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Mariana Meireles marimeireles @quantstack Berlin https://psychonautgirl.space :octocat: octocatnaut & tech witch 🧙🏼‍♀️ (she/her)

cytoscape/ipycytoscape 162

A Cytoscape Jupyter widget

jupyter-xeus/xeus-sqlite 121

Jupyter kernel for SQLite

jupyter-xeus/xeus-sql 104

xeus-sql is a Jupyter kernel for general SQL implementations.

mamba-org/rhumba 34

The R package manager that is blazingly fast ⚡. Powered by mamba.

ckw017/vader-sentiment-rust 18

Rust port of the VADER sentiment analysis tool.

eblur/woc-code 3

Notes, scheduling, and wiki for WoCCode – an Astropy IDE supported program

jupyter-xeus/xvega-bindings 3

xvega bindings for xeus

marimeireles/camara-deputados 1

Análise das atividades da câmara de deputados federais do Brasil em 2018

issue commentjupyter-xeus/xeus-sql

WITH clause doesn't work with SQLite

Hum! This is where my lack of knowledge in SQL attacks again! Sorry for this, I'm mostly a C++/Python dev and just know the very basics of SQL.

Yeah, seems a bit complicated. If I understand correctly this WITH clause is like a "variable(? did I get that right?)" that you can store the values of the query? And then you have the RECURSIVE modifier, even.

I can't tell if SOCI offers support for it, because they have no entries about WITH in their docs. And looking further, they have no WITH tests nor examples, maybe they don't support it. So first step as I said, is making sure they do. Maybe one could even open an issue upstream asking about it and how to use it.

Afterwards... I'd say the steps to fix this would be:

  • create an example that uses WITH (you've done this already)
  • check the method process_SQL_input and print on the console the output of this code :), using this and maybe the help of the SOCI people we can figure out how to treat this result. Do we have to store this var ourselves? What type does it have? If we have to create a type for it is probably very complicated to tackle, if there's a type, should be easy, we can just create another if we another check and add it before the other words
n87

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issue commentjupyter-xeus/xeus-sql

WITH clause doesn't work with SQLite

Hey @n87, thank you for opening the issue :) That's true. I don't understand why it's not being picked up by SOCI though. We treat this case in the following lines:

            else
            {
                if (this->sql)
                {
                    /* Shows rich output for tables */
                    if (xv_bindings::case_insentive_equals("SELECT", tokenized_input[0]) ||
                        xv_bindings::case_insentive_equals("DESC", tokenized_input[0]) ||
                        xv_bindings::case_insentive_equals("DESCRIBE", tokenized_input[0]) ||
                        xv_bindings::case_insentive_equals("SHOW", tokenized_input[0]))
                    {
                        nl::json data = process_SQL_input(code, xv_sql_df);


                        publish_execution_result(execution_counter,
                                                 std::move(data),
                                                 nl::json::object());


                    }
                    /* Execute all SQL commands that don't output tables */
                    else
                    {
                        *this->sql << code;
                    }
                }

https://github.com/jupyter-xeus/xeus-sql/blob/master/src/xeus_sql_interpreter.cpp#L295-L317

Here are some things I'm thinking we should do to fix it:

  • check upstream if SOCI deals with the WITH keyword, maybe it's not supported by them
  • does this command requires some special treatment? For everything that's not acting directly in the database we have to create special cases called magics, see for example how we call LOAD: %LOAD sqlite3 db=chinook.db timeout=2 shared_cache=true I believe this might be the case for WITH and then we want to do something similar to what we're doing with LOAD :)

I'm not sure, these are just some hints. If you or anyone want to tackle this issue I'm here to help. Unfortunately I can't dedicate so much time to this project right now. (Maybe in the future!) But thanks again for opening this and please feel free to ask questions.

n87

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pull request commentjupyter-xeus/xeus

Add out method

It was supposed to print the next thing on the next test: std::cout << "the extract_filename is never starting bc of the other test" << std::endl;

marimeireles

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pull request commentjupyter-xeus/xeus

Add out method

so, this is the output I get:

(xeus) mariana@wintermute ~/dev/xeus/build/test (output*?) $ ./test_unit_kernel
[doctest] doctest version is "2.4.6"
[doctest] run with "--help" for options
this print is running 4 ever...

After running the following code:

        TEST_CASE("print_starting_message")
        {
            auto context = make_context<zmq::context_t>();

            using interpreter_ptr = std::unique_ptr<test_kernel::test_interpreter>;
            interpreter_ptr interpreter = interpreter_ptr(new test_kernel::test_interpreter());
            xkernel kernel(get_user_name(),
                         std::move(context),
                         std::move(interpreter),
                         make_xserver_zmq);
            std::string kernel_config = print_starting_message(kernel.get_config());
            bool found = kernel_config.find(" Starting kernel...\n"
                                            "\n"
                                            "If you want to connect to this kernel from an other client, just copy and paste the following content inside of a `kernel.json` file. And then run for example:\n"
                                            "\n"
                                            "# jupyter console --existing kernel.json\n"
                                            "\n"
                                            "kernel.json\n"
                                            "```\n"
                                            "{\n"
                                            "    \"transport\": \"tcp\",\n");
            std::cout << "this print is running 4 ever..." << std::endl;
            REQUIRE_EQ(found, true);
        }

    TEST_CASE("extract_filename")
    {
        std::cout << "the extract_filename is never starting bc of the other test" << std::endl;
        char** argv = new char*;
        argv[0] = (char*)"-f";
        argv[1] = (char*)"connection.json";
        std::string file_name = extract_filename(3, argv);
        REQUIRE_EQ(file_name, "connection.json");
    }

is just stuck in the first test, @JohanMabille

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Messages are now moved in comm

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Pull request review commentjupyter-xeus/xeus

Add out method

 #include "gtest/gtest.h"  #include <string>+#include <memory>  #include "nlohmann/json.hpp" +#include "test_interpreter.hpp"+ #include "xeus/xkernel.hpp" #include "xeus/xmiddleware.hpp" #include "xeus/xsystem.hpp" +#include "xeus/xhelper.hpp"+ namespace nl = nlohmann;  namespace xeus {+    // TEST(kernel, print_starting_message)+    // {+    //     std::string file_name = "connection.json";+    //     xconfiguration config = load_configuration(file_name);++    //     using interpreter_ptr = std::unique_ptr<test_kernel::test_interpreter>;+    //     interpreter_ptr interpreter = interpreter_ptr(new test_kernel::test_interpreter());+    //     xkernel kernel(config, get_user_name(), std::move(interpreter));++    //     print_starting_message(config);+    // }++    TEST(kernel, extract_filename)+    {+        char** argv;+        argv[0] = "-f connection.json";+        std::string file_name = extract_filename(1, argv);+        EXPECT_EQ(file_name, "connection.json");+    }

This also fails and I don't understand why because I can't really debug the test outputs? I'm using ctest -VV --output-on-failure but can't see anything. Is there a way of seeing test outputs?

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Pull request review commentjupyter-xeus/xeus

Add out method

 #include "gtest/gtest.h"  #include <string>+#include <memory>  #include "nlohmann/json.hpp" +#include "test_interpreter.hpp"+ #include "xeus/xkernel.hpp" #include "xeus/xmiddleware.hpp" #include "xeus/xsystem.hpp" +#include "xeus/xhelper.hpp"+ namespace nl = nlohmann;  namespace xeus {+    // TEST(kernel, print_starting_message)+    // {+    //     std::string file_name = "connection.json";+    //     xconfiguration config = load_configuration(file_name);++    //     using interpreter_ptr = std::unique_ptr<test_kernel::test_interpreter>;+    //     interpreter_ptr interpreter = interpreter_ptr(new test_kernel::test_interpreter());+    //     xkernel kernel(config, get_user_name(), std::move(interpreter));++    //     print_starting_message(config);+    // }

I don't understand how to initialize a Kernel. Maybe the problem here is because I'm using this connection.json that doesn't exist? I thought it should work regardless because it has default values. Anyway, I'm getting the following when trying to compile:

(xeus)  ✘  ~/dev/xeus/build   output ●✚  make install -j12
[  2%] Built target gtest
[  4%] Built target gtest_main
[ 81%] Built target xeus
[ 84%] Built target xeus-static
Consolidate compiler generated dependencies of target test_unit_kernel
[ 86%] Built target test_xin_memory_history_manager
[ 90%] Built target test_kernel_shell
[ 93%] Built target test_kernel
[ 97%] Built target test_kernel_control
[ 98%] Building CXX object test/CMakeFiles/test_unit_kernel.dir/test_unit_kernel.cpp.o
/Users/mariana/dev/xeus/test/test_unit_kernel.cpp:51:19: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        argv[0] = "--version";
                  ^
1 warning generated.
[100%] Linking CXX executable test_unit_kernel
Undefined symbols for architecture x86_64:
  "vtable for test_kernel::test_interpreter", referenced from:
      xeus::kernel_print_starting_message_Test::TestBody() in test_unit_kernel.cpp.o
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [test/test_unit_kernel] Error 1
make[1]: *** [test/CMakeFiles/test_unit_kernel.dir/all] Error 2
make: *** [all] Error 2

Can you help me with this @JohanMabille? :)

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pull request commentjupyter-xeus/xeus

Add out method

I haven't finished it yet! I'm working on some tests. I added other helper functions.

marimeireles

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issue closedjupyter-xeus/xeus-sqlite

Needs fix for xeus 2.0.0

While rebuilding xeus-sqlite 0.3.0 against xeus 2.0.0, I get the following errors:

[ 87%] Building CXX object CMakeFiles/xsqlite.dir/src/main.cpp.o /usr/bin/clang++ -DGUID_CFUUID -DJSON_DIAGNOSTICS=0 -DJSON_USE_IMPLICIT_CONVERSIONS=1 -DSQLITE_DEBUG=1 -DSQLITE_ENABLE_COLUMN_METADATA -DSQLITE_ENABLE_EXPLAIN_COMMENTS=1 -DSQLITE_MEMDEBUG=1 -DXEUS_SQLITE_EXPORTS -DXVEGA_EXPORTS -Dxsqlite_EXPORTS -I/opt/local/var/macports/build/_Users_marius_Development_MacPorts_ports_databases_xeus-sqlite/xeus-sqlite/work/xeus-sqlite-0.3.0/include -isystem /opt/local/include -isystem /opt/local/include/openssl -pipe -Os -DNDEBUG -I/opt/local/include -stdlib=libc++ -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -O3 -DNDEBUG -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -mmacosx-version-min=10.14 -Wunused-parameter -Wextra -Wreorder -mtune=generic -march=native -std=gnu++17 -MD -MT CMakeFiles/xsqlite.dir/src/main.cpp.o -MF CMakeFiles/xsqlite.dir/src/main.cpp.o.d -o CMakeFiles/xsqlite.dir/src/main.cpp.o -c /opt/local/var/macports/build/_Users_marius_Development_MacPorts_ports_databases_xeus-sqlite/xeus-sqlite/work/xeus-sqlite-0.3.0/src/main.cpp /opt/local/var/macports/build/_Users_marius_Development_MacPorts_ports_databases_xeus-sqlite/xeus-sqlite/work/xeus-sqlite-0.3.0/src/main.cpp:62:36: error: no member named 'make_xserver_shell_main' in namespace 'xeus' xeus::make_xserver_shell_main); ~~~~~~^ /opt/local/var/macports/build/_Users_marius_Development_MacPorts_ports_databases_xeus-sqlite/xeus-sqlite/work/xeus-sqlite-0.3.0/src/main.cpp:78:36: error: no member named 'make_xserver_shell_main' in namespace 'xeus' xeus::make_xserver_shell_main); ~~~~~~^ 2 errors generated.

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Schamschula

issue commentjupyter-xeus/xeus-sqlite

Needs fix for xeus 2.0.0

Johan pushed a PR fixing it :) Soon we will have a new version out on conda-forge, but must be working now from master. If not, feel free to reopen this issue. Thank you.

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tag0.4.0

Jupyter kernel for SQLite

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