Documentation and installer helpers (#454)

* Documentation and installer helpers
LibreHealthIO · Mar 6, 2017 · 321cae9 · 321cae9
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diff --git a/Documentation/1_Installing/InstallingLibreEHR.html b/Documentation/1_Installing/InstallingLibreEHR.html
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+<!DOCTYPE HTML>
+<html>
+<head>
+	<meta http-equiv="content-type" content="text/html; charset=windows-1252"/>
+</head>
+<body>
+<p align="center"  background: transparent">
+<font size="5" style="font-size: 20pt"><b>Installing LibreHealth<font color="#ff420e">EHR</font></b></font></p>
+<p align="center" style="margin-left: -0.75in; margin-right: -0.81in; margin-bottom: 0in; line-height: 100%; background: transparent">
+<font color="#280099"><font size="3" style="font-size: 12pt"><u><b>Quick
+Start Guide</b></u>
+<BR>
+<TABLE>
+
+<TR>
+<TD>
+<BR>
+<font color="#000000"><font size="4" style="font-size: 14pt">After
+you have run the installer, please follow these steps:
+<BR></TD></TR>
+
+<TR>
+<TD>
+<img src="images/1_install/installer1.png" name="Image1" align="left" width="1109" height="483" border="0"/>
+</TR>
+</TD>
+
+
+<TR><TD><HR>
+<p align="center"><font color="#280099"><font size="4" style="font-size: 16pt"><b>NEXT</b></p>
+<BR><HR></TD></TR>
+
+
+
+<TR><TD>
+<img src="images/1_install/installer2.png" name="Image2" align="left" width="910" height="304" border="0"/>
+<BR></TD></TR>
+
+<TR><TD><HR>
+<p align="center"><font color="#280099"><font size="4" style="font-size: 16pt"><b>THEN...</b></p>
+<BR><HR></TD></TR>
+
+<TR><TD>
+<img src="images/1_install/installer3.png" name="Image3" align="left" width="766" height="231" border="0"/>
+<BR></TD></TR>
+
+<TR><TD><HR>
+<p align="center"><font color="#280099"><font size="4" style="font-size: 16pt"><b>AND</b></p>
+<BR><HR></TD></TR>
+
+<TR><TD>
+<img src="images/1_install/installer4.png" name="Image4" align="left" width="951" height="475" border="0"/>
+<BR></TD></TR>
+
+<TR><TD><HR>
+<p align="center"><font color="#280099"><font size="4" style="font-size: 16pt"><b>Now
+Step 5 of 9</b></p>
+<BR><HR></TD></TR>
+
+<TR><TD>
+<img src="images/1_install/installer5.png" name="Image5" align="left" width="589" height="370" border="0"/>
+<BR></TD></TR>
+
+<TR><TD><HR>
+<p align="center"><font color="#280099"><font size="4" style="font-size: 16pt"><b>Step6</b></p>
+<BR><HR></TD></TR>
+
+<TR><TD>
+<img src="images/1_install/installer6.png" name="Image6" align="left" width="866" height="459" border="0"/>
+<BR></TD></TR>
+
+<TR><TD><HR>
+<p align="center"><font color="#280099"><font size="4" style="font-size: 16pt"><b>On to Step 7</b></p>
+<BR><HR></TD></TR>
+
+<TR><TD>
+<img src="images/1_install/installer7.png" name="Image7" align="left" width="924" height="381" border="0"/>
+<BR></TD></TR>
+
+<TR><TD><HR>
+<p align="center"><font color="#280099"><font size="4" style="font-size: 16pt"><b>Then Step 8 of 9...Getting Close...</b></p>
+<BR><HR></TD></TR>
+
+<TR><TD>
+<img src="images/1_install/installer8.png" name="Image8" align="left" width="797" height="297" border="0"/>
+<BR></TD></TR>
+
+<TR><TD><HR>
+<p align="center"><font color="#280099"><font size="4" style="font-size: 16pt"><b>And Last of All...</b></p>
+<BR><HR></TD></TR>
+
+<TR><TD>
+<img src="images/1_install/installer9.png" name="Image9" align="left" width="1023" height="514" border="0"/>
+<HR></TD></TR>
+
+</body>
+</html>
diff --git a/Documentation/Setup-SQL-Database-Admin.odt → ...1_Installing/Setup-SQL-Database-Admin.odt b/Documentation/Setup-SQL-Database-Admin.odt → ...1_Installing/Setup-SQL-Database-Admin.odt
diff --git a/Documentation/Setup-SQL-Database-Admin.pdf → ...1_Installing/Setup-SQL-Database-Admin.pdf b/Documentation/Setup-SQL-Database-Admin.pdf → ...1_Installing/Setup-SQL-Database-Admin.pdf
diff --git a/Documentation/1_Installing/images/1_install/installer1.png b/Documentation/1_Installing/images/1_install/installer1.png
diff --git a/Documentation/1_Installing/images/1_install/installer10.png b/Documentation/1_Installing/images/1_install/installer10.png
diff --git a/Documentation/1_Installing/images/1_install/installer3.png b/Documentation/1_Installing/images/1_install/installer3.png
diff --git a/Documentation/1_Installing/images/1_install/installer4.png b/Documentation/1_Installing/images/1_install/installer4.png
diff --git a/Documentation/1_Installing/images/1_install/installer5.png b/Documentation/1_Installing/images/1_install/installer5.png
diff --git a/Documentation/1_Installing/images/1_install/installer6.png b/Documentation/1_Installing/images/1_install/installer6.png
diff --git a/Documentation/1_Installing/images/1_install/installer7.png b/Documentation/1_Installing/images/1_install/installer7.png
diff --git a/Documentation/1_Installing/images/1_install/installer8.png b/Documentation/1_Installing/images/1_install/installer8.png
diff --git a/Documentation/1_Installing/images/1_install/installer9.png b/Documentation/1_Installing/images/1_install/installer9.png
diff --git a/Documentation/2_Configuration/configurations.md b/Documentation/2_Configuration/configurations.md
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+Placeholder file for adding special configuration notes.
diff --git a/Documentation/Payment_Posting_ZHH.pdf → ...ntation/3_Billing/Payment_Posting_ZHH.pdf b/Documentation/Payment_Posting_ZHH.pdf → ...ntation/3_Billing/Payment_Posting_ZHH.pdf
diff --git a/...tation/Clinical_Decision_Rules_Manual.pdf → ...anuals/Clinical_Decision_Rules_Manual.pdf b/...tation/Clinical_Decision_Rules_Manual.pdf → ...anuals/Clinical_Decision_Rules_Manual.pdf
diff --git a/Documentation/Direct_Messaging_README.txt → ...eatureManuals/Direct_Messaging_README.txt b/Documentation/Direct_Messaging_README.txt → ...eatureManuals/Direct_Messaging_README.txt
diff --git a/Documentation/Emergency_User_README.txt → ..._FeatureManuals/Emergency_User_README.txt b/Documentation/Emergency_User_README.txt → ..._FeatureManuals/Emergency_User_README.txt
diff --git a/Documentation/README-Log-Backup.md → ...on/4_FeatureManuals/README-Log-Backup.txt b/Documentation/README-Log-Backup.md → ...on/4_FeatureManuals/README-Log-Backup.txt
diff --git a/Documentation/Readme_edihistory.html → ...n/4_FeatureManuals/Readme_edihistory.html b/Documentation/Readme_edihistory.html → ...n/4_FeatureManuals/Readme_edihistory.html
diff --git a/...p the Patient flow board for libreehr.pdf → ...p the Patient flow board for libreehr.pdf b/...p the Patient flow board for libreehr.pdf → ...p the Patient flow board for libreehr.pdf
diff --git a/...ing The End of Day Report in libreehr.pdf → ...ing The End of Day Report in libreehr.pdf b/...ing The End of Day Report in libreehr.pdf → ...ing The End of Day Report in libreehr.pdf
diff --git a/Documentation/Complete_Vaccine_Listing.pdf → ...5_Healthcare/Complete_Vaccine_Listing.pdf b/Documentation/Complete_Vaccine_Listing.pdf → ...5_Healthcare/Complete_Vaccine_Listing.pdf
diff --git a/Documentation/8_ForDevelopers/3rd_Party_Form_API.txt b/Documentation/8_ForDevelopers/3rd_Party_Form_API.txt
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+3rd Party Form API
+LibreEHR suite v2.0
+doc revision 2
+
+Pennington Firm
+PennFirm.com
+San Diego, California
+888-480-5050
+
+
+ ******* Introduction *******
+
+LibreEHR is more than a simple EMR suite, it is a modular platform that allows for customized modifications to meet specific needs.
+
+To create a set of patient encounter forms for use with LibreEHR, at least a limited knowledge of the PHP scripting language and the MySQL syntax is needed. The script _must_ be stored in the interface/forms/your_script_name/ directory, with at least these four files:
+	new.php		<-- will be acessed for new data entry
+	view.php	<-- will be used to view your form
+	print.php	<-- should be used to print your form
+	SQL.php		<-- contains sql table creation scripts
+
+ ******* Initialization *******
+
+To initialize the 3rd party php library (from interface/forms/your_script_name/myfile.php):
+	include_once("../../../library/api.inc");
+
+
+ ******* Functions *******
+
+--->>	formHeader("my form title name here")
+	This is the suggested title header for forms. It maintains the style used by the rest of the suite for consistency.
+
+
+--->>	formFooter()
+	Our suggested footer.
+
+
+--->>	formSubmit("my_table", $array_to_import, "0")
+	Submit will submit your array into the database, in the table created during your script install process.  The array to import should be a single dimension such as the following:
+
+		$myArray['column_name1']  = 'my column1 value';
+
+The third argument to formSubmit() is a url to redirect to after the data from a form has been saved.  If you set this to "0" (its default) then it will forward back to "libreehr/interface/patient_file/encounter/patient_encounter.php". This is the preferred operation, since users expect to be taken back to the Patient Encounter screen after saving a new form.
+
+
+--->>	formFetch("my_table", 'record id', 'columns wanted', 'activity state')
+	This function will retrieve one record of data.  The record id must be a numeric entry in the database.  The columns wanted defaults to "*", or all columns. If only a few columns are needed, setting columns wanted manually as follows: "id, activity, column-x" for example - usually id and activity are needed by the form, so it's a good idea to include those.  The activity state controls the visibility, or activity, of the records - you can view normal records with it set to "1" (its default) or view deleted records with "0" or both with "all".
+
+
+--->>	formGetIds("my_table", 'wanted columns', 'limit', 'start point', 
+'activity state')
+	This function retrieves a set of ids ordered by date descending from the most recent.  "wanted columns" will once again have a default of "*".  Limit defaults to "all" with returns unlimited results.  Placing a number in its place with limit the results.  'start point' is a starting point or offset for the limited results, and 'activity state' acts as stated above.
+
+
+--->>	formDisappear("my_table", 'record id')
+	This effectively sets the activity state to 0, causing the records to be invisible during normal suite usage. This is equivalent to letting the user delete a record. However, for maximum legal compliance, all data entered into LibreEHR should be saved. Instead of deleting records then, we merely make them invisible to normal user interface operations.
+
+
+--->>	formReappear("my_table", 'record id)
+	This function will reverse the effects of formDisappear, cause the record to once again be active. Use this if you allow the user to modify the active or inactive flag.
diff --git a/Documentation/8_ForDevelopers/Direct_Messaging_README.txt b/Documentation/8_ForDevelopers/Direct_Messaging_README.txt
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+Direct Messaging with LibreEHR and EMR Direct phiMail(R)
+Version 1.3, 19 Jul 2014
+
+A. Purpose: To provide a secure method from within LibreEHR for sending/receiving 
+protected health information to/from another Direct address using the Direct Project 
+messaging standard, as a step toward the goal of satisfying the three MU2 criteria 
+requiring the use of Direct messaging.  (For general information about Direct messaging, 
+see http://www.emrdirect.com/about-directed-exchange-and-secure-direct-messaging.html)
+
+B. IMPORTANT:  Please be aware of the following limitations when using the LibreEHR 
+Direct Messaging features with PHI in a production environment:
+
+1. the current code only supports a single shared "group" Direct Address for each LibreEHR 
+installation. Note that this model is fully compliant with the Direct Project 
+requirements for Direct messaging, but we may add additional models in the future 
+should we determine that doing so would provide a higher degree of interoperability for 
+LibreEHR users.
+
+2. the current code only sends the CCR or CCD XML data that is already available in LibreEHR; 
+these files as currently generated by existing LibreEHR code do not meet the requirements 
+of the MU2 criteria, and the current CCD files do not pass strict CDA validation tests.
+
+C. Problems Solved:
+
+1. Patient-initiated transmission of clinical data from the Report section of the Patient 
+Portal interface.
+
+2. Provider-initiated transmission of clinical data from the Report section of the Patient 
+pane in the main LibreEHR interface.
+
+3. Log all data transmissions including date/time, patient, and whether transmission 
+was initiated by the patient through the Patient Portal or by an LibreEHR user through the 
+main interface.
+
+4. Receive Direct messages from other sources.
+
+D. How it Works:
+Once configured, LibreEHR will interface with a phiMail Direct messaging server to complete the
+required message transactions. The phiMail platform is described on the EMR Direct website, 
+http://www.emrdirect.com and http://www.emrdirect.com/phimail-faq.html.
+
+E. What you need before enabling Direct Messaging in LibreEHR:
+
+1. Test Mode: Developers may request a complimentary test address at 
+https://www.emrdirect.com/subscribe-developer  
+Access to a sandbox server is available for testing and development purposes.
+
+2. Production Mode: Healthcare provider users should begin by signing up for a production 
+Direct messaging account with EMR Direct by registering at https://www.emrdirect.com/subscribe
+
+Subscribers will receive the username, password, and server address information with which to 
+configure LibreEHR.  
+
+F. How to enable the Direct Messaging Features in LibreEHR:
+Setup of phiMail Direct messaging Service is done in the Administration::Globals::Connectors 
+tab
+
+1. Check the "Enable phiMail Direct Messaging Service" checkbox.
+
+2. Enter the Server Address, Username, and Password provided to you. The server address
+will be of the form "ssl://servername.example.com:32541" - replace the hostname and port
+with the values provided to you by EMR Direct. The Username is your Direct Address. Do not 
+enter the server URL into your browser address bar, as this will not work.
+
+3. Specify the LibreEHR user who will receive notification of new incoming Direct messages. 
+Enter their LibreEHR username in the notification user field.
+
+4. Specify the interval for automatic message checking; we suggest 5 or 10 minutes as a
+starting point, but installations processing a large number of Direct messages may want a 
+shorter interval. To disable automatic message checking through LibreEHR's background service
+manager, set the interval to 0 (zero). Disabling automatic checking would be appropriate 
+if message checking is managed through another mechanism, such as a system cron job.
+
+5. Optionally check "phiMail Allow CCD Send" and/or "phiMail Allow CCR Send" to enable
+the Transmit feature for these data types. If you do not select at least one of these,
+LibreEHR will operate in a receive-only mode.
+
+6. Click the "Save" button.
+
+7. Confirm that a valid Notification Email Address is set in the Administration::
+Globals::Notifications tab to receive error notifications from the Direct Messaging service.
+
+8. Install the EMR Direct trust anchor certificate.  
+
+Note: This is *not* your Direct certificate; it is the trust anchor for the SSL 
+certificate issued to our servers, and is used only to validate the SSL certificate 
+presented by the phiMail server on the other side of LibreEHR's connection.  Your Direct private
+key and certificate are managed by the phiMail Server and are not installed in LibreEHR.
+Your Direct certificate is made availabe for your review by EMR Direct, but you will not
+need to install it anywhere.
+
+For added security, the trust anchor for the phiMail Server should be installed in the LibreEHR 
+installation tree at:
+
+[installation_root]/sites/[site_id]/documents/phimail_server_pem/phimail_server.pem
+
+This phimail_server_pem directory and its contents should be readable by the the 
+webserver process, but only writable by trusted local users. The certificate file 
+itself must be PEM encoded. You can identify a PEM encoded certificate file because 
+it begins with the text "-----BEGIN CERTIFICATE-----". Although LibreEHR will connect 
+to phiMail servers without installing this certificate, this is a required configuration 
+step for all production  accounts to ensure that you are connecting to the correct 
+server. You can obtain the correct certificate at the following URLs:
+
+  a. Test accounts: http://certs.emrdirect.com/EMRDirectTestCA.crt
+     Important: Don't forget to rename the file to phimail_server.pem and install it
+     in the correct directory.
+
+  b. Production accounts: https://www.phicert.com/certs/phiCertDirectRootCA.crt
+     Important: The production root must be converted to PEM format as follows:
+     $ openssl x509 -in phiCertDirectRootCA.crt -inform DER -out phimail_server.pem
+     Don't forget to install phimail_server.pem in the correct directory. As an added
+     security measure, please call us to confirm the thumbprint on this certificate.
+
+G. Debugging background connections to the server.
+
+You may review the connection activity to the server by Selecting Administration::Other::Logs,
+selecting "direct-message" in the "Name of events:" drop-down menu, and clicking "[Refresh]".
+If the background service is succesfully connecting, you will see "message check completed"
+events in the log as well as any message related entries (see below for instructions to
+view more detailed message related status information). If you see no entries, make sure that
+the background service is enabled (See F.4 above). If you see "could not connect to server"
+entries, each entry will also contain an error code:
+
+  C1: phiMail is disabled in the global configuration. Fix: enable.
+  C2: the phiMail server URL entered in the global configuration is invalid. Fix: Confirm
+      the URL has been entered correctly. It should be of the form 
+      "ssl://server.example.com:32541".
+  C3: unable to create stream context. Fix: Usually this is because the server certificate 
+      file installed in F.8 above is not the correct certificate or is in the wrong format.
+  C4: failed to open connection. Fix: Confirm you Internet service and local DNS servers are
+      online and your firewall is not blocking connections to the phiMail Server.
+
+H. Checking the status and history of the Direct Messaging Service in LibreEHR:
+Administrators may view the status of the service by Selecting Reports::Services::Background 
+Services from the main LibreEHR left navigation bar. The "View Log" link on this page or 
+Reports::Services::Direct Message Log will open the messaging history log showing each message 
+sent or received and the current status of that message (Received, Sent, Delivery Confirmed, 
+or Failed).
+
+I. Note of message status messages: Receiving message status updates requires that Direct message
+checking be enabled. When receiving messages, the phiMail back-end is fully compliant with the 
+Direct messaging protocols to notify the sender and provide final delivery confirmation, but 
+please note that  many other Direct providers do not yet support these features. If a message 
+is sent to a recipient using one of these other systems, LibreEHR probably won't ever receive a 
+final delivery confirmation for that message.
+
+J. How to use the Direct Messaging Features in LibreEHR:
+
+1. Sending:
+When the phiMail Direct Messaging service is enabled, an additional "Transmit" button will
+appear in the Continuity of Care Record (CCR) and/or Continuity of Care Document (CCD) block 
+of the Reports section in both the Patient Portal and the Patient pane of the main provider 
+interface. 
+
+To transmit a CCR or CCD, first click the "Transmit" button. This will open a small dialog 
+immediately below the button with a form field to enter the intended recipient's Direct Address. 
+Clicking "Transmit" again will hide the dialog.
+
+A Direct Address should have the same form as a regular email address, e.g. 
+[email protected]. Enter the address in the field and click the "Send" button 
+immediately to the right of the field. Only a single recipient may be specified in the field.
+The Send button will be temporarily disabled while LibreEHR is communicating with the phiMail 
+server. This will only work for properly-configured Direct addresses. Attempts to send to a 
+regular email address or Direct address outside of our test mode "trust sandbox" will fail
+during testing. Production accounts have wide interoperability with other Direct service
+providers. Should you encounter a trust community with which LibreEHR does not interoperate,
+please let us know at [email protected].
+
+LibreEHR will then display a status message immediately below the Address field, the 
+success or failure of the message transmission, or an error message. If the message is
+successfully submitted to the server, the Address field will be cleared to prevent accidental
+re-transmission. If multiple recipients are required, the next recipient can now be entered.
+
+If you receive an error message, it will be followed by an error code. For a discussion
+of error codes beginning with the letter "C" please see section G above. Error codes
+beginning with "EC" are listed here:
+
+  EC 1: phiMail disabled in global configuration. Fix: enable.
+  EC 4: authentication failure. Fix: The Username and Password entered in the
+        global configuration must be corrected.
+  EC 5: request to add text failed. Fix: Confirm total message length < 5MB.
+  EC 6: problem sending the text. Fix: Confirm your local network connectivity is stable.
+  EC 7: request to add clinical document failed. Fix: see EC 5.
+  EC 8: problem sending the clinical document. Fix: see EC 6.
+
+2. Receiving:
+When the phiMail Direct Messaging service is enabled, and message checking is enabled either 
+through the background services manager of another mechanism, LibreEHR will automatically process 
+message status updates and new messages. Status updates will be reflected immediately in the 
+Direct Messaging log. Additionally, if a "Failed" notification is received for a previously sent 
+message, a regular email message will be generated to the Notification Email Address specified 
+in the Notifications tab of the Global Settings panel (accessed by selecting Administration::
+Globals from the main left navigation menu).
+
+New Direct messages will be processed as follows. A new "Patient Note" will be generated and 
+sent to the phiMail notification user specified in the Connectors tab of the Global settings. 
+The patient note will contain information about the message, including any text at the beginning 
+of the message from the sender. Any attachments (and any non-text content) will be automatically 
+converted to separate LibreEHR Documents, which will be referenced in the new Patient Note.  
+The Documents and the Patient Note are initially created without an assigned patient. 
+
+At this time, the envisioned workflow is that the notification user will review the message text
+and any included Documents to determine which patient the content belongs to and will then set the 
+patient using the existing Patient Note interface for choosing a patient. Once the patient is sent, 
+the Patient Note can be forwarded to another provider or staff member as appropriate using the 
+existing forwarding mechanism for Patient Notes. The unassigned Documents can be viewed by Selecting 
+Miscellaneous::New Documents from the main left navigation menu, which opens a Documents list. Once 
+the specified document is opened, the user can optionally categorize the document and, when 
+appropriate, assign the document to a specific patient using the "Move to Patient #" feature in the 
+Documents interface.
+
+
+Trademark Notice: phiMail is a registered trademark of EMR Direct.
+
+Copyright (c) 2013-2014 EMR Direct.
+
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		Placeholder file for adding special configuration notes.