400
Modified test data to work with network graph
Modified the test data set so that the master_top_table and master_bottom_table work with the network graph. Specifically, I filtered the sub-table data for each gene in the master tables so that they only contain genes in the test data set.
commit f1de11dc877c15f9e9fd4763beaa65d01a17b4ac
Merge: a3ece63 570ee49
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Oct 19 13:31:18 2020 -0400
Merge pull request #35 from matthewhirschey/28-slurm-array-job-v2
Use slurm array job for pathway subset generation
commit 570ee49ffa78e528598780a4ce4e7318e3a0d706
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Oct 19 10:06:00 2020 -0400
Use slurm array job for pathway subset generation
Switches to using slurm array job to generate pathways data.
Changes
- code/generate_data.R support for more steps. Changes steps to numeric identifiers to clearly define the order they should be run in. The pathway data subset files can now be generated by themselves.
- code/current_release.R adds number of pathway subset files global variable
- submit-slurm-jobs.sh - updates existing script to call new slurm scripts
- slurm/data-gen-step*.sh - scripts to generate steps with different slurm requirements
- slurm/rscript.sh - script to wrap up singularity Rscript call
- slurm/upload-data.sh - moved from root directory upload-slurm.sh
Logs for the slurm jobs will be stored in the logs directory.
The workflow for running on slurm will not change with these changes.
Continue to just run submit-slurm-jobs.sh.
Fixes #28
commit a3ece63e8a6bc5eff40dd065482f0b5c69f6393c
Merge: 2bef814 da0e959
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Oct 15 10:12:29 2020 -0400
Merge pull request #34 from matthewhirschey/11-remove-return-js
remove returnClick.js
commit da0e95922adfc562bd6688b788576e126ad01624
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Oct 15 09:21:30 2020 -0400
remove returnClick.js
Removes un-necessary custom javascript code for search input.
Changes querySearchServer to observe gene_or_pathway instead
of gene_or_pathway_search which is not fired when the user
presses enter. I added code to ignore empty search strings
since the gene_or_pathway_search event is fired when the
the page loads.
commit 35c64673628e32116ec4182713577c9d05adfc4e
Merge: 818468a 6a2edaa
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Oct 13 11:17:07 2020 -0400
Merge branch 'data-viz-update' of https://github.com/matthewhirschey/ddh.com into data-viz-update
commit 818468a4c9b1e404c54b6c846d72e309cf32e474
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Oct 13 11:17:04 2020 -0400
update legends
update legends + minor re-org
commit 6a2edaa19827123ce54c41ca62ef6aecdaeb1530
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Oct 13 17:06:43 2020 +0200
:art: ridges sorted from neg to pos + smaller axis texts
commit 92b95ee20e2b20409f2d6d671c16de3dd6204977
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Oct 13 17:00:04 2020 +0200
:art: old order interval stripes, new order ridge plot
commit c3dcb296a43042873e6d6c84148964cec663ada8
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Oct 13 16:57:20 2020 +0200
:art: reverse order (sub)lineages in interval plots
commit 0bd66fade11ee99decc478110cb705ae9da7e9e4
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Oct 13 16:36:06 2020 +0200
:art: fix order
commit a16ae69e961d4965b9aa304c8ad38f20e521c087
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Oct 13 16:34:37 2020 +0200
:art: updates all dependency plots
- interval stripes
- grey box
- add top axis labs + title (sub)lineages
- remove bottom title (sub)lineages
- legend on top
- halfeyes
- grey box
- colored cutoff
- source colors (main, light, dark) + palette
commit 0440d61ecd5cef0b0f0b4755a74acfe69f75e77a
Merge: 4cf74d2 1170037
Author: Z3tt <cedricphilippscherer@gmail.com>
Date: Tue Oct 13 15:47:27 2020 +0200
Merge branch 'master' into data-viz-update
commit 2bef814c3e5cf0516f63e4604ccb6a3a0254a695
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Oct 12 07:31:01 2020 -0400
move generate_drug_data.R to step 2 for more memory allocation
Will rename later.
commit 949fe4bc2079701a99450113a71eedd288ee84bb
Author: matthewhirschey <matthew@hirschey.org>
Date: Sun Oct 11 06:47:31 2020 -0400
fix col_types error
commit bfdd9ca6363ffb079ee2f440e53f6ca47defb941
Author: matthewhirschey <matthew@hirschey.org>
Date: Sat Oct 10 15:15:43 2020 -0400
remove vroom
Not needed, throws error
commit 2809ae4fc6328bf18a72f089c0ab8d50942f0745
Merge: ec71d5a a482a69
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Oct 10 10:28:19 2020 -0400
Merge pull request #33 from matthewhirschey/cell_line
Adds cell line and compound data
commit a482a692f5a67bc8f92710755499511734ad7116
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Oct 10 10:23:24 2020 -0400
add generate_drug_data to generate_data.R
commit caac837504b7e5c98ff913d4498d672c7bc0eb13
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Oct 10 10:23:03 2020 -0400
remove unused gene_summary from generate_drug_data
commit 07a14ffa250447cf601ca71e8232ed5e61b1ea91
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Oct 10 09:58:05 2020 -0400
move cell/compound summary modules to shiny_text
commit cf1f493fe3fb1395148d2b5005d812436de5907a
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Oct 10 09:53:18 2020 -0400
add null checks to fix console errors
Adding checks for nulls to prevent the following console errors:
```
Warning: Error in : Problem with `filter()` input `..1`.
x Input `..1` must be of size 462 or 1, not size 0.
ℹ Input `..1` is `approved_symbol == input$id`.
```
The problems seems to be the reactivity temporarily updates
while we are navigating away from the page.
commit ec71d5a9cc1918c1232f6397ee67fde9e0b7140d
Merge: 1170037 9a7790d
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Oct 10 09:27:02 2020 -0400
Merge pull request #32 from matthewhirschey/nginx-django-deploy-yaml
Nginx django deploy yaml
commit 6d98495a6ff009658a1c17191bb950035d238c35
Merge: 6b35bab 1170037
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Oct 10 09:25:50 2020 -0400
Merge branch 'master' into cell_line
commit 6b35babf2ba2e0a09d15cf8e97b171ca45088f0d
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Oct 10 09:04:47 2020 -0400
add compound/mo/compound_list page
Adds code to search prism_names for compounds and return search results.
Adds page_compound that renders detail for the three types with
basic placeholder content.
commit 2e9d7ee6fd7231e330f69db0ea9f945850500106
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Oct 9 10:07:25 2020 -0400
add moa to prism_names
Adding moa to the prism_names file (which we will use for search) will act as a defined group of drugs.
commit e0e5a4d6fab2c7926e51c96d37a427646123ca7c
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Oct 8 07:10:36 2020 -0400
add test
Add a single line to get top drug-gene correlations out of entire dataset
commit 62b04b28ae92ba741a3a056c05708e6444ba9d65
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Oct 7 15:43:56 2020 -0400
first pass metabolite data
Add metabolite data from HMDB
commit 178547f19a60ecef04ba11a1b3017e82158e4457
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Oct 7 12:56:07 2020 -0400
update drugs to search on ID
imperfect, but working. searching on ID causes errors in duplicates and drugs IDs that share common gene names.
commit 228a4327dd42a0feeb150fef72573e3f161d45af
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Oct 5 16:12:13 2020 -0400
generate drug data
Update current_release.R to put prism URLs into release. Also add new generate_drug_data.R file to begin generating datafile that will allow searching. Current problem: multiple entries sharing same name
commit 11700371ed6a8b9b4dfbbe19f837056edb15de13
Merge: 5123eff dcfb524
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Oct 1 09:44:00 2020 -0400
Merge pull request #31 from matthewhirschey/retry-entrez-summary
retry entrez_summary
commit dcfb524b4818184bb61c8bd62673d931ecbd6f42
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Sep 29 14:06:25 2020 -0400
retry entrez_summary
Adds retry logic to create_gene_summary.R fetching entrez data.
This is to handle sporatic errors like this:
> No esummary records found in file.
commit 5123eff5c1951229524f7b752ec350ebb34870d9
Merge: 7c34ee8 fc4e87e
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Sun Sep 27 13:34:05 2020 -0400
Merge pull request #30 from matthewhirschey/gene-page-fillout
20Q3 + other minor fixes.
commit fc4e87ebc1adb93719b53ad70a897bf245eff2fd
Author: matthewhirschey <matthew@hirschey.org>
Date: Sat Sep 26 14:34:31 2020 -0400
add methods for 20Q3
This adds the rendered HTML file, as well as a new R script to generate the methods doc post new release, pre-full data
commit 32d094e4b20961b2e30c25f9eaac27af14a07508
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Sep 26 13:46:56 2020 -0400
calculate search rank with appropriate fields
Calculate rank with the correct fields. Also moves rank into the group by so top level
code can sort by ranking.
commit 1de41b7456f58752fe09b036bc4e6f9fbc3a36bb
Author: matthewhirschey <matthew@hirschey.org>
Date: Sat Sep 26 13:06:56 2020 -0400
Update code to generate 20Q3 data
Added code to generate tables for P 53 Jeanne that will then allow a network graph to be made. Previous problem was needing to generate data before generating methods. A better solution is to generate a subset of the data, Render the methods, and then push the entire change to github. This code also changed how some of the master tables were made. I broke out two small functions, that are now called in the script. Part of the reason I did this was to be able to reuse some of the code in generating the test data set.
commit bf8ff1f882a5718328a07c21a548aef4f994242d
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Sep 26 12:00:58 2020 -0400
fixes to show lineage and sublinage pages correctly
commit 131efbdcb171a6c349090fca0a067e7c82f2c7fc
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Sep 26 11:38:58 2020 -0400
sort search results by rank
Adds sorting step that shows closest matches first.
commit d13c39e00e531975081a7a23872b0a445225dc1c
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Sep 25 17:07:14 2020 -0400
allow searching lineage subtypes
commit 4cf74d25ad297b58bc79b7b2d532335f1e0b07bb
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Fri Sep 25 22:42:43 2020 +0200
:art: ridges colored by dep score
commit 42c306ac21872486bcda035357932d0c88c91fe8
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Sep 25 16:21:08 2020 -0400
only show custom list search results if something was known
commit 1051d8f1fb726340b84c6b49fde64daa38998a62
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Sep 25 14:08:25 2020 -0400
display custom cell list summary
commit 0700f35b160a1e78ebc7a7db6fc514b7ce85a3a8
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Sep 25 11:48:42 2020 -0400
update search for cell lines, lineage, can custom cell lines
commit 9a7790d3eb2275e642bdab2d94915aa0620c8725
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Sep 24 09:02:14 2020 -0400
update README and placeholder index.html
commit d8f8961a83ad73313e2ee4f0858e342caded9bbe
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Sep 24 08:49:31 2020 -0400
add OpenShift yaml for Django,PostgreSQL,Nginx
Django - deploys authentication app
Postgres - holds data for Django auth app
Nginx - routes auth to Django and otherwise shiny app
commit c79df1e9f425751877b183fe47aa116351eb68f3
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Sep 23 17:45:31 2020 -0400
first attempt at cell search
Made dummy page_cell.R, and added three types of cell line searches (single cell, many cells defined by lineage, or custom list) analogous to gene searches
commit 0d8c5f30d5022bbfa0e0ce70d7da064d4a20e7d2
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Sep 23 11:09:09 2020 -0400
add placeholder nginx index.html
commit f5f26d7c60f465528fc2cd009eca9915aa91dc80
Merge: 0f1422d 7c34ee8
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Sep 18 14:48:08 2020 -0400
Merge branch 'master' into gene-page-fillout
# Conflicts:
# code/current_release.R
commit 0f1422d66c171880e0fadc7dc5dd0bca7798d037
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Sep 18 13:53:18 2020 -0400
20Q3 urls
commit 6913b2f78d072b47704c32706c9b76685d69247e
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Sep 18 13:52:57 2020 -0400
test code for public/private pages
commit 7c34ee89efe588644fcc4b59c47cfff8d909049d
Merge: caf4be9 f1f2a18
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Sep 18 13:11:47 2020 -0400
Merge pull request #29 from matthewhirschey/25-retry-enrichr-on-error
Retry enrichr calls when invalid data is returned
commit f1f2a1856192ea5945e33c99ed5563f85e37cfbc
Author: John Bradley <johnbradley2008@gmail.com>
Date: Fri Sep 18 09:26:22 2020 -0400
remove outfile flag from makeCluster for stability
Removing outfile="" from makeCluster since it caused the processes to
hang after a while. This flag caused stdout/stderr from the
background process to be passed back to the main process.
commit 2cd227ce23fee549dce509e697aa3322a6303213
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Sep 16 14:24:37 2020 -0400
remove debug gene names limiting
commit ef9de6828a244381121f85d5bd0f823da6611ec1
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Sep 16 08:47:56 2020 -0400
make sure enrichr response includes Adjusted.P.value for all libraries
commit a10d6028bea4282231453072f6aaabe8b1d70424
Author: John Bradley <johnbradley2008@gmail.com>
Date: Wed Sep 16 08:45:15 2020 -0400
save stdout and stderr for background processes
This is to help debugging failures in pathway data generation.
commit 732077ead54d9445a9e61670c5e204562c737a55
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Sep 15 13:06:00 2020 -0400
retry if enrichr results is missing Adjusted.P.value column
commit a95d106e1b401cea6b9dfe2f3f69fc009e8bc8fa
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Sep 14 10:18:55 2020 -0400
put back generate_data dopar
commit 54d31fefe3a1b49d6022f8d1a3589b56526ac9be
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Sep 14 10:07:01 2020 -0400
improve retrying "path" step in generate_data.R
We have seen problems with enrichr failing after several
hours when running the "path" step. This results in no subset
files being created and requiring starting over. To better
handle this scenario we increase the number of subset files
so progress is saved and do not re-create subset files.
After the pathway files are created the subset files are now
deleted.
commit da37177dae70b254c1028103648427d2cf3eef8a
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Sep 14 10:05:57 2020 -0400
add retry logic to enrichr call to generate_depmap_pathways.R
Adds 3 retries for null results from enrichr after sleeping for 30 seconds.
commit 406ee9a5087a6b2a73a9b547cdef1e08da44d06e
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Sep 8 10:42:57 2020 -0400
fix dissimilar gene linkout
dissimilar gene table had old URL in a href for gene link out
commit a3566caeba9302ea5d883a87ca3afb7749d6ca6f
Author: matthewhirschey <matthew@hirschey.org>
Date: Sat Sep 5 07:22:57 2020 -0400
Add target="_blank" to hrefs
Want to open link outs into new tabs, so added target="_blank"to each linkout href
commit 0ec3f1982703017aa9a8a9bfa74b62a2bda76dc8
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Sep 2 11:10:28 2020 -0400
new logo
Added new logo
commit caf4be909cb6d1108a6c49280cd6ff58c8b05b6a
Merge: 07b2df7 5fe6588
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Tue Sep 1 08:40:10 2020 -0400
Merge pull request #27 from matthewhirschey/gene-page-fillout
Gene page fillout (step 2)
commit 07b2df77939ae3fc903e3407eb7f0a25a083c8c5
Merge: e20b377 a1bf48e
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Sep 1 08:38:46 2020 -0400
Merge pull request #26 from matthewhirschey/25-data-generation-fixes
Fixes to data generation and deployment
commit 5fe65883da7bcd61ef4a63f4d24c56a15b2b323b
Author: matthewhirschey <matthew@hirschey.org>
Date: Mon Aug 31 12:11:12 2020 -0400
load data, not test data
commit a1bf48ecc5bdf8056dbb46febdf9e757548bf96e
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Aug 31 10:34:23 2020 -0400
add requirements for docker tests
commit 218894ff3ffa4a508b3f32753439c740b5b587b8
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Aug 31 10:00:26 2020 -0400
test cast_enrichr_data
commit 31ad7fdfdf3f12167be5a28e4d2300882c7f3121
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Aug 31 09:06:36 2020 -0400
cleanup base-shiny/Dockerfile
This Dockerfile had two places installing r packages. Combined
it into one location.
commit 3bd387afecc22cf211d2f4293140f5b9077848a9
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Aug 31 08:59:49 2020 -0400
fix error when enrichr_loop is run on empty gene list
Some genes have no negatively associated genes that pass the threadshold.
When this happens an empty gene_list is passed to enrichr_loop which returned
an empty tibble. We then arranged this and received an error since the colum
we were arranging by (Adjusted.P.valuej) didn't exist.
https://github.com/matthewhirschey/ddh.com/issues/25#issuecomment-682985439
commit d39e71207816d2ad48e5ca156b2c19314e6c1ec2
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Aug 31 08:36:46 2020 -0400
remove duplicate ggdist install
commit 50441d556cafd137d7ca3feb9623a242eb0b60dd
Author: John Bradley <johnbradley2008@gmail.com>
Date: Sat Aug 29 09:43:12 2020 -0400
move ggdist later in base-shiny installation
It was failing due to missing dplyr across function.
commit 50086fe40f5c37924c316a7fd29d8c35ce888700
Author: matthewhirschey <matthew@hirschey.org>
Date: Sat Aug 29 09:30:21 2020 -0400
add linkout to EC
Add link to EC def on wikipedia, and then to search expasy for EC id
commit 9c729f94882d06ec98521d9f097989974e85d15b
Author: matthewhirschey <matthew@hirschey.org>
Date: Sat Aug 29 08:54:06 2020 -0400
fix protein sequence output
Add data to get proteins.Rds that contains sequence information, and then added this as an output to the shiny app. Had a problem with getting proper breaks, but verbatimTextOutput solves that problem by giving the long string on one page (and makes it copy-able!)
commit 291ff35fdd97bdeb6b193518d7fd761a8bfe7dc5
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Aug 28 14:10:09 2020 -0400
Add ability to filter raw depedency data table
commit 1e2ed2fe6c7c8974a4f4f7add92bdc3997b65357
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Aug 28 14:09:50 2020 -0400
Move depedency table to conditional panel below plots
I still think the plots are messy, but like hiding the raw data here, if it's needed
commit 9f32f233dbcc5027bc4e9cafc69a197c8eeb3370
Author: matthewhirschey <matthew@hirschey.org>
Date: Fri Aug 28 09:44:21 2020 -0400
Add generate_proteins_data.R to generate_data script
Add generate_proteins_data.R to generate_data.R script, so this will run durng data generation.
No need to update the slurm jobs.sh script, because we did not add a new step.
commit 4bc570c39bf9fb94e789c92ea2653d4afb63161a
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Aug 27 15:52:03 2020 -0400
fixes for enrichr data
Addresses "Combining problems with enrichr data" in issue #25.
commit ec2e13dd1f9143121c8867f6a829e91f7a69fb66
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Aug 27 15:49:04 2020 -0400
fix gene_summary filename in generate_pubmed_data.R
commit a1190db5b9fb63960ebcca98a870c010b94ed555
Author: John Bradley <johnbradley2008@gmail.com>
Date: Thu Aug 27 15:47:46 2020 -0400
install later tidyselect version
Similar fix in data generation to https://github.com/matthewhirschey/ddh/pull/101
commit e4a8a8686dacca99d9836b1facc2610c9ba6433a
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Aug 27 12:47:09 2020 -0400
add CCLE cell expression back
After mysterious deletion with some recent PRs, added the code back to page_gene to get the cellExpressionPlot back
commit ad34345227508207fd966824a7cf2de33ed0fbe8
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Aug 27 12:44:59 2020 -0400
working proteins summary
Added function to get proteins summary out of proteins df, made objects in shiny function, and added to page.
commit 7837650446f0f0958d5f6ee0ba6b3a3bdeb261d2
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Aug 27 10:57:11 2020 -0400
add where() back
Assuming john fixes this :]
commit 670241e3dd9359bcaf7f2f42e91366fcd9797a45
Author: matthewhirschey <matthew@hirschey.org>
Date: Thu Aug 27 10:49:17 2020 -0400
add proteins data
Added proteins data v1 from zenodo download, which is linked to the proteins package. Will need to update this to v1.1 when we have more information that we'd like to include, such as the 'description' field. Also added proteins to the test data generation. And added the URL to zenodo to the current_release.R, with other URLs.
commit e20b3770775556ddb6e5f49b54916243e3f218eb
Merge: db7f980 01b39d6
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Thu Aug 27 09:31:25 2020 +0200
Merge pull request #21 from matthewhirschey/theme-update
New Shiny theme! 🎉
commit 01b39d60ad48af0596829181c74109e711d9c3c7
Merge: aee2612 db7f980
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Wed Aug 26 19:49:52 2020 +0200
Merge branch 'master' into theme-update
commit db7f9802b0b5d20adad5a9189db75290d5ac3621
Merge: e419762 e01d7fd
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Wed Aug 26 10:18:16 2020 -0400
Merge pull request #24 from matthewhirschey/gene-page-fillout
Gene page fillout: step 1
commit e01d7fd8b68a938639b68e4136c26d34b9ec7d65
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Aug 26 07:20:21 2020 -0400
change dir from tests to data
commit 6be76e46f90f34754ad00e5513a07dc2862968ed
Merge: 1ed629d e419762
Author: matthewhirschey <matthew@hirschey.org>
Date: Wed Aug 26 07:11:43 2020 -0400
merge master after data-viz-update
Some changes required after merging with master after data-viz-update, which were conflicted with this branch. Most important was the rename of expression_join to expression and expression_names
Merge branch 'master' into gene-page-fillout
# Conflicts:
# code/fun_plots.R
# code/shiny_plots.R
commit aee2612fa20b9b37332bedbeb5fe2e3373110989
Merge: 890be3b e419762
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Wed Aug 26 09:03:20 2020 +0200
Merge branch 'master' into theme-update
commit e4197629ebc0b0f4fceb0966ecf13fb8c72c03b4
Merge: aba3f2f ab690d8
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Wed Aug 26 00:02:30 2020 +0200
Merge pull request #20 from matthewhirschey/data-viz-update
New Plots 📈🎉
commit ab690d8f58d4fadeabd2199043c6d15aa59cd302
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 22:39:33 2020 +0200
:lipstick: remove font package dependencies as well for now
commit 424befe93f71c02ed19208d3983c06cda2cf0886
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 22:36:30 2020 +0200
:lipstick: go back to default ggplot fonts for now
commit f20d85463af6f875a2af721fa3b66de642e2abc5
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 22:29:05 2020 +0200
:lipstick: replace font with system font for now
font: Franklin Gothic Book
commit edddf685ec39a341ec95eb9aff3b3ba1e81c0e74
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 22:22:36 2020 +0200
:lipstick: fix printing ridgeline plot
commit 48983c06f8611ae036b0ef87ab7f65e1924f97b1
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 22:04:12 2020 +0200
:lipstick: remove conditional legends
commit e6ba05f7cb25ba704af4a30a2a7dc227ab7d1a04
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 22:02:40 2020 +0200
:lipstick: reverse lineage + sublineage order
commit 8b27a30998e7441bbf7841cfa13ceebbe3c0a3a4
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Aug 25 12:12:59 2020 -0400
add ragg, scico, ggdist requirements
commit 890be3b6e87780a152b328f1e97d7b0243d3c2d2
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 17:35:13 2020 +0200
:lipstick: use Roboto Slab for h4 as well
commit c46d5cefc73e8144499f23e0e6564a75710ce655
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 17:31:18 2020 +0200
:art: theme updates title font + weight
commit d7132d204a5862674330983e8e0aeb2058bf0e32
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 16:39:57 2020 +0200
:art: use ggplot2:scale_viridis_d() for cell anatogram
commit 62671cbdee178e11f309a545922ebdb57a0c3611
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 16:37:29 2020 +0200
:lipstick: add libraries to app.R
commit 3942ec22c42a5c168f605909eda064d3ab205983
Merge: e5bc8b6 2fdb048
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 16:37:01 2020 +0200
Merge branch 'data-viz-update' of https://github.com/matthewhirschey/ddh.com into data-viz-update
commit e5bc8b6fe2883ca8cfe98839133e72155c64bdca
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 16:35:35 2020 +0200
:lipstick: remove viridis call ridgeline plot
commit 2fdb04838965bc55ddb62cb46ad2978597f4f95e
Author: Matthew Hirschey <matthew.hirschey@duke.edu>
Date: Tue Aug 25 10:34:22 2020 -0400
Update fun_plots.R
typo
commit 72aa68d066886247221166967386e22f14eb3265
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 16:25:40 2020 +0200
:package: add library call ggdist
commit 7ee2736c95943bb4fe4020081500c083d949763c
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 16:20:04 2020 +0200
:lipstick: fix typo
commit ae138f33bf883393a47381f0e619b9bb1136af22
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 16:19:22 2020 +0200
:art: fix font title to Nunito as default
commit ff96224d142c85c3c6857708ad0023d598005d58
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 16:18:56 2020 +0200
:art: new theming
new fonts, new color navbar, all caps navbar, new link color
commit a877ea9ba1b0e3047b9f1a20f5f0c51b1307c647
Merge: 6899e60 aba3f2f
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 15:38:05 2020 +0200
Merge branch 'master' into theme-update
commit 139d36b38fc2f276d31aad78ee0a759aa2cf97be
Merge: 1f3c42d aba3f2f
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 15:31:47 2020 +0200
Merge branch 'master' into data-viz-update
commit 1f3c42d2f046a9eebd81ae21f817699d2981f0a7
Author: Cédric Scherer <cedricphilippscherer@gmail.com>
Date: Tue Aug 25 15:29:29 2020 +0200
:pencil2: new captions
commit 1ed629d155bb87f74d392ea5fa2ff0fc227f6bd5
Merge: 3f64587 aba3f2f
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Aug 25 08:11:01 2020 -0400
merge master
Merge branch 'master' into gene-page-fillout
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
commit 3f64587ba336b727035b8ebe0a5d943e5a7fdfaa
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Aug 25 08:10:09 2020 -0400
Move anatograms
Moved anatograms to expression tab from summary tab
commit bbfb6fc96a7882a2fff6f7e81e4468fda3a94e85
Author: matthewhirschey <matthew@hirschey.org>
Date: Tue Aug 25 08:09:04 2020 -0400
lineage counter
small script to count lineages & subs in order to determine how dynamic the height variable needs to be in the ridgeline plots; the answer: they are the same within data releases, but likely different upon a new data release.
commit aba3f2fe5c59801fbff1646316e9be2fc0313e2c
Merge: 198b43b ad4adbc
Author: John Bradley <johnbradley2008@gmail.com>
Date: Tue Aug 25 08:07:05 2020 -0400
Merge pull request #19 from matthewhirschey/search-in-nav-bar
move search input to nav bar
commit ad4adbc18749ed8baeb703aaff7b67a7a10d2603
Author: John Bradley <johnbradley2008@gmail.com>
Date: Mon Aug 24 19:15:14 2020 -0400
add styles.css to fix searchInput textbox…
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Currently if we configure openshift to run two pods
for the website new deployments fail due to memory quotas.
This change will allow us to run two pods and gracefully
deploy new changes.
Based on openshift Memory metrics we are using ~ 1040 MiB.
This is just the requested amount and the app is allowed
to utilize more than this.