diff --git a/README.md b/README.md index fe35f6d..0b67033 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ PHPCap makes accessing REDCap from a PHP program easier by providing: REDCap is a web application for building and managing online surveys and databases. For information about REDCap, please see http://www.project-redcap.org. -Developers: [Jim Mullen](https://github.com/mullen2); [Andy Arenson](https://github.com/aarenson), aarenson@iu.edu +Developers: [Jim Mullen](https://github.com/mullen2); [Andy Arenson](https://github.com/aarenson), aarenson@iu.edu; [Nancy Long](https://github.com/naalong) [![Packagist](https://img.shields.io/github/v/release/iuredcap/PHPCap.svg)](https://packagist.org/packages/iu-redcap/phpcap) [![PHP 5.6+](https://img.shields.io/badge/php-%3E%3D%205.6-8892BF.svg)](https://php.net/) diff --git a/composer.json b/composer.json index 36140b6..c0cf0ed 100644 --- a/composer.json +++ b/composer.json @@ -1,37 +1,37 @@ { - "name" : "iu-redcap/phpcap", - "license" : "BSD-3-Clause", - "description" : "PHP library for accessing the REDCap API", - "keywords" : [ - "REDCap" - ], - "require" : { - "php" : ">=5.6.0", - "ext-curl" : "*", - "ext-openssl" : "*" - }, - "require-dev" : { - "phpunit/phpunit" : "11.4.4", - "squizlabs/php_codesniffer" : "3.11.1", - 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"version": "v1.31.0", + "version": "v1.33.0", "source": { "type": "git", "url": "https://github.com/symfony/polyfill-mbstring.git", - "reference": "85181ba99b2345b0ef10ce42ecac37612d9fd341" + "reference": "6d857f4d76bd4b343eac26d6b539585d2bc56493" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/symfony/polyfill-mbstring/zipball/85181ba99b2345b0ef10ce42ecac37612d9fd341", - "reference": "85181ba99b2345b0ef10ce42ecac37612d9fd341", + "url": "https://api.github.com/repos/symfony/polyfill-mbstring/zipball/6d857f4d76bd4b343eac26d6b539585d2bc56493", + "reference": "6d857f4d76bd4b343eac26d6b539585d2bc56493", "shasum": "" }, "require": { + "ext-iconv": "*", "php": ">=7.2" }, "provide": { @@ -1890,7 +2054,7 @@ "shim" ], "support": { - "source": "https://github.com/symfony/polyfill-mbstring/tree/v1.31.0" + "source": "https://github.com/symfony/polyfill-mbstring/tree/v1.33.0" }, "funding": [ { @@ -1901,32 +2065,36 @@ "url": "https://github.com/fabpot", "type": "github" }, + { + "url": "https://github.com/nicolas-grekas", + "type": "github" + }, { "url": "https://tidelift.com/funding/github/packagist/symfony/symfony", "type": "tidelift" } ], - "time": "2024-09-09T11:45:10+00:00" + "time": "2024-12-23T08:48:59+00:00" }, { "name": "theseer/tokenizer", - "version": "1.2.3", + "version": "2.0.1", "source": { "type": "git", "url": "https://github.com/theseer/tokenizer.git", - "reference": "737eda637ed5e28c3413cb1ebe8bb52cbf1ca7a2" + "reference": "7989e43bf381af0eac72e4f0ca5bcbfa81658be4" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/theseer/tokenizer/zipball/737eda637ed5e28c3413cb1ebe8bb52cbf1ca7a2", - "reference": "737eda637ed5e28c3413cb1ebe8bb52cbf1ca7a2", + "url": "https://api.github.com/repos/theseer/tokenizer/zipball/7989e43bf381af0eac72e4f0ca5bcbfa81658be4", + "reference": "7989e43bf381af0eac72e4f0ca5bcbfa81658be4", "shasum": "" }, "require": { "ext-dom": "*", "ext-tokenizer": "*", "ext-xmlwriter": "*", - "php": "^7.2 || ^8.0" + "php": "^8.1" }, "type": "library", "autoload": { @@ -1948,7 +2116,7 @@ "description": "A small library for converting tokenized PHP source code into XML and potentially other formats", "support": { "issues": "https://github.com/theseer/tokenizer/issues", - "source": "https://github.com/theseer/tokenizer/tree/1.2.3" + "source": "https://github.com/theseer/tokenizer/tree/2.0.1" }, "funding": [ { @@ -1956,12 +2124,12 @@ "type": "github" } ], - "time": "2024-03-03T12:36:25+00:00" + "time": "2025-12-08T11:19:18+00:00" } ], "aliases": [], "minimum-stability": "stable", - "stability-flags": [], + "stability-flags": {}, "prefer-stable": false, "prefer-lowest": false, "platform": { @@ -1969,6 +2137,6 @@ "ext-curl": "*", "ext-openssl": "*" }, - "platform-dev": [], - "plugin-api-version": "2.2.0" + "platform-dev": {}, + "plugin-api-version": "2.9.0" } diff --git a/docs-md/DeveloperGuide.md b/docs-md/DeveloperGuide.md index b9a115e..9db0833 100644 --- a/docs-md/DeveloperGuide.md +++ b/docs-md/DeveloperGuide.md @@ -195,6 +195,22 @@ __super.token__ to a valid super token value. Note that the tests for project cr have no way to delete the projects that are created, so they will need to be deleted manually. +#### Setup for Optional Randomization Tests + +To run the randomization tests, use the following steps: + +1. In REDCap, create a project for the "Randomization" project test file in the __tests/projects__ directory, and import the project test file into that project. +2. Request an API token for the project imported in the step above. Make sure that user setting allows API import and export. +3. If you have not already done so, copy the "config-example.ini" file to a file named _config.ini_. Edit _config,ini_ and set __randomization.api.token__ + to the API token created in the previous step. +4. In REDCap, edit the project. In the "Applications" section on the left side of screen, click on the __Randomization__ link. You should see the _Summary_ tab of the _Randomization_ page that lists one target, _randomization_group_. +5. Make note of the __Randomization ID__ for _randomization_group_. +6. Edit the _config.ini_ file and set __randomization.id__ to the _randomization_group_ value. +7. In REDCap, return to the "Randomization" page for the project. Click on the __Setup__ icon for _randomization_group_. The "Setup1" tab should appear. +8. In section "STEP 3: Upload your allocation table (CSV file)", for _Upload allocation table (CSV file) for use in DEVELOPMENT status_, + browse to the __tests/data__ directory where you installed PHPCap and upload the file __randomization_dev_allocation.csv__. + You should see a brief message that the upload was successful. + #### Set the Timezone Set the timezone property in the __config.ini__ file. diff --git a/docs/CACertificateFile.html b/docs/CACertificateFile.html index e26c4af..3269f96 100644 --- a/docs/CACertificateFile.html +++ b/docs/CACertificateFile.html @@ -68,31 +68,45 @@

CA Certificate File Info

Creating a CA Certificate File with Firefox

To use the Firefox web browser to create a CA (Certificate Authority) certificate file for use with PHPCap, use the following steps:

    -
  1. Access your REDCap site with Firefox.
  2. -

    Click on the padlock icon to the left of the URL displayed in Firefox, and then the connection, and then "More Information".

    +

    Access your REDCap site with Firefox.

    +
    3. +
  3. +

    Click on the padlock icon to the left of the URL displayed in Firefox, and then the connection, and then "More Information".

    Page Information

  4. -

    If the previous step succeeded, a "Page Info" window should open up. In this window, -click on the "Security" tab, if it is not already selected.

    +

    If the previous step succeeded, a "Page Info" window should open up. In this window, +click on the "Security" tab, if it is not already selected.

    Page Information

    5. -
  5. Click on the "View Certificate" button
  6. -

    Click on the "Detail" tab of the "Certificate Viewer" dialog.

    +

    Click on the "View Certificate" button

    +
    7. +
  7. +

    Click on the "Detail" tab of the "Certificate Viewer" dialog.

    Certificate Viewer

    8. -
  8. Select the top entry in the "Certificate Hierarchy" box.
    9. -
  9. Click the "Export..." button.
  10. -

    In the "Save Certificate to File" window that should appear:

    +

    Select the top entry in the "Certificate Hierarchy" box.

    +
    11. +
  11. +

    Click the "Export..." button.

    +
    12. +
  12. +

    In the "Save Certificate to File" window that should appear:

      -
    1. navigate to where you want to save the file
      2. -
    2. change the name of the file if you don't want to use the default name
      3. -
    3. set "Save as type" to "X.509 Certificate (PEM)"
    4. -

      click on the "Save" button.

      +

      navigate to where you want to save the file

      +
      5. +
    5. +

      change the name of the file if you don't want to use the default name

      +
      6. +
    6. +

      set "Save as type" to "X.509 Certificate (PEM)"

      +
      7. +
    7. +

      click on the "Save" button.

      Save Certificate to File

    diff --git a/docs/DeveloperGuide.html b/docs/DeveloperGuide.html index 4cbaab4..a61a6c0 100644 --- a/docs/DeveloperGuide.html +++ b/docs/DeveloperGuide.html @@ -71,30 +71,30 @@

    Setup

  13. Get PHPCap:

    -
    git clone https://github.com/iuredcap/phpcap
    +
     git clone https://github.com/iuredcap/phpcap

  14. Get Composer. Composer is needed to download the development dependencies for PHPCap. See: https://getcomposer.org/download/. -You can either install the composer.phar file to the root directory of PHPCap (the .gitignore +You can either install the composer.phar file to the root directory of PHPCap (the .gitignore file is set to ignore this file), or install it globally at the system or account level.

  15. Install PHPCap's development dependencies:

    -
    # If you installed the composer.phar file in PHPCap's root directory:
-php composer.phar install
+
     # If you installed the composer.phar file in PHPCap's root directory:
+ php composer.phar install
 
-# If you installed composer globally:
-composer install
+ # If you installed composer globally:
+ composer install
 
-# The dependencies should be installed into a "vendor" directory
-# (which will be ignored by Git).    
    
+ # The dependencies should be installed into a "vendor" directory
+ # (which will be ignored by Git).

  16. Install phpDocumentor, which is used for generating API documentation from PHPDoc comments in the code. It should be set up so that it can be run from the command line using:

    -
    phpdoc
    +
     phpdoc

Example Setup on Ubuntu 20

@@ -112,25 +112,25 @@

Example Setup on Ubuntu 20

sudo mv phpDocumentor.phar /usr/local/bin/phpdoc

Development

Automated Tests

-

PHPCap uses PHPUnit for running automated tests. PHPUnit should get installed as a dependency for your PHPCap project when you run the "composer install" command. +

PHPCap uses PHPUnit for running automated tests. PHPUnit should get installed as a dependency for your PHPCap project when you run the "composer install" command. PHPCap has the following types of automated tests:

    -
  1. unit tests - +

You can test your PHPUnit installation by running the following in the root PHPCap directory, which will run the unit tests for PHPCap:

    ./vendor/bin/phpunit --testsuite unit
-

If the above command succeeds, you should see an "OK" message with the number of tests and assertions that were run, and you should see no errors of failures.

-

To run all the automated tests (the unit tests as well as the integration tests), setup steps needs to be completed. Some of the integration tests are considered optional. If +

If the above command succeeds, you should see an "OK" message with the number of tests and assertions that were run, and you should see no errors of failures.

+

To run all the automated tests (the unit tests as well as the integration tests), setup steps needs to be completed. Some of the integration tests are considered optional. If you don't do the setup steps for these optional tests, they will not be run. But if you don't do the setup steps for the non-optional integration tests, phpunit will fail when you try to run them.

Setup for Non-Optional Integration Tests

@@ -139,22 +139,22 @@

Setup for Non-Optional Integration Tests

  1. Log in to your REDCap site.
  2. Create an empty project in REDCap.
    3. -
  3. Create a project in REDCap for the "Basic Demography," "DAG," and "Longitudinal Data" test projects in directory tests/projects/, and import each of those test project files into the REDCap project created for it.
    4. +
  4. Create a project in REDCap for the "Basic Demography," "DAG," and "Longitudinal Data" test projects in directory tests/projects/, and import each of those test project files into the REDCap project created for it.
  5. In REDCap, request API tokens for the empty project and the projects imported in the step above. Make sure that user setting for each project allow API import and export.
    6. -
  6. Once you have your tokens, copy the "config-example.ini" file to a file -named "config.ini" and then set the URL in that file to be the +
  7. Once you have your tokens, copy the "config-example.ini" file to a file +named "config.ini" and then set the URL in that file to be the URL for the API of your REDCap instance, and set the tokens to be the tokens requested in the previous step.
    8. -
  8. In the Control Center in REDCap, download the "Date Calculated Fields" external module and then enable it.
    9. -
  9. In REDCap, enable the "Date Calculated Fields" external module for the "Basic Demography" project.
    10. -
  10. In REDCap, add a test user to the DAG project, assigning only default, basic permissions. -
      +
    1. In the Control Center in REDCap, download the "Date Calculated Fields" external module and then enable it.
      2. +
    2. In REDCap, enable the "Date Calculated Fields" external module for the "Basic Demography" project.
      3. +
    3. In REDCap, add a test user to the DAG project, assigning only default, basic permissions.
      1. Add the test user to the 'group1' DAG
        2. -
      2. Using the "DAG Switcher" in REDCap, assign the test user access to DAGs 'group1' and 'group2'
        3. +
      3. Using the "DAG Switcher" in REDCap, assign the test user access to DAGs 'group1' and 'group2'
      4. Create an API token for the test user with export/import/update permission for the DAG project
      5. Set the dags.test.user.api.token property in your test config.ini file to the value for the API token created in the previous step
        6. -
      4. +
    +

Setup for Optional CA Certificate File Integration Tests

To run the optional tests involving the CA certificate file, you will need to set up @@ -167,81 +167,121 @@

Setup for Optional Report Integration Tests

To run all of the optional report tests, you will need to manually set up 2 reports.

You need to set up a report for the basic demography project. -and then set the +and then set the basic.demography.report.id property in your tests/config.ini file to the ID of the report. If the ID property is not set, then the tests -that use the report will not be run. You need to set up an "Exercise" report +that use the report will not be run. You need to set up an "Exercise" report as follows:

You need to set up a report for the longitudinal data project -and then set the +and then set the longitudinal.data.report.id property in your tests/config.ini file to the ID of the report. If the ID property is not set, then the tests -that use the report will not be run. You need to set up an "Exercise" report +that use the report will not be run. You need to set up an "Exercise" report as follows:

Setup for Optional Survey Integration Tests

To run the survey tests, use the following steps:

    -
  1. In REDCap, create a project for the "Repeatable Survey" project test file in the tests/projects directory, and import the project test file into that project.
    2. -
  2. In the "Project Setup" tab for the project created in the step above, click on the Enable button for "Use surveys for this project?"
    3. -
  3. In the "Project Setup" tab, click on the Designer button
    4. -
  4. In the "Online Designer" tab, click on the Enable button for instrument "Basic Information", and then: +
  5. +

    In REDCap, create a project for the "Repeatable Survey" project test file in the tests/projects directory, and import the project test file into that project.

    +
    6. +
  6. +

    In the "Project Setup" tab for the project created in the step above, click on the Enable button for "Use surveys for this project?"

    +
    7. +
  7. +

    In the "Project Setup" tab, click on the Designer button

    +
    8. +
  8. +

    In the "Online Designer" tab, click on the Enable button for instrument "Basic Information", and then:

      -
    1. Select "Yes" for "Allow 'Save & Return Later' option for respondents?"
      2. +
    2. Select "Yes" for "Allow 'Save & Return Later' option for respondents?"
    3. Click on the Save Changes button
      4. -
    9. -
  9. In the "Online Designer" tab, click on the Enable button for instrument "Weight", and then: +
+ +
  • +

    In the "Online Designer" tab, click on the Enable button for instrument "Weight", and then:

      -
    1. Select "Yes" for "Allow 'Save & Return Later' option for respondents?"
      2. -
    2. Check the box for "(Optional) Allow respondents to repeat the survey"
      3. +
    3. Select "Yes" for "Allow 'Save & Return Later' option for respondents?"
      4. +
    4. Check the box for "(Optional) Allow respondents to repeat the survey"
    5. Click on the Save Changes button
      6. -
    • -
  • In the "Online Designer" tab, click on the "Survey Queue" button
    • -
  • In the "Set up Survey Queue" dialog: + +
    • +
  • +

    In the "Online Designer" tab, click on the "Survey Queue" button

    +
    • +
  • +

    In the "Set up Survey Queue" dialog:

      -
    1. Click on the Activate button for "Weight"
      2. -
    2. Check "When the following survey is completed:"
      3. -
    3. In the selection below "When the following survey is completed:", select "Basic Information"
      4. +
    4. Click on the Activate button for "Weight"
      5. +
    5. Check "When the following survey is completed:"
      6. +
    6. In the selection below "When the following survey is completed:", select "Basic Information"
    7. Click on the Save button
      8. -
    • -
  • Click on the "Manage Survey Participants" or "Survey Distribution Tools" link on the left (depending on your REDCap version)
    • -
  • Go to the "Participant List" tab
    • -
  • Click on the Add participants button
    • -
  • Add an e-mail that you have access to and click on the Add participants button
    • -
  • Click on the Enable button for participant identifiers, and confirm this action
    • -
  • Enter an identifier for the participant for the e-mail that you entered above and then click on the Save button
    • -
  • Click on the Compose Survey Invitations button
    • -
  • In the "Send a Survey Invitation to Participants" dialog: + +
    • +
  • +

    Click on the "Manage Survey Participants" or "Survey Distribution Tools" link on the left (depending on your REDCap version)

    +
    • +
  • +

    Go to the "Participant List" tab

    +
    • +
  • +

    Click on the Add participants button

    +
    • +
  • +

    Add an e-mail that you have access to and click on the Add participants button

    +
    • +
  • +

    Click on the Enable button for participant identifiers, and confirm this action

    +
    • +
  • +

    Enter an identifier for the participant for the e-mail that you entered above and then click on the Save button

    +
    • +
  • +

    Click on the Compose Survey Invitations button

    +
    • +
  • +

    In the "Send a Survey Invitation to Participants" dialog:

      -
    1. Make sure that "Immediately" is selected for when the e-mail should be sent
      2. +
    2. Make sure that "Immediately" is selected for when the e-mail should be sent
    3. Make sure that the participant you create above is selected
    4. Click on the Send Invitations button
      5. -
    • -
  • Open the e-mail that should have been sent (you may need to wait a few minutes to receive it)
    • -
  • Click on the "Basic Information" link in the e-mail and fill out the survey, and then at least one "Weight" survey
    • -
  • In your project window in REDCap, click on the "API" link on the left and request (or create if you are an admin) an API token with at least API Export rights
    • + + +
  • +

    Open the e-mail that should have been sent (you may need to wait a few minutes to receive it)

    +
    • +
  • +

    Click on the "Basic Information" link in the e-mail and fill out the survey, and then at least one "Weight" survey

    +
    • +
  • +

    In your project window in REDCap, click on the "API" link on the left and request (or create if you are an admin) an API token with at least API Export rights

    +

  • Once you have your API token, use it and the e-mail and identifier entered earlier to set the following properties in the config.ini file in the tests directory:

    -
    repeatable.survey.api.token
-survey.participant.email
-survey.participant.identifier
    +
     repeatable.survey.api.token
+ survey.participant.email
+ survey.participant.identifier

    • Setup for the Optional Repeating Forms Tests

    To run the repeating forms tests, use the following steps:

      -
    1. In REDCap, create a project for the "Repeating Forms" project test file in the tests/projects directory, and import the project test file into that project.
      2. -
    2. In your project window in REDCap, click on the "API" link on the left and request (or create if you are an admin) an API token with at least API Export rights
      3. +
    3. +

      In REDCap, create a project for the "Repeating Forms" project test file in the tests/projects directory, and import the project test file into that project.

      +
      4. +
    4. +

      In your project window in REDCap, click on the "API" link on the left and request (or create if you are an admin) an API token with at least API Export rights

      +

    5. Once you have your API token, use it to set the following property in the config.ini file in the tests directory:

      -
      repeating.forms.api.token
      +
       repeating.forms.api.token

    Setup for Optional Project Creation Tests

    @@ -249,6 +289,21 @@

    Setup for Optional Project Creation Tests

    super.token to a valid super token value. Note that the tests for project creation have no way to delete the projects that are created, so they will need to be deleted manually.

    +

    Setup for Optional Randomization Tests

    +

    To run the randomization tests, use the following steps:

    +
      +
    1. In REDCap, create a project for the "Randomization" project test file in the tests/projects directory, and import the project test file into that project.
      2. +
    2. Request an API token for the project imported in the step above. Make sure that user setting allows API import and export.
      3. +
    3. If you have not already done so, copy the "config-example.ini" file to a file named config.ini. Edit config,ini and set randomization.api.token +to the API token created in the previous step.
      4. +
    4. In REDCap, edit the project. In the "Applications" section on the left side of screen, click on the Randomization link. You should see the Summary tab of the Randomization page that lists one target, _randomizationgroup.
      5. +
    5. Make note of the Randomization ID for _randomizationgroup.
      6. +
    6. Edit the config.ini file and set randomization.id to the _randomizationgroup value.
      7. +
    7. In REDCap, return to the "Randomization" page for the project. Click on the Setup icon for _randomizationgroup. The "Setup1" tab should appear.
      8. +
    8. In section "STEP 3: Upload your allocation table (CSV file)", for Upload allocation table (CSV file) for use in DEVELOPMENT status, +browse to the tests/data directory where you installed PHPCap and upload the file randomization_dev_allocation.csv. +You should see a brief message that the upload was successful.
      9. +

    Set the Timezone

    Set the timezone property in the config.ini file.

    Note: the .gitignore file in PHPCap is set to ignore the tests/config.ini file, so that your @@ -334,7 +389,7 @@

    Documentation

    API Document Generation

    To generate the API documentation (stored in ./docs/api), execute the following command in PHPCap's root directory:

    phpdoc
    -

    Note: For this command to work, phpDocumentor needs to have been installed as command "phpdoc". +

    Note: For this command to work, phpDocumentor needs to have been installed as command "phpdoc". The configuration file used by this command is phpdoc.xml in the root directory of PHPCap.

    The API documentation is stored in Git to eliminate the need for non-developer users to install Composer and the developer dependencies.

    @@ -346,13 +401,13 @@

    HTML Document Generation

    execute the following command in PHPCap's root directory:

    php generate-html-docs.php

    Tagging Releases

    -

    Releases should be tagged in accordance with semantic versioning: +

    Releases should be tagged in accordance with semantic versioning: http://semver.org/

    Developer Dependencies

    PHPCap uses a few development dependencies.

    To check for out of date dependencies, use:

    composer outdated --direct
    -

    The "--direct" option above only checks dependencies directly used by PHPCap (i.e., specified in the +

    The "--direct" option above only checks dependencies directly used by PHPCap (i.e., specified in the composer.json file).