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AlexMili/torch-dataframe 64

Utility class to manipulate dataset from CSV file

gforge/htmlTable 63

An R package for generating advanced tables

gforge/Gmisc 42

An R package for table creating, plotting and more

gforge/forestplot 22

Advanced forest plots in R using grid graphics

gforge/comorbidities.icd10 13

Comorbidities calculator for R using ICD-9 and ICD-10 based scores

gforge/pngjs3 8

Simple PNG encoder/decoder for Node.js and browsers with no dependencies.

gforge/ftp 7

Fast-track publishing - set-up, example and more

gforge/atom-git-control 5

Provides a GUI interface to manage all commonly-used git commands.

gforge/Greg 5

This R-package provides additional functions that help you convey regression models. It has also a few functions for handling robust confidence intervals for the ols() regression in the rms-package.

gforge/fixed-data-table-addons 3

Addons for fixed-data-table

issue closedgforge/forestplot

Different rows/covariates/studies in different colors

Hello.

I would like to make a forest plot that has each row in a different color. By each row, I mean the boxes and the respective confidence intervals.

Taking an example from the vignette [https://cran.r-project.org/web/packages/forestplot/vignettes/forestplot.html],

library(forestplot)
# Cochrane data from the 'rmeta'-package
cochrane_from_rmeta <- 
  structure(list(
    mean  = c(NA, NA, 0.578, 0.165, 0.246, 0.700, 0.348, 0.139, 1.017, NA, 0.531), 
    lower = c(NA, NA, 0.372, 0.018, 0.072, 0.333, 0.083, 0.016, 0.365, NA, 0.386),
    upper = c(NA, NA, 0.898, 1.517, 0.833, 1.474, 1.455, 1.209, 2.831, NA, 0.731)),
    .Names = c("mean", "lower", "upper"), 
    row.names = c(NA, -11L), 
    class = "data.frame")

tabletext<-cbind(
  c("", "Study", "Auckland", "Block", 
    "Doran", "Gamsu", "Morrison", "Papageorgiou", 
    "Tauesch", NA, "Summary"),
  c("Deaths", "(steroid)", "36", "1", 
    "4", "14", "3", "1", 
    "8", NA, NA),
  c("Deaths", "(placebo)", "60", "5", 
    "11", "20", "7", "7", 
    "10", NA, NA),
  c("", "OR", "0.58", "0.16", 
    "0.25", "0.70", "0.35", "0.14", 
    "1.02", NA, "0.53"))

forestplot(tabletext, 
           cochrane_from_rmeta,new_page = TRUE,
           is.summary=c(TRUE,TRUE,rep(FALSE,8),TRUE),
           clip=c(0.1,2.5), 
           xlog=TRUE, 
           col=fpColors(box="royalblue",line="darkblue", summary="royalblue"))

I want each study to have its own color. Auckland can be blue, Block can be red, Doran can be green, and so on.

Is there any way to do this?

closed time in 7 days

vaibhav-k

issue commentgforge/forestplot

Different rows/covariates/studies in different colors

Sorry, this is a quotation for stack overflow

vaibhav-k

comment created time in 7 days

issue commentgforge/Gmisc

Gmisc: connectGrob not plotting correctly since update to R 4.03

Thanks - with a good issue report it is easy to help. If you feel that the docs could be improved then send a PR and I'll update it in the next release.

lhunsicker

comment created time in 10 days

issue closedgforge/Gmisc

Gmisc: connectGrob not plotting correctly since update to R 4.03

Yesterday I created a Consort diagram for a clinical trial that I am reporting. Fortunately I saved a copy of the printout (attached). CIT Consort diagram..docx This AM I updated R to 4.03 and reran the r program below:

#  CIT long-term outcomes Consort diagram
library(Gmisc, quietly = TRUE)
library(glue, quietly = TRUE)
library(htmlTable, quietly = TRUE)
library(grid, quietly = TRUE)
library(magrittr, quietly = TRUE)

CIT07 <- boxGrob(glue("Transplanted in", "CIT-07, n = 48", .sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.92, x = 0.14)
EarlyX07 <- boxGrob(glue("Failed, n = 2", "Withdrew*, n = 5",.sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.78, x = 0.38)
Comp07 <- boxGrob(glue("Completed CIT-07", "n = 48", .sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.64, x = 0.14)
Not8_07 <- boxGrob(glue("Exited CIT*, n= 5", "n = 48", .sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.50, x = 0.38)
CIT8_07 <- boxGrob(glue("Entered CIT-08", "n = 5", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.36, x = 0.14)
EarlyX8_07 <- boxGrob(glue("Failed, n = 4", "Withdrew*, n = 3", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.22, x = 0.28)
Complete07 <-boxGrob(glue("Completed CIT-08", "n = 5", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = .08, x = 0.14)
                     
CIT06 <- boxGrob(glue("Transplanted", "in CIT-06, n = 24", .sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.92, x = 0.86)
EarlyX06 <- boxGrob(glue("Failed, n = 5", "Withdrew*, n = 5",.sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.78, x = 0.64)
Comp06 <- boxGrob(glue("Completed CIT-06", "n = 3", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.64, x = 0.86)
Not8_06 <- boxGrob(glue("Exited CIT*, n= 5", "n = 48", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.50, x = 0.64)
CIT8_06 <- boxGrob(glue("Entered CIT-08", "n = 48", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.36, x = 0.70)
EarlyX8_6 <- boxGrob(glue("Failed, n = 4", "Withdrew*, n = ",.sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.22, x = 0.55)
CompIn06 <- boxGrob(glue("Completed CIT", "in CIT-06, n = 5", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.08, x = 0.86)
CompIn08 <- boxGrob(glue("Completed CIT", "in CIT-08, n = 5", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.08, x = 0.54)
                    
windows(height = 9, width = 6.5)
CIT07; EarlyX07; Comp07; Not8_07; CIT8_07; EarlyX8_07; Complete07
CIT06; EarlyX06; Comp06; Not8_06; CIT8_06; EarlyX8_6; CompIn06; CompIn08 

connectGrob(CIT07, Comp07, type = 'N')
connectGrob(CIT07, EarlyX07, type = 'L')
connectGrob(Comp07, CIT8_07, type = 'N')
connectGrob(Comp07, Not8_07, type = 'L')
connectGrob(CIT8_07, Complete07, type = 'N')
connectGrob(CIT8_07, EarlyX8_07, type = 'L')
connectGrob(CIT06, Comp06, type = 'N')
connectGrob(Comp06, CompIn06, type = 'N')
connectGrob(CIT06, EarlyX06, type = 'L')
connectGrob(Comp06, Not8_06, type = 'L')
connectGrob(Comp06, CIT8_06, type = 'L')
connectGrob(CIT8_06, EarlyX8_6, type = 'N')
connectGrob(CIT8_06, CompIn08, type = 'L')


The boxGrobs are plotting correctly, but the connectGrobs are messed up. Repeatable on two Windows 10 desktops.

messed up Consort.docx

Something in the new version of R is messing up the mapping or something. I suspect that this is not your bug, but you folks will probably be stuck with fixing it. Meanwhile I may have to drop back to R 4.02. Many thanks for any help you can give me. Larry Hunsicker

closed time in 11 days

lhunsicker

issue commentgforge/Gmisc

Gmisc: connectGrob not plotting correctly since update to R 4.03

Oh, you set the size of the boxes after they've been created: windows(height = 9, width = 6.5) must be before the firs section

lhunsicker

comment created time in 11 days

issue commentgforge/Gmisc

Gmisc: connectGrob not plotting correctly since update to R 4.03

No worries. My guess is that you resized the image at some stage - the connections are fixed to a certain point and thus if you resize the image later they will not automatically be updated.

lhunsicker

comment created time in 12 days

starteddcmjs-org/dcmjs

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Final https fix (?)

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Updates to vignettes Merge branch 'master' of github.com:gforge/htmlTable # Conflicts: # vignettes/general.Rmd

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issue commentjkettmann/graphql-passport

don't need to await login?

Not sure about that, my feeling is that the async is within the authenticate action where the login just moves the user into the express-session - the login function is defined in Passport.

kbyatnal

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startedUrigo/graphql-scalars

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issue commentgforge/Gmisc

Change font in transition diagram

Excellent idea although I don't think I can manage to add this anytime soon. You're welcome to do PR on a fix and I can have a look at it.

dkaufman-w2o

comment created time in 24 days

PR opened DefinitelyTyped/DefinitelyTyped

Fix invalid indexFields in mongoose-delete
  • [x] Use a meaningful title for the pull request. Include the name of the package modified.
  • [x] Test the change in your own code. (Compile and run.)
  • [x] Add or edit tests to reflect the change. (Run with npm test mongoose-delete.)
  • [x] Follow the advice from the readme.
  • [x] Avoid common mistakes.
  • [x] Run npm run lint package-name (or tsc if no tslint.json is present).
  • [x] Provide a URL to documentation or source code which provides context for the suggested changes: https://github.com/dsanel/mongoose-delete/blob/79d7f611bd47238ecd02feb3b87b96c84c060673/index.js#L64-L68
  • [x] Include tests for your changes

This fixes a simple error with the indexFields that is parsed using:

function parseIndexFields (options) {
    var indexFields = {
        deleted: false,
        deletedAt: false,
        deletedBy: false
    };

    if (!options.indexFields) {
        return indexFields;
    }

    if ((typeof options.indexFields === 'string' || options.indexFields instanceof String) && options.indexFields === 'all') {
        indexFields.deleted = indexFields.deletedAt = indexFields.deletedBy = true;
    }

    if (typeof(options.indexFields) === "boolean" && options.indexFields === true) {
        indexFields.deleted = indexFields.deletedAt = indexFields.deletedBy = true;
    }

    if (Array.isArray(options.indexFields)) {
        indexFields.deleted = options.indexFields.indexOf('deleted') > -1;
        indexFields.deletedAt = options.indexFields.indexOf('deletedAt') > -1;
        indexFields.deletedBy = options.indexFields.indexOf('deletedBy') > -1;
    }

    return indexFields;
}
+4 -1

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Fix for indexFields in mongoose-delete

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The repository for high quality TypeScript type definitions.

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issue commentjkettmann/graphql-passport

Login() takes Credentials instead of UserObjectType

Hmm... that seems like an error from my part. The login function is controlled by the main passport library as I understand it: https://github.com/jaredhanson/passport/blob/master/lib/http/request.js#L10-L57

It suggests that the login should accept a full user object. Although - every time I look into the passport code I seem to end up in an evil loop searching for where the different functions are defined and I can't claim that I fully grasp passport. My grasp of this is just too weak.

sproott

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Merge pull request #77 from gforge/develop Minor CRAN updates

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Merge pull request #78 for 2.0.1 Changes for 2.0.1

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Merge pull request #82 from gforge/develop The 2.1 release

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CRAN-fixes with https

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Found some more possible http -> https issues

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Fixed new website address for ght-tables (last CRAN-thing?)

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created taggforge/htmlTable

tagv2.1

An R package for generating advanced tables

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PR merged gforge/htmlTable

The 2.1 release
  • Added spacer cell option for vertical borders
  • Fixed ignored align.header
  • Fix for wrapped styles (issue #80)
  • Updated old http:/ urls to https
  • Minor theme updates
+678 -244

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gforge

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PR opened gforge/htmlTable

The 2.1 release
  • Added spacer cell option for vertical borders
  • Fixed ignored align.header
  • Fix for wrapped styles (issue #80)
  • Updated old http:/ urls to https
  • Minor theme updates
+678 -244

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Forgot to update docs for urls

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issue commentgforge/htmlTable

tidyHtmlTable does not accept multiple rgroup

Closing the issue as it seems resolved

HoneyBuddha

comment created time in a month

issue closedgforge/htmlTable

tidyHtmlTable does not accept multiple rgroup

Describe the bug Hi, Thank you for this wonderful package.

I have noticed that - the tidyHtmlTable wrapper does not allow rnames or rgroup to accept anything other than a character string. Thus, nested row groups are not able to be passed to the function.

To Reproduce

tidy.DF_FULL  %>%
  tidyHtmlTable(x = .,
                header = "ColumnLevel02",
                cgroup1 = "ColumnLevel01",
                value = "formattedValue",
                rnames = "RowLevel03",
                rgroup = c("RowLevel01", "RowLevel02"))

creates the following error:

Error in argument_checker(x, value = value, header = header, rnames = rnames, : The following parameters must be of type character: rgroup

Expected behavior Row Level 2 would be nested within Row Level 1 - just like Row Level 3 is nested within Row Level 2 i.e. Rows would be nested Level 1 > Level 2 > Level 3

Versions (please complete the following information):

  • OS: Windows 10
  • R IDE: RStudio
  • Package version: 1.13.1

Additional context The Tidy Html Table wrapper is fantastic and works perfectly in all over situations. It is simply not responding to multiple nested groups. Is it possible to get an interim data structure out that could be manipulated before rendering in html?

closed time in a month

HoneyBuddha

issue closedgforge/htmlTable

Auto add border styles to columns with grouped headers

I looked through the documentation but did not find an option that suits my needs. When adding grouped headers using cgroup and n.cgroup I want to have borders to the left and right of those grouped columns. I ended up extracting the raw HTML table code, parsing it using xml2, use the n.cgroup indices to identify the td elements to which I need to add the CSS border styles and return the modified HTML code into the htmlTable object.

did I miss anything or is this the only way to go?

closed time in a month

martinschmelzer

issue closedgforge/htmlTable

Use `addHtmlTableStyle` inside a custom function and passing argument throws an error

Take the MWE:


library(htmlTable)

customTable <- function(x, css = c("custom-table", "custom-table-small")) {
  css.table <- match.arg(css)

  x <- addHtmlTableStyle(x, css.table = css.table)
  htmlTable(x)
}

customTable(x = mtcars)

I basically want to add different values for css.table . My real customTable is a little more complex. I get the error thet css.table cannot be found. I guess that this is a scoping issue. Is it intentional and what is the work-around besides adding the styles outside of my customTable function?

I am using the current developer branch feature/flexible_spacer_cells.

closed time in a month

martinschmelzer

issue commentgforge/htmlTable

Use `addHtmlTableStyle` inside a custom function and passing argument throws an error

Thanks! That was certainly an evil bug :imp: as the argument had to be manually traversed through the environments. Should work now. It has been merged into develop. Please check that it works. I'll try to submit 2.1 to CRAN within a few days.

martinschmelzer

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Added some Google theme options incl. vertical align Fixed align.header not being used

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Merge pull request #81 from gforge/feature/flexible_spacer_cells Feature/flexible spacer cells

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PR merged gforge/htmlTable

Feature/flexible spacer cells
  • Added options for how the empty spacer cell appears (see addHtmlTableStyle() spacer.* options)
  • Fixed ignored align.header
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PR opened gforge/htmlTable

Feature/flexible spacer cells
  • Added options for how the empty spacer cell appears (see addHtmlTableStyle() spacer.* options)
  • Fixed ignored align.header
+631 -226

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issue commentgforge/forestplot

fpShapesGp from vignette does not exist

The current version of forestplot is 1.10, have you tried upgrading?

annaoj2

comment created time in a month

issue closedgforge/Greg

etm dependency

Greg seems to have dependency on the etm package, which was removed from CRAN. Using R version 4,.0.2, loading Greg gives the following error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘etm’

Would be great if you could look into it!

closed time in a month

pmakai

issue commentgforge/Greg

etm dependency

I'm not getting any errors... The deps are:

Imports:
    Hmisc,
    stringr,
    rms,
    sandwich,
    stats,
    nlme,
    methods,
    htmlTable (>= 2.0.0),
    magrittr,
    knitr,
    Epi,
    utils,
    graphics,
    grDevices
Depends:
    forestplot,
    Gmisc (>= 1.0.3)
Suggests:
    boot,
    testthat,
    cmprsk,
    survival,
    dplyr,
    ggplot2,
    parallel,
    rmarkdown,
    rmeta

Can't find an etm package

pmakai

comment created time in a month

issue commentSouthern/node-x509

Error installing x509: error x509@0.3.4 install: `node-gyp rebuild` on macOS

I don't think this bug is MacOS specific, similar issue appears in Ubuntu. When running NodeJS 12 and above the below Dockerfile will fail, here is the simplest possible container that I could think of that triggers the error:

FROM ubuntu:20.04

RUN apt-get update && \
  apt-get install curl -y

RUN curl -sL https://deb.nodesource.com/setup_12.x | bash -
RUN apt-get install -y nodejs build-essential

RUN mkdir -p /root/test

WORKDIR /root/test
RUN npm init -y
RUN npm install node-gyp
RUN npm install x509

CMD ["/bin/bash"]

The error does not occur at the RUN npm install node-gyp step but at the RUN npm install x509 that rebuilds the node-gyp package.

For the purpose of this error being easier to Google the main error seems to be these lines:

../../nan/nan_implementation_12_inl.h:356:37: error: no matching function for call to 'v8::StringObject::New(v8::Local<v8::String>&)'
  356 |   return v8::StringObject::New(value).As<v8::StringObject>();
      |                                     ^
In file included from /root/.cache/node-gyp/12.18.3/include/node/node.h:67,
                 from ../include/addon.h:4,
                 from ../src/addon.cc:4:
/root/.cache/node-gyp/12.18.3/include/node/v8.h:5531:23: note: candidate: 'static v8::Local<v8::Value> v8::StringObject::New(v8::Isolate*, v8::Local<v8::String>)'
 5531 |   static Local<Value> New(Isolate* isolate, Local<String> value);
      |                       ^~~
/root/.cache/node-gyp/12.18.3/include/node/v8.h:5531:23: note:   candidate expects 2 arguments, 1 provided
In file included from ../../nan/nan_new.h:189,
                 from ../../nan/nan.h:223,
                 from ../include/x509.h:7,
                 from ../src/addon.cc:5:
../../nan/nan_implementation_12_inl.h:356:58: error: expected primary-expression before '>' token
  356 |   return v8::StringObject::New(value).As<v8::StringObject>();
      |                                                          ^
../../nan/nan_implementation_12_inl.h:356:60: error: expected primary-expression before ')' token
  356 |   return v8::StringObject::New(value).As<v8::StringObject>();

With the end section having looking like this:

make: *** [x509.target.mk:116: Release/obj.target/x509/src/addon.o] Error 1
make: Leaving directory '/root/test/node_modules/x509/build'
gyp ERR! build error 
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/lib/node_modules/npm/node_modules/node-gyp/lib/build.js:194:23)
gyp ERR! stack     at ChildProcess.emit (events.js:315:20)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:275:12)
gyp ERR! System Linux 5.4.0-45-generic
gyp ERR! command "/usr/bin/node" "/usr/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /root/test/node_modules/x509
gyp ERR! node -v v12.18.3
gyp ERR! node-gyp -v v5.1.0
DigitalLeaves

comment created time in 2 months

issue commentgforge/htmlTable

Auto add border styles to columns with grouped headers

Actually "double" should work as I use match.arg(). One thought I had was that maybe "center" or "split" would be more intuitive where you don't specify how the cells work

martinschmelzer

comment created time in 2 months

issue commentgforge/htmlTable

Auto add border styles to columns with grouped headers

Great! I've been wanting to do this for a while but haven't really gotten around to it.

Do you have any input on the documentation and naming of the arguments? Will people understand "double_cell" - it's probably a bit technical...

martinschmelzer

comment created time in 2 months

startedtsconfig/bases

started time in 2 months

push eventgforge/htmlTable

Max Gordon

commit sha 121beddf0c9e0441ece286da2a23bbcbed9ed1c9

Added some Google theme options incl. vertical align Fixed align.header not being used

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issue commentgforge/htmlTable

Auto add border styles to columns with grouped headers

I think I've fixed it in the feature/flexible_spacer_cells branch (checkout https://github.com/gforge/htmlTable/tree/). Do you mind testing it a bit before I push it to CRAN?

martinschmelzer

comment created time in 2 months

push eventgforge/htmlTable

Max Gordon

commit sha 2b0175a96d762518a61dc015c9563a6ad7637a13

Added spacer cell options to style * Major refactor to getAlign functionality * Started implementing stringr::str_interp instead of relying on sprintf * Added getHtmlTableStyle * Improved how options are matched with match.arg in style handlers

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create barnchgforge/htmlTable

branch : feature/flexible_spacer_cells

created branch time in 2 months

issue commentgforge/htmlTable

Auto add border styles to columns with grouped headers

Yeah, the empty column is there so that the header bottom border doesn't blend into one unit. I guess an option could be added for removing it but the question is if the result will be what you truly want. Another would be to use css.cell or add an argument similar to col.columns that takes not only color but also CSS-rules.

martinschmelzer

comment created time in 2 months

issue commentgforge/htmlTable

Auto add border styles to columns with grouped headers

And the option of align = "rr|rr|rr|r" doesn't give you the desired outcome?

martinschmelzer

comment created time in 2 months

issue commentjkettmann/graphql-passport

Support other strategies

This should be doable but I've never worked with the more advanced strategies. The GraphQLLocalStrategy is implemented but it would be awesome if all of the strategies passport provides could be available.

DarkLite1

comment created time in 2 months

issue commentgforge/htmlTable

Auto add border styles to columns with grouped headers

Could you show the HTML-code, what you get together with a small PNG and then what you want and the CSS. Shouldn't bee too difficult to fix.

martinschmelzer

comment created time in 2 months

startednodeca/js-yaml

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startedbondz/react-epic-spinners

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issue commentjkettmann/graphql-passport

Typescript Context for Apollo Server

Sorry for the delayed response. The project where I had been using this package was put on hold and I got some new test-errors after updating the packages. First, if anyone stumbles upon issues with your Request not being valid, make sure that you have the correct definitions (see this issue) by deleting your lock-files and re-installing everything.

I'm not sure that I actually understand the original code example. The definition for the PassportContext requires 4 arguments:

export declare type PassportContext<
  UserObjectType extends {}, 
  Credentials extends {}, 
  AuthInfoTemplate extends {} = {}, 
  Request extends object = ExpressRequest
> = SharedPassportContext<UserObjectType, Credentials, AuthInfoTemplate, Request>;

In the example provided there are only two arguments provided, Context and ExpressRequest. My definitions look something like this:

export interface Credentials {
  username: string;
  password: string;
}

declare interface MyContext extends PassportContext<UserModelInterface, Credentials, {}, express.Request> {
  dataSources: MyDataSourcesInterface;
}

As of TS 2.2 there you can add the prisma and smtpTransport just as I did with dataSources even though the original context is a type and not an interface. If you want it stricter then perhaps an intersection is a better choice.

tnolan8

comment created time in 3 months

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