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HiCAL is a system for efficient high-recall retrieval with an adaptable assessing interface.

Home Page: https://hical.github.io/

License: GNU General Public License v3.0

Makefile 0.34% Python 42.96% Shell 3.92% C++ 35.77% C 2.88% CSS 0.87% JavaScript 12.69% Dockerfile 0.57%
information-retrieval high-recall search-engine machine-learning active-learning test-collection document-assessment cal

hical's Introduction

HiCAL

Want to find all relevant documents?

HiCAL is a system for efficient high-recall retrieval. The system allows retrieving and assessing relevant documents with high data processing performance and a user-friendly document assessment interface.

To learn more about HiCAL, read our paper or visit the project's website.

@inproceedings{10.1145/3209978.3210176,
    author = {Abualsaud, Mustafa and Ghelani, Nimesh and Zhang, Haotian and Smucker, Mark D. and Cormack, Gordon V. and Grossman, Maura R.},
    title = {A System for Efficient High-Recall Retrieval},
    year = {2018},
    isbn = {9781450356572},
    publisher = {Association for Computing Machinery},
    address = {New York, NY, USA},
    url = {https://doi.org/10.1145/3209978.3210176},
    doi = {10.1145/3209978.3210176},
    booktitle = {The 41st International ACM SIGIR Conference on Research & Development in Information Retrieval},
    pages = {1317–1320},
    numpages = {4},
    keywords = {high-recall, systematic review, electronic discovery},
    location = {Ann Arbor, MI, USA},
    series = {SIGIR ’18}
}

Install

Visit hical.github.io for usage and installation instruction. For component specific details, check the README in their respective directory.

Relevant Papers

Learn more about HiCAL and its performance in the following papers:

License

GNU GPL v3.0

hical's People

Contributors

ammsa avatar angshumanghosh avatar hatianzhang avatar hazhang-wish avatar nims11 avatar profsmucker avatar

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hical's Issues

no /begin endpoint

Hi there,

I was trying to interact with the engine through command line. I tried to call the APIs using the python binding. However, when I begin a session, but it seems not to be able to find the /begin endpoints. The code and error messages are as follows:

`import json
import requests

h = httplib2.Http()
URL = "http://localhost:9000/CAL/"

data = {'session_id': '0001',
'seed_query': 'prepay',
'async': True,
'mode': 'doc',
'judgments_per_iteration': 1}

resp = requests.post(url = URL+'begin/', data=data)
print(resp.text)`

`

<title>Page not found at /CAL/begin/</title> <style type="text/css"> html * { padding:0; margin:0; } body * { padding:10px 20px; } body * * { padding:0; } body { font:small sans-serif; background:#eee; } body>div { border-bottom:1px solid #ddd; } h1 { font-weight:normal; margin-bottom:.4em; } h1 span { font-size:60%; color:#666; font-weight:normal; } table { border:none; border-collapse: collapse; width:100%; } td, th { vertical-align:top; padding:2px 3px; } th { width:12em; text-align:right; color:#666; padding-right:.5em; } #info { background:#f6f6f6; } #info ol { margin: 0.5em 4em; } #info ol li { font-family: monospace; } #summary { background: #ffc; } #explanation { background:#eee; border-bottom: 0px none; } </style>

Page not found (404)

</table>
  <p>
  Using the URLconf defined in <code>config.urls</code>,
  Django tried these URL patterns, in this order:
  </p>
  <ol>
    
      <li>
        
            ^
            
        
            ^$
            [name='home']
        
      </li>
    
      <li>
        
            ^
            
        
            ^sessions/$
            [name='sessions']
        
      </li>
    
      <li>
        
            ^
            
        
            ^practice/$
            [name='practice']
        
      </li>
    
      <li>
        
            ^
            
        
            ^practice_complete/$
            [name='practice_complete']
        
      </li>
    
      <li>
        
            ^
            
        
            ^post_ctrlf/$
            [name='post_ctrlf']
        
      </li>
    
      <li>
        
            ^
            
        
            ^post_find_keystroke/$
            [name='post_find_keystroke']
        
      </li>
    
      <li>
        
            ^
            
        
            ^post_visit/$
            [name='post_visit']
        
      </li>
    
      <li>
        
            ^
            
        
            ^post_log/$
            [name='post_log_msg']
        
      </li>
    
      <li>
        
            ^
            
        
            ^get_session_details/$
            [name='get_session_details']
        
      </li>
    
      <li>
        
            ^about/$
            [name='about']
        
      </li>
    
      <li>
        
            ^admin/
            
        
      </li>
    
      <li>
        
            ^users/
            
        
      </li>
    
      <li>
        
            ^accounts/
            
        
      </li>
    
      <li>
        
            ^CAL/
            
        
            ^$
            [name='main']
        
      </li>
    
      <li>
        
            ^CAL/
            
        
            ^post_log/$
            [name='post_log_msg']
        
      </li>
    
      <li>
        
            ^CAL/
            
        
            ^get_docs/$
            [name='get_docs']
        
      </li>
    
      <li>
        
            ^iterative/
            
        
      </li>
    
      <li>
        
            ^search/
            
        
      </li>
    
      <li>
        
            ^topic/
            
        
      </li>
    
      <li>
        
            ^judgment/
            
        
      </li>
    
      <li>
        
            ^media\/(?P&lt;path&gt;.*)$
            
        
      </li>
    
      <li>
        
            ^400/$
            
        
      </li>
    
      <li>
        
            ^403/$
            
        
      </li>
    
      <li>
        
            ^404/$
            
        
      </li>
    
      <li>
        
            ^500/$
            
        
      </li>
    
  </ol>
  <p>The current URL, <code>CAL/begin/</code>, didn't match any of these.</p>

You're seeing this error because you have DEBUG = True in your Django settings file. Change that to False, and Django will display a standard 404 page.

`
Request Method: GET
Request URL: http://localhost:9000/CAL/begin/

COPY source files into the docker images

Coming back to HiCAL after a bit. I went through and cleaned out all my old images related to this. I found that I had the same error following the documentation, but if I did 'make clean' in the src directory, then 'make corpus_parser' would work. I suspect there are stale .o objects coming from somewhere.

Originally posted by @isoboroff in #7 (comment)

Installation instruction create data in wrong dir.

Thanks for open sourcing this.

If you follow these instructions:

cd sample-dataset
python process.py athome4_sample.tgz
# Create the data directory which is mounted to the docker containers
mkdir ../data
cp athome4_sample.tgz athome4_sample_para.tgz ../data/

then it creates data in the root directory and copies the tgz files in there. It does not place them in the HiCAL/data directory. As a result the ./corpus_parser program in docker fails because /data in docker is empty.

I believe the instructions should say:

cd sample-dataset
python process.py athome4_sample.tgz
# Create the data directory which is mounted to the docker containers
cp athome4_sample.tgz athome4_sample_para.tgz ../HiCAL/data/

Thanks.

GET /get_ranklist returns scores of 0.00 for all documents

I am trying to return a list of the documents and their classifier scores per the HTTP API documentation. I am able to successfully get a list of document IDs and scores, but all the scores are zero.

>>> curl http://localhost:9001/CAL/get_ranklist\?session_id\=ef3ccebf-de2d-4c8b-9f1c-a89061cba2c0 | head -20

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 16217    0 16217    0     0  30455      0 --:--:-- --:--:-- --:--:-- 30425

082d6c85-77a2-4006-b3e1-d2db1770c94a 0.000000
e68bb8f3-f2ba-4cf3-8692-3e4c7cb8a49a 0.000000
eaf2ad85-77a3-49e6-b49d-d1c8383a942f 0.000000
7ed61a2a-6ace-440f-8915-f196ce04e143 0.000000
471eaccf-811b-4cda-b96f-2b3e1a5c5882 0.000000
ba3dbb95-f279-41bd-9fec-5a693bc33888 0.000000
e896fb04-99c1-4d50-b6e9-c2dccb96e357 0.000000
f9b011b6-9455-48d9-992f-7ad35f8b499d 0.000000
f495ff23-35f6-45b0-b2aa-47c23ca996e8 0.000000
5ebf8fcf-e75c-4e99-bd32-e376e4488ab0 0.000000
b58d2e87-c447-466f-98e4-8ab6c2f75e46 0.000000
a8c5a77f-fb2b-4404-90d5-0150d8b8df0d 0.000000
397cbc5e-c305-4f1d-8232-29414ffe6cfc 0.000000
1c4ef4ba-9aa9-45f1-afeb-9d3d7fc8d326 0.000000
ae221c61-b628-47b8-a328-4083490af6ce 0.000000
edbe93db-76bd-4bf4-8b05-d43ce61b9361 0.000000
4a76e35a-18fe-4d69-afd2-210d4509b89e 0.000000
675af8b9-07b0-4c11-911d-a9827c3c5473 0.000000
424aea81-54f6-4037-b806-0dee04a3e33a 0.000000
e31b899a-9356-40bf-818b-e0f6e3480eb5 0.000000

Am I hitting this endpoint incorrectly?

Issue with Django - "Postgres is unavailable - sleeping"

Hello. First, thanks for making HiCAL available and so easy to spin up with Docker containers! It's made it much more convenient to test out.

The Problem

I recently ran into an error when trying to start HiCAL. I followed all of the instructions here and ran into the error on the last step (DOC_BIN=/data/athome4_sample.bin PARA_BIN=/data/athome4_para_sample.bin docker-compose -f HiCAL.yml up -d). I got the following error in the Django image, which prevented it from finishing bringing up the web server (i.e. you get a 502 Bad Gateway error when you navigate to http://localhost:9000/).

django_1    | Traceback (most recent call last):
django_1    |   File "<stdin>", line 2, in <module>
django_1    |   File "/usr/local/lib/python3.5/site-packages/psycopg2/__init__.py", line 50, in <module>
django_1    |     from psycopg2._psycopg import (                     # noqa
django_1    | ImportError: /usr/local/lib/python3.5/site-packages/psycopg2/.libs/libresolv-2-c4c53def.5.so: symbol __res_maybe_init version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
django_1    | Postgres is unavailable - sleeping

I did some searching and came across this thread that seems to indicate some issue with the psycopg2 binary.

The Fix

This issue seems to be solved by upgrading pyscopg2 to a newer version. I bumped the version to 2.8.0, which solved the issue for me.

I don't know enough about all of the interdependencies of this project or the new psycopg2 release to know if this affects anything else, but it at least fixed the issue for me.

System Setup

This was tested in Terminal on a Macbook running the Mojave OS 10.14.6 and Docker version 18.03.0-ce-mac60 (23751).

Let me know if you have any more questions about my setup or anything. Thanks!

Failed to retrieve docs

I get the above message if I select a topic ("Women in Parliaments") or try to create a new one, then click the lightbulb icon. I'm trying to run the Docker setup as laid out on the hical.github.io page on athome4.

How do I debug this?

Results meaning for CALEngine

Is there anywhere that explains the output for CALEngine (especially bmi_cli).
Sample output for bmi:

064578 0
047277 2
050307 2
050457 2
047817 1
047799 2
273177 0
273551 2
047347 0
273611 0
086457 0
080529 2
085197 2
...

Thanks (sorry to bother)

Cleanup logging extraneous actions

There’s still many instances in the front end that I feel need to be cleaned. These were mainly for studying user behaviour for our first study/experiment where we needed to capture interactions as much as needed.

Having them now is unnecessary.

Compilation fail building cal for the the HiCAL docker

I get a compile fail trying to 'docker-compose':

$ /Applications/Docker.app/Contents/Resources/bin/docker-compose -f HiCAL.yml up --no-recreate cal
WARNING: The DEBUG variable is not set. Defaulting to a blank string.
WARNING: The DOC_BIN variable is not set. Defaulting to a blank string.
WARNING: The PARA_BIN variable is not set. Defaulting to a blank string.
Creating network "hical_default" with the default driver
Creating volume "hical_postgres_data_local" with default driver
Creating volume "hical_postgres_backup_local" with default driver
Building cal
Step 1/3 : FROM ubuntu:16.04
16.04: Pulling from library/ubuntu
7b8b6451c85f: Pull complete
ab4d1096d9ba: Pull complete
e6797d1788ac: Pull complete
e25c5c290bde: Pull complete
Digest: sha256:e547ecaba7d078800c358082088e6cc710c3affd1b975601792ec701c80cdd39
Status: Downloaded newer image for ubuntu:16.04
 ---> a51debf7e1eb
Step 2/3 : RUN apt-get update -y && apt-get install -y     libfcgi-dev spawn-fcgi g++ libarchive-dev make git
 ---> Running in 909e31652a88
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  binutils ca-certificates cpp cpp-5 g++-5 gcc gcc-5 git-man ifupdown iproute2
  isc-dhcp-client isc-dhcp-common krb5-locales less libarchive13 libasan2
  libasn1-8-heimdal libatm1 libatomic1 libbsd0 libc-dev-bin libc6-dev libcc1-0
  libcilkrts5 libcurl3-gnutls libdns-export162 libedit2 liberror-perl
  libexpat1 libfcgi0ldbl libffi6 libgcc-5-dev libgdbm3 libgmp10 libgnutls30
  libgomp1 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal
  libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal
  libicu55 libidn11 libisc-export160 libisl15 libitm1 libk5crypto3
  libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2
  liblsan0 liblzo2-2 libmnl0 libmpc3 libmpfr4 libmpx0 libnettle6 libp11-kit0
  libperl5.22 libpopt0 libquadmath0 libroken18-heimdal librtmp1 libsasl2-2
  libsasl2-modules libsasl2-modules-db libsqlite3-0 libssl1.0.0
  libstdc++-5-dev libtasn1-6 libtsan0 libubsan0 libwind0-heimdal libx11-6
  libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxmuu1 libxtables11
  linux-libc-dev manpages manpages-dev netbase openssh-client openssl patch
  perl perl-modules-5.22 rename rsync sgml-base xauth xml-core
Suggested packages:
  binutils-doc cpp-doc gcc-5-locales g++-multilib g++-5-multilib gcc-5-doc
  libstdc++6-5-dbg gcc-multilib autoconf automake libtool flex bison gdb
  gcc-doc gcc-5-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
  libasan2-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
  libmpx0-dbg libquadmath0-dbg gettext-base git-daemon-run
  | git-daemon-sysvinit git-doc git-el git-email git-gui gitk gitweb git-arch
  git-cvs git-mediawiki git-svn ppp rdnssd iproute2-doc resolvconf
  avahi-autoipd isc-dhcp-client-ddns apparmor lrzip glibc-doc gnutls-bin
  krb5-doc krb5-user libsasl2-modules-otp libsasl2-modules-ldap
  libsasl2-modules-sql libsasl2-modules-gssapi-mit
  | libsasl2-modules-gssapi-heimdal libstdc++-5-doc make-doc man-browser
  ssh-askpass libpam-ssh keychain monkeysphere ed diffutils-doc perl-doc
  libterm-readline-gnu-perl | libterm-readline-perl-perl openssh-server
  sgml-base-doc debhelper
The following NEW packages will be installed:
  binutils ca-certificates cpp cpp-5 g++ g++-5 gcc gcc-5 git git-man ifupdown
  iproute2 isc-dhcp-client isc-dhcp-common krb5-locales less libarchive-dev
  libarchive13 libasan2 libasn1-8-heimdal libatm1 libatomic1 libbsd0
  libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libcurl3-gnutls libdns-export162
  libedit2 liberror-perl libexpat1 libfcgi-dev libfcgi0ldbl libffi6
  libgcc-5-dev libgdbm3 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2
  libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libicu55 libidn11
  libisc-export160 libisl15 libitm1 libk5crypto3 libkeyutils1
  libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 liblsan0
  liblzo2-2 libmnl0 libmpc3 libmpfr4 libmpx0 libnettle6 libp11-kit0
  libperl5.22 libpopt0 libquadmath0 libroken18-heimdal librtmp1 libsasl2-2
  libsasl2-modules libsasl2-modules-db libsqlite3-0 libssl1.0.0
  libstdc++-5-dev libtasn1-6 libtsan0 libubsan0 libwind0-heimdal libx11-6
  libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxmuu1 libxtables11
  linux-libc-dev make manpages manpages-dev netbase openssh-client openssl
  patch perl perl-modules-5.22 rename rsync sgml-base spawn-fcgi xauth
  xml-core
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Get:33 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtasn1-6 amd64 4.7-3ubuntu0.16.04.3 [43.5 kB]
Get:34 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgnutls30 amd64 3.4.10-4ubuntu1.4 [548 kB]
Get:35 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsqlite3-0 amd64 3.11.0-1ubuntu1 [396 kB]
Get:36 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libssl1.0.0 amd64 1.0.2g-1ubuntu4.13 [1083 kB]
Get:37 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxtables11 amd64 1.6.0-2ubuntu3 [27.2 kB]
Get:38 http://archive.ubuntu.com/ubuntu xenial/main amd64 netbase all 5.3 [12.9 kB]
Get:39 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 openssl amd64 1.0.2g-1ubuntu4.13 [492 kB]
Get:40 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 ca-certificates all 20170717~16.04.1 [168 kB]
Get:41 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 krb5-locales all 1.13.2+dfsg-5ubuntu2 [13.2 kB]
Get:42 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libroken18-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [41.4 kB]
Get:43 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libasn1-8-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [174 kB]
Get:44 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5support0 amd64 1.13.2+dfsg-5ubuntu2 [30.8 kB]
Get:45 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libk5crypto3 amd64 1.13.2+dfsg-5ubuntu2 [81.2 kB]
Get:46 http://archive.ubuntu.com/ubuntu xenial/main amd64 libkeyutils1 amd64 1.5.9-8ubuntu1 [9904 B]
Get:47 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5-3 amd64 1.13.2+dfsg-5ubuntu2 [273 kB]
Get:48 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgssapi-krb5-2 amd64 1.13.2+dfsg-5ubuntu2 [120 kB]
Get:49 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libhcrypto4-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [85.0 kB]
Get:50 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libheimbase1-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [29.3 kB]
Get:51 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwind0-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [47.8 kB]
Get:52 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libhx509-5-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [107 kB]
Get:53 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5-26-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [202 kB]
Get:54 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libheimntlm0-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [15.1 kB]
Get:55 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgssapi3-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [96.1 kB]
Get:56 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-14ubuntu0.1 [14.5 kB]
Get:57 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-14ubuntu0.1 [48.6 kB]
Get:58 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2ubuntu3.3 [161 kB]
Get:59 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d-1ubuntu0.1 [54.4 kB]
Get:60 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libcurl3-gnutls amd64 7.47.0-1ubuntu2.11 [185 kB]
Get:61 http://archive.ubuntu.com/ubuntu xenial/main amd64 libedit2 amd64 3.1-20150325-1ubuntu2 [76.5 kB]
Get:62 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libicu55 amd64 55.1-7ubuntu0.4 [7646 kB]
Get:63 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libsasl2-modules amd64 2.1.26.dfsg1-14ubuntu0.1 [47.5 kB]
Get:64 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libxml2 amd64 2.9.3+dfsg1-1ubuntu0.6 [697 kB]
Get:65 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxmuu1 amd64 2:1.1.2-2 [9674 B]
Get:66 http://archive.ubuntu.com/ubuntu xenial/main amd64 manpages all 4.04-2 [1087 kB]
Get:67 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 openssh-client amd64 1:7.2p2-4ubuntu2.6 [584 kB]
Get:68 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 rsync amd64 3.1.1-3ubuntu1.2 [329 kB]
Get:69 http://archive.ubuntu.com/ubuntu xenial/main amd64 xauth amd64 1:1.0.9-1ubuntu2 [22.7 kB]
Get:70 http://archive.ubuntu.com/ubuntu xenial/main amd64 xml-core all 0.13+nmu2 [23.3 kB]
Get:71 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 binutils amd64 2.26.1-1ubuntu1~16.04.7 [2309 kB]
Get:72 http://archive.ubuntu.com/ubuntu xenial/main amd64 libisl15 amd64 0.16.1-1 [524 kB]
Get:73 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 cpp-5 amd64 5.4.0-6ubuntu1~16.04.10 [7671 kB]
Get:74 http://archive.ubuntu.com/ubuntu xenial/main amd64 cpp amd64 4:5.3.1-1ubuntu1 [27.7 kB]
Get:75 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libcc1-0 amd64 5.4.0-6ubuntu1~16.04.10 [38.8 kB]
Get:76 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgomp1 amd64 5.4.0-6ubuntu1~16.04.10 [55.1 kB]
Get:77 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libitm1 amd64 5.4.0-6ubuntu1~16.04.10 [27.4 kB]
Get:78 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libatomic1 amd64 5.4.0-6ubuntu1~16.04.10 [8888 B]
Get:79 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libasan2 amd64 5.4.0-6ubuntu1~16.04.10 [264 kB]
Get:80 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 liblsan0 amd64 5.4.0-6ubuntu1~16.04.10 [105 kB]
Get:81 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtsan0 amd64 5.4.0-6ubuntu1~16.04.10 [244 kB]
Get:82 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libubsan0 amd64 5.4.0-6ubuntu1~16.04.10 [95.3 kB]
Get:83 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libcilkrts5 amd64 5.4.0-6ubuntu1~16.04.10 [40.1 kB]
Get:84 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmpx0 amd64 5.4.0-6ubuntu1~16.04.10 [9764 B]
Get:85 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libquadmath0 amd64 5.4.0-6ubuntu1~16.04.10 [131 kB]
Get:86 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgcc-5-dev amd64 5.4.0-6ubuntu1~16.04.10 [2228 kB]
Get:87 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 gcc-5 amd64 5.4.0-6ubuntu1~16.04.10 [8426 kB]
Get:88 http://archive.ubuntu.com/ubuntu xenial/main amd64 gcc amd64 4:5.3.1-1ubuntu1 [5244 B]
Get:89 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libc-dev-bin amd64 2.23-0ubuntu10 [68.7 kB]
Get:90 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 linux-libc-dev amd64 4.4.0-139.165 [862 kB]
Get:91 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libc6-dev amd64 2.23-0ubuntu10 [2079 kB]
Get:92 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libstdc++-5-dev amd64 5.4.0-6ubuntu1~16.04.10 [1426 kB]
Get:93 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 g++-5 amd64 5.4.0-6ubuntu1~16.04.10 [8319 kB]
Get:94 http://archive.ubuntu.com/ubuntu xenial/main amd64 g++ amd64 4:5.3.1-1ubuntu1 [1504 B]
Get:95 http://archive.ubuntu.com/ubuntu xenial/main amd64 liberror-perl all 0.17-1.2 [19.6 kB]
Get:96 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 git-man all 1:2.7.4-0ubuntu1.5 [736 kB]
Get:97 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 git amd64 1:2.7.4-0ubuntu1.5 [2714 kB]
Get:98 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libarchive13 amd64 3.1.2-11ubuntu0.16.04.4 [262 kB]
Get:99 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libarchive-dev amd64 3.1.2-11ubuntu0.16.04.4 [424 kB]
Get:100 http://archive.ubuntu.com/ubuntu xenial/main amd64 libfcgi0ldbl amd64 2.4.0-8.3 [161 kB]
Get:101 http://archive.ubuntu.com/ubuntu xenial/main amd64 libfcgi-dev amd64 2.4.0-8.3 [30.1 kB]
Get:102 http://archive.ubuntu.com/ubuntu xenial/main amd64 make amd64 4.1-6 [151 kB]
Get:103 http://archive.ubuntu.com/ubuntu xenial/main amd64 manpages-dev all 4.04-2 [2048 kB]
Get:104 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 patch amd64 2.7.5-1ubuntu0.16.04.1 [90.5 kB]
Get:105 http://archive.ubuntu.com/ubuntu xenial/main amd64 rename all 0.20-4 [12.0 kB]
Get:106 http://archive.ubuntu.com/ubuntu xenial/universe amd64 spawn-fcgi amd64 1.6.4-1 [14.5 kB]
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Removing intermediate container 909e31652a88
 ---> 53bbc2ba1960
Step 3/3 : RUN mkdir -p /src/
 ---> Running in 0f0be909f7c4
Removing intermediate container 0f0be909f7c4
 ---> 90d2399a504e
Successfully built 90d2399a504e
Successfully tagged hical_cal:latest
WARNING: Image for service cal was built because it did not already exist. To rebuild this image you must use `docker-compose build` or `docker-compose up --build`.
Creating cal ... done
Attaching to cal
cal         | rm -f bmi_fcgi bmi_cli corpus_parser
cal         | rm -r obj
cal         | rm: cannot remove 'obj': No such file or directory
cal         | make: *** [clean] Error 1
cal         | Makefile:45: recipe for target 'clean' failed
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/bmi_fcgi.cc -o obj/src/bmi_fcgi.cc.o
cal         | src/bmi_fcgi.cc: In function 'std::__cxx11::string parse_action_from_uri(std::__cxx11::string)':
cal         | src/bmi_fcgi.cc:20:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |      while(st < uri.length() && uri[st] == '/') st++;
cal         |               ^
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/dataset.cc -o obj/src/dataset.cc.o
cal         | src/dataset.cc: In function 'std::vector<int> generate_parent_documents(const Dataset&, const SparseVectors&)':
cal         | src/dataset.cc:19:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |      for(int i = 0; i < parent_documents.size(); i++){
cal         |                       ^
cal         | src/dataset.cc: In member function 'virtual void Dataset::score_docs_priority_queue(const std::vector<float>&, int, int, std::priority_queue<std::pair<float, int> >&, std::mutex&, int, const std::map<int, int>&)':
cal         | src/dataset.cc:78:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |                  if(top_docs.size() < num_top_docs)
cal         |                                     ^
cal         | src/dataset.cc: In member function 'virtual void ParagraphDataset::score_docs_priority_queue(const std::vector<float>&, int, int, std::priority_queue<std::pair<float, int> >&, std::mutex&, int, const std::map<int, int>&)':
cal         | src/dataset.cc:117:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |                  if(top_docs.size() < num_top_docs)
cal         |                                     ^
cal         | src/dataset.cc: In member function 'virtual std::vector<int> ParagraphDataset::rescore(const std::vector<float>&, int, int, const std::map<int, int>&)':
cal         | src/dataset.cc:170:36: warning: 'prev_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
cal         |          if(i != 0) start = prev_end;
cal         |                                     ^
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/bmi_para.cc -o obj/src/bmi_para.cc.o
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/bmi_para_scal.cc -o obj/src/bmi_para_scal.cc.o
cal         | src/bmi_para_scal.cc: In member function 'virtual void BMI_para_scal::record_judgment_batch(std::vector<std::pair<std::__cxx11::basic_string<char>, int> >)':
cal         | src/bmi_para_scal.cc:33:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |              if(paragraphs->translate_index(judgment_queue[i]) == id){
cal         |                                                                ^
cal         | src/bmi_para_scal.cc:58:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |          for(int i = 0; i < selector.size(); i++)
cal         |                           ^
cal         | src/bmi_para_scal.cc:61:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |          for(int i = 0; i < batch.size(); i++){
cal         |                           ^
cal         | mkdir -p obj/src/utils/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/utils/utils.cc -o obj/src/utils/utils.cc.o
cal         | mkdir -p obj/src/utils/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/utils/feature_writer.cc -o obj/src/utils/feature_writer.cc.o
cal         | mkdir -p obj/src/utils/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/utils/feature_parser.cc -o obj/src/utils/feature_parser.cc.o
cal         | src/utils/feature_parser.cc: In constructor 'BinFeatureParser::BinFeatureParser(const string&)':
cal         | src/utils/feature_parser.cc:8:53: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
cal         |      fread(&dict_end_offset, sizeof(uint32_t), 1, fp);
cal         |                                                      ^
cal         | src/utils/feature_parser.cc:19:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
cal         |          fread(&df, sizeof(uint32_t), 1, fp);
cal         |                                             ^
cal         | src/utils/feature_parser.cc:22:52: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
cal         |      fread(&num_records, sizeof(num_records), 1, fp);
cal         |                                                     ^
cal         | src/utils/feature_parser.cc: In constructor 'BinFeatureParser::BinFeatureParser(const string&, const string&)':
cal         | src/utils/feature_parser.cc:36:52: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
cal         |      fread(&num_records, sizeof(num_records), 1, fp);
cal         |                                                     ^
cal         | src/utils/feature_parser.cc: In member function 'virtual std::unique_ptr<SfSparseVector> BinFeatureParser::next()':
cal         | src/utils/feature_parser.cc:66:48: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
cal         |      fread(&num_pairs, sizeof(num_pairs), 1, fp);
cal         |                                                 ^
cal         | src/utils/feature_parser.cc:71:43: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
cal         |          fread(&x, sizeof(uint32_t), 1, fp);
cal         |                                            ^
cal         | src/utils/feature_parser.cc:73:49: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
cal         |          fread(&fvp.value_, sizeof(float), 1, fp);
cal         |                                                  ^
cal         | mkdir -p obj/src/utils/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/utils/text_utils.cc -o obj/src/utils/text_utils.cc.o
cal         | In file included from src/utils/text_utils.cc:4:0:
cal         | src/utils/porter.c:25:32: warning: unknown option after '#pragma GCC diagnostic' kind [-Wpragmas]
cal         |  #pragma GCC diagnostic ignored "-Wmisleading-indentation"
cal         |                                 ^
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/bmi.cc -o obj/src/bmi.cc.o
cal         | In file included from src/bmi.cc:7:0:
cal         | src/classifier.h: In constructor 'LRPegasosWeightedRecencyClassifier::LRPegasosWeightedRecencyClassifier(int, int)':
cal         | src/classifier.h:35:9: warning: 'LRPegasosWeightedRecencyClassifier::c' will be initialized after [-Wreorder]
cal         |      int c;
cal         |          ^
cal         | src/classifier.h:51:101: warning:   base 'LRPegasosClassifier' [-Wreorder]
cal         |      LRPegasosWeightedRecencyClassifier(int _c, int _num_iters):c(_c), LRPegasosClassifier(_num_iters){}
cal         |                                                                                                      ^
cal         | src/classifier.h:51:5: warning:   when initialized here [-Wreorder]
cal         |      LRPegasosWeightedRecencyClassifier(int _c, int _num_iters):c(_c), LRPegasosClassifier(_num_iters){}
cal         |      ^
cal         | In file included from src/bmi.cc:6:0:
cal         | src/bmi.h: In constructor 'BMI::BMI(Seed, Dataset*, int, int, bool, int, bool)':
cal         | src/bmi.h:45:16: warning: 'BMI::seed' will be initialized after [-Wreorder]
cal         |      const Seed seed;
cal         |                 ^
cal         | src/bmi.h:21:9: warning:   'int BMI::training_iterations' [-Wreorder]
cal         |      int training_iterations;
cal         |          ^
cal         | src/bmi.cc:11:1: warning:   when initialized here [-Wreorder]
cal         |  BMI::BMI(Seed _seed,
cal         |  ^
cal         | src/bmi.cc: In member function 'void BMI::sync_training_cache()':
cal         | src/bmi.cc:141:67: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |                      if(documents->get_index(positives[i]->doc_id) == training.first){
cal         |                                                                    ^
cal         | src/bmi.cc:148:67: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |                      if(documents->get_index(negatives[i]->doc_id) == training.first){
cal         |                                                                    ^
cal         | mkdir -p obj/src/sofiaml/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/sofiaml/sf-sparse-vector.cc -o obj/src/sofiaml/sf-sparse-vector.cc.o
cal         | src/sofiaml/sf-sparse-vector.cc: In member function 'void SfSparseVector::PushPair(uint32_t, float)':
cal         | src/sofiaml/sf-sparse-vector.cc:47:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |    if (id > 0 && NumFeatures() > 0 && id <= FeatureAt(NumFeatures() - 1) ) {
cal         |                                          ^
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/features.cc -o obj/src/features.cc.o
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/bmi_reduced_ranking.cc -o obj/src/bmi_reduced_ranking.cc.o
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/bmi_precision_delay.cc -o obj/src/bmi_precision_delay.cc.o
cal         | src/bmi_precision_delay.cc: In member function 'virtual void BMI_precision_delay::record_judgment_batch(std::vector<std::pair<std::__cxx11::basic_string<char>, int> >)':
cal         | src/bmi_precision_delay.cc:47:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |          if(judgment_queue.size() > 0 && id == judgment_queue.back()){
cal         |                                             ^
cal         | src/bmi_precision_delay.cc:53:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |          if(q.size() > window){
cal         |                      ^
cal         | src/bmi_precision_delay.cc:65:26: warning: 'last_rel' may be used uninitialized in this function [-Wmaybe-uninitialized]
cal         |          if(last_rel <= 0 && rel / (float)q.size() < threshold){
cal         |                           ^
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/bmi_online_learning.cc -o obj/src/bmi_online_learning.cc.o
cal         | mkdir -p obj/src/
cal         | g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/classifier.cc -o obj/src/classifier.cc.o
cal         | In file included from src/classifier.cc:25:0:
cal         | src/classifier.h: In constructor 'LRPegasosWeightedRecencyClassifier::LRPegasosWeightedRecencyClassifier(int, int)':
cal         | src/classifier.h:35:9: warning: 'LRPegasosWeightedRecencyClassifier::c' will be initialized after [-Wreorder]
cal         |      int c;
cal         |          ^
cal         | src/classifier.h:51:101: warning:   base 'LRPegasosClassifier' [-Wreorder]
cal         |      LRPegasosWeightedRecencyClassifier(int _c, int _num_iters):c(_c), LRPegasosClassifier(_num_iters){}
cal         |                                                                                                      ^
cal         | src/classifier.h:51:5: warning:   when initialized here [-Wreorder]
cal         |      LRPegasosWeightedRecencyClassifier(int _c, int _num_iters):c(_c), LRPegasosClassifier(_num_iters){}
cal         |      ^
cal         | src/classifier.cc: In function 'void ScaleToOne(std::vector<float>&, double&)':
cal         | src/classifier.cc:44:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cal         |      for (int i = 0; i < weights.size(); ++i) {
cal         |                        ^
cal         | g++  obj/src/dataset.cc.o obj/src/bmi_para.cc.o obj/src/bmi_para_scal.cc.o obj/src/utils/utils.cc.o obj/src/utils/feature_writer.cc.o obj/src/utils/feature_parser.cc.o obj/src/utils/text_utils.cc.o obj/src/bmi.cc.o obj/src/sofiaml/sf-sparse-vector.cc.o obj/src/features.cc.o obj/src/bmi_reduced_ranking.cc.o obj/src/bmi_precision_delay.cc.o obj/src/bmi_online_learning.cc.o obj/src/classifier.cc.o obj/src/bmi_fcgi.cc.o -o bmi_fcgi -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3
cal         | Error.  --doc-features needs a value, but is given none.
cal exited with code 1

Building corpus_parser on macOS 10.14 in Docker

The docker container comes up fine, but in the shell, when I try to compile corpus_parser, I get an ld error.

root@c671d9c26a58:/# cd src
root@c671d9c26a58:/src# make corpus_parser
mkdir -p obj/src/
g++ -MMD -MP -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3 -c src/corpus_parser.cc -o obj/src/corpus_parser.cc.o
src/corpus_parser.cc: In function 'int main(int, char**)':
src/corpus_parser.cc:125:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < dictionary.size(); i++){
                    ~~^~~~~~~~~~~~~~~~~~~
src/corpus_parser.cc: In function 'std::__cxx11::string get_tempfile()':
src/corpus_parser.cc:29:12: warning: ignoring return value of 'int mkstemp(char*)', declared with attribute warn_unused_result [-Wunused-result]
     mkstemp(file_template);
     ~~~~~~~^~~~~~~~~~~~~~~
g++  obj/src/dataset.cc.o obj/src/bmi_para.cc.o obj/src/bmi_para_scal.cc.o obj/src/utils/utils.cc.o obj/src/utils/feature_writer.cc.o obj/src/utils/feature_parser.cc.o obj/src/utils/text_utils.cc.o obj/src/bmi.cc.o obj/src/sofiaml/sf-sparse-vector.cc.o obj/src/features.cc.o obj/src/bmi_reduced_ranking.cc.o obj/src/bmi_precision_delay.cc.o obj/src/bmi_online_learning.cc.o obj/src/classifier.cc.o obj/src/corpus_parser.cc.o -o corpus_parser -Wall -pthread --std=c++14 -lfcgi -lfcgi++ -larchive -O3
/usr/bin/ld: obj/src/dataset.cc.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/bmi_para.cc.o: relocation R_X86_64_32 against symbol `__pthread_key_create@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/bmi_para_scal.cc.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/utils/utils.cc.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/utils/feature_writer.cc.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/utils/feature_parser.cc.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/utils/text_utils.cc.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/bmi.cc.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/sofiaml/sf-sparse-vector.cc.o: relocation R_X86_64_32 against symbol `_ZSt4cerr@@GLIBCXX_3.4' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/features.cc.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/bmi_reduced_ranking.cc.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/bmi_precision_delay.cc.o: relocation R_X86_64_32 against symbol `__pthread_key_create@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/bmi_online_learning.cc.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: obj/src/classifier.cc.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:32: recipe for target 'corpus_parser' failed
make: *** [corpus_parser] Error 1

Clean Judgment model

  • Clean up Judgment model and all requests to make judgments to only record important fields.

  • Add meta field for any other information (e.g. paragraph excerpt content, etc)

Changes to the judgment model will cause earlier versions not to work, unless the database is cleaned.

Multiple data collections

Should we allow users to select and switch between different data collections? We now support only one collection by default.

Django error creating a new topic

I set things up with the athome sample collection, created a user, and chose to create a new topic. The title was 'Social Security', the initial query was 'social security', the strategy was paragraphs, and I checked view-full-documents. I then got the following error.

Environment:

Request Method: POST
Request URL: http://localhost:9000/

Django Version: 1.10.7
Python Version: 3.5.6
Installed Applications:
['django.contrib.auth',
'django.contrib.contenttypes',
'django.contrib.sessions',
'django.contrib.sites',
'django.contrib.messages',
'django.contrib.staticfiles',
'django.contrib.admin',
'crispy_forms',
'allauth',
'allauth.account',
'raven.contrib.django.raven_compat',
'hicalweb.users.apps.UsersConfig',
'hicalweb.progress',
'hicalweb.CAL',
'hicalweb.topic',
'hicalweb.judgment',
'hicalweb.search',
'hicalweb.iterative',
'hicalweb.archive',
'django_extensions']
Installed Middleware:
['raven.contrib.django.middleware.DjangoRestFrameworkCompatMiddleware',
'raven.contrib.django.middleware.SentryMiddleware',
'django.middleware.security.SecurityMiddleware',
'django.contrib.sessions.middleware.SessionMiddleware',
'django.middleware.common.CommonMiddleware',
'django.middleware.csrf.CsrfViewMiddleware',
'django.contrib.auth.middleware.AuthenticationMiddleware',
'django.contrib.messages.middleware.MessageMiddleware',
'django.middleware.clickjacking.XFrameOptionsMiddleware',
'hicalweb.middleware.pagefile.PageHTMLMiddleware']

Traceback:

File "/usr/local/lib/python3.5/site-packages/django/db/backends/utils.py" in execute
64. return self.cursor.execute(sql, params)

The above exception (null value in column "show_full_document_content" violates not-null constraint
DETAIL: Failing row contains (2, de6b267d-d523-4a48-b1e8-c5f1a1984238, 0, null, 51, 5, 2019-02-21 16:42:31.592377+00, 2019-02-21 16:42:31.592406+00, 1000, para, null).
) was the direct cause of the following exception:

File "/usr/local/lib/python3.5/site-packages/django/core/handlers/exception.py" in inner
42. response = get_response(request)

File "/usr/local/lib/python3.5/site-packages/django/core/handlers/base.py" in _get_response
187. response = self.process_exception_by_middleware(e, request)

File "/usr/local/lib/python3.5/site-packages/django/core/handlers/base.py" in _get_response
185. response = wrapped_callback(request, *callback_args, **callback_kwargs)

File "/usr/local/lib/python3.5/contextlib.py" in inner
30. return func(*args, **kwds)

File "/usr/local/lib/python3.5/site-packages/django/views/generic/base.py" in view
68. return self.dispatch(request, *args, **kwargs)

File "/usr/local/lib/python3.5/site-packages/braces/views/_access.py" in dispatch
102. request, *args, **kwargs)

File "/usr/local/lib/python3.5/site-packages/django/views/generic/base.py" in dispatch
88. return handler(request, *args, **kwargs)

File "./hicalweb/progress/views.py" in post
93. strategy=strategy

File "/usr/local/lib/python3.5/site-packages/django/db/models/manager.py" in manager_method
85. return getattr(self.get_queryset(), name)(*args, **kwargs)

File "/usr/local/lib/python3.5/site-packages/django/db/models/query.py" in create
399. obj.save(force_insert=True, using=self.db)

File "./hicalweb/progress/models.py" in save
50. super(Task, self).save(*args, **kwargs)

File "/usr/local/lib/python3.5/site-packages/django/db/models/base.py" in save
796. force_update=force_update, update_fields=update_fields)

File "/usr/local/lib/python3.5/site-packages/django/db/models/base.py" in save_base
824. updated = self._save_table(raw, cls, force_insert, force_update, using, update_fields)

File "/usr/local/lib/python3.5/site-packages/django/db/models/base.py" in _save_table
908. result = self._do_insert(cls._base_manager, using, fields, update_pk, raw)

File "/usr/local/lib/python3.5/site-packages/django/db/models/base.py" in _do_insert
947. using=using, raw=raw)

File "/usr/local/lib/python3.5/site-packages/django/db/models/manager.py" in manager_method
85. return getattr(self.get_queryset(), name)(*args, **kwargs)

File "/usr/local/lib/python3.5/site-packages/django/db/models/query.py" in _insert
1045. return query.get_compiler(using=using).execute_sql(return_id)

File "/usr/local/lib/python3.5/site-packages/django/db/models/sql/compiler.py" in execute_sql
1054. cursor.execute(sql, params)

File "/usr/local/lib/python3.5/site-packages/django/db/backends/utils.py" in execute
79. return super(CursorDebugWrapper, self).execute(sql, params)

File "/usr/local/lib/python3.5/site-packages/raven/contrib/django/client.py" in execute
127. return real_execute(self, sql, params)

File "/usr/local/lib/python3.5/site-packages/django/db/backends/utils.py" in execute
64. return self.cursor.execute(sql, params)

File "/usr/local/lib/python3.5/site-packages/django/db/utils.py" in exit
94. six.reraise(dj_exc_type, dj_exc_value, traceback)

File "/usr/local/lib/python3.5/site-packages/django/utils/six.py" in reraise
685. raise value.with_traceback(tb)

File "/usr/local/lib/python3.5/site-packages/django/db/backends/utils.py" in execute
64. return self.cursor.execute(sql, params)

Exception Type: IntegrityError at /
Exception Value: null value in column "show_full_document_content" violates not-null constraint
DETAIL: Failing row contains (2, de6b267d-d523-4a48-b1e8-c5f1a1984238, 0, null, 51, 5, 2019-02-21 16:42:31.592377+00, 2019-02-21 16:42:31.592406+00, 1000, para, null).

screen shot 2019-02-21 at 11 45 08 am

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