EMERSE Virtual Machine Guide

Once the virtual machine (VM) is up and running, launching EMERSE should be simple. The servers that run EMERSE should already automatically start up, so all you need to do is launch the browser (preferably Chrome). This can be found on the Linux VM under Applications → Internet → Chrome or by double clicking on the Chrome icon on the Desktop. Then, simply go to the URL:

username: emerse
password: demouser

This username and password combination are used throughout the VM, for the Linux OS, for the EMERSE application, for Oracle, etc.

In addition to the main EMERSE interface that most users will interact with, there are other areas that may be worth exploring.

EMERSE uses Apache Solr for indexing documents. Solr can handle several file formats, but not all file formats are supported. If your documents are already plain text (.txt) or HTML (.html or .htm) then no additional conversion is required, and you can skip this section.

Files in other formats should be converted to either plain text or HTML. HTML is ideal for files with formatting (e.g., tables, bold text, etc) since HTML files can generally preserve that formatting whereas plain text files will not.

If file conversion is needed because the documents are not already in plain text (.txt) or HTML (.html or .htm) format, there are various ways to convert files, including several commercial options. The following directions were made for the Mac, using tools already provided with the Mac to perform file conversions. Other file conversions options are available for Windows machines. On Mac OS X there is a file converter built into the operating system. This can convert Microsoft Word documents (.doc or .docx) into HTML files which can then be imported into EMERSE. This file converter can also transform RTF documents into HTML. The following directions describe a simple approach for converting Word documents into HTML. Similar steps would be needed for converting RTF into HTML.

The converted files should all have a .html extension. You can now either delete or remove the original files, or simply copy the new HTML files to a new folder to separate them out. Note that you can sort the folder by Kind to get all of the HTML files together in the list, which makes it easier to just select that file type

On the Mac it is also possible to convert PDF files, but the process is a bit more involved. This can be done using the Automator app, and developing a workflow. The PDF conversion component in the Automator app can be found under the PDFs → Extract PDF Text workflow. One can use this Automator workflow to save the files in RTF format, and then follow the directions about using the textutil app to convert RTF to HTML.

EMERSE was designed to incorporate data from electronic health records. As such, it was designed to include documents that are connected to patients via a medical record number (MRN). Documents can have various sources (e.g., Radiology, Pathology, Epic, etc), and each document might have different metadata depending on the source (e.g., date, author, document type, clinical service, authoring clinician, etc). EMERSE also expects to have a list of all patients for which documents are loaded.

While this was the intended use, it is still possible to include documents even if they are not actually tied to a known patient. In such a case, when setting up the data import you will need to essentially create a fake “patient” MRN to connect to the document as well as filler data about the patient name, date of birth, sex, etc. This should not affect the performance of the system.

Following are details about the data files needed to import your own data into the VM, their expected structure, and contents. Four files in Microsoft Excel (.xlsx) are required to define the metadata, and a separate folder (simply called documents) is required to hold the actual documents that will be indexed.

It is probably easiest to create these Excel files on your own (host) computer and then move them to the virtual machine (details for moving the files are provided within this document). However, if there is a desire to open/view Microsoft Excel xlsx files on the Linux virtual machine, this can be done using a free program called OpenOffice, which has been pre-installed on the virtual machine on which EMERSE is distributed.

There are four components for which you need to provide data: the document source names, the metadata about the document sources, the document metadata, and the patient data. These four files are called:

A fifth file is required by the loading scripts, but does not require any editing. It is called solrmap.xlsx and it should already be located on the virtual machine in /app/data/emerse_pdi_job/. In the event that it is missing or deleted, it can simply be re-created by pasting the table below into an Excel spreadsheet and naming it solrmap.xlsx.

The contents of the solrmap.xlsx file:

The first file to define is related to the document sources. In EMERSE, documents are displayed according to source system which helps distinguish where a document came from. In general, a source can be thought of as a source system, such as a radiology system, a pathology system, or the EHR itself. You can include just one source, or you can have multiple sources. These sources are defined in the file called:

There are 2 columns where the metadata about the document sources should be defined. Each is explained below. The order in which the sources are displayed in the EMERSE “Overview” section (from left to right) are defined by the order in which they are listed in this spreadsheet (from top to bottom).

Example documentSources.xlsx spreadsheet:

For every document source there are, at a minimum, two required metadata fields (other than the text of the document itself). These are the date in which the clinical encounter occurred (often called the service date or encounter date), and the date when the document was last updated. However, each document source may have additional metadata that could be displayed for the users and can include items such as the clinical department, the clinician’s name who authored the document, or even the document/note type (e.g., progress report, discharge note, etc.). The types of metadata are defined in this Excel spreadsheet which is called:

This file contains 3 columns, described below. The order in which these elements are listed (top to bottom) are the order in which they will appear in EMERSE (from left to right), with the caveat that the text snippet showing any text found for a note will always appear on the left, and, the order is only considered within each document source.

The full list of elements for the nameFromDocumentSheet are defined in the table below. Note that these names are essentially placeholders, so even if a name appears to have a specific intended use, it can be overridden simply by providing a new display name. There are also two data types supported, date and text. Note that the table below is just for information to define what the elements are, it is not meant to be a spreadsheet used for importing data into EMERSE.

*This is only provided for those wishing to look deeper into the underlying Solr configuration to understand how the fields are being mapped.

Every document indexed will have its own metadata which relates to the types defined in the sourceMetadata.xlsx sheet. For example, if service is defined in the sourceMetadata.xlsx sheet, then the specific metadata elements for a document could be ‘cardiology’, ‘pulmonology’, ‘rheumatology’, etc.

The file in which these document-specific metadata are defined is called:

Every row in this spreadsheet represents a single document to be indexed. Every document must have a unique identifier, and must be connected to a patient through a medical record number. The filename of the document to be loaded (from the documents folder) must also be specified here. For the metadata elements related to the documents that will be displayed in EMERSE, each element has its own column in the spreadsheet, regardless of whether or not any metadata for that element actually exists for the documents. The specific cells related to those columns should be left blank if no metadata exists. The following table details the elements present in this spreadsheet.

*Other columns should appear, as defined elsewhere in the previous table, but are not shown here due to space limitations. In addition, the order of the columns should not change, and all columns must be in this spreadsheet even if no metadata exist for them.

Every document that is imported must be associated with a patient through a medical record number. A patient can have one or (more likely) many associated documents. Patients are defined in a simple Excel spreadsheet called:

In this spreadsheet every patient is listed in a row with some additional metadata about them including date of birth, sex, race, ethnicity, and, most importantly, medical record number (MRN). Ethnicity is not required, but can be added if desired. Race, sex, and ethnicity must be coded according to the EMERSE lookup tables, which can be viewed with the SQL Developer tool. (See section on Oracle database). These lookup tables can also be modified for local needs, but for the purposes of this demonstration you can just map your data to the existing codes. The codes, in additional to an example patient spreadsheet, are described below.

The following directions were created for a Mac, but the process should be very similar for Windows. The directions below were based on those found at helpdeskgeek.com:

http://helpdeskgeek.com/virtualization/virtualbox-share-folder-host-guest/

The virtual machine is essentially another computer (operating system) running on your computer. The VM is often called the guest and the main operating system on your computer is called the host. As such the guest OS has it’s own disk space and can’t “see” the files on your main (host) computer unless you set it up so that they can communicate. Once this is set up you can then copy files from the host OS to the guest VM. In these directions, the term “folder” and “directory” are used essentially interchangeably.

There are several ways to moves files to the VM for data import into EMERSE, and the directions below describe only one such approach. Depending on your setup, the default VM environment may not able to connect to the outside Internet, so using services connected to the internet for moving files may not be possible. There are ways to configure the VM to allow for internet connections, but this is not described here. Further, if the data destined for import contains sensitive patient information, it might not be ideal to move them via the internet anyway.

Then enter the password: demouser
Close the Terminal window.
At this point if you open the vboxsharedfolder on the Linux OS you should be able to see any files that are in the equivalent folder on the Mac Desktop.

If it is still not possible to access the vboxsharedfolder on the Mac from the Linux OS, it may be necessary to verify that the privileges on the folder on the Mac side are set correctly. To check, click once on the folder (on the Mac side) to select it, then press command-I for Get Info. Look at the bottom of the small info window where it shows Sharing & Permissions and make sure that for "everyone" it displays Read only or Read & Write. See screen shot below for an example.

Once the shared folder has been created, and the correct ‘permissions’ have been granted for access (see the prior section, “Setting up a shared directory for copying data to the VM”), you can then copy the data files to the VM. The directions for this are below.

documentMetadata.xlsx
patientMetadata.xlsx
sourceMetadata.xlsx
documentSources.xlsx
documents/ folder

If other files or folders with the same name are already there, replace them with the ones you are moving (or delete the older ones before copying over the new ones).

Make sure that the solrmap.xlsx file remains in the emerse_pdi_job folder. This file does not need to be edited but must be there for proper data import to occur. If it is not there, copy it there. Details about the file, and how to create a new one if necessary, are provided elsewhere in this document.

The directions in this section are based on the assumption that you have already created your metadata files for import and have the documents located in the documents folder as described in the previous sections of this manual. The following scripts will clear out the existing data in the system, load in the new data, and then index the documents so that they are ready to be searched. For this to work, you will need to first make sure that you have copied the updated metadata files into the emerse_pdi_job folder, and in that same emerse_pdi_job directory you have all of the documents that need to be indexed, located within a directory called documents. This includes:

documentMetadata.xlsx
patientMetadata.xlsx
sourceMetadata.xlsx
documentSources.xlsx
documents/ folder

The runPatientLoadJob.sh script loads the patient data into a database table. The patient data must then get copied from that database table into a Solr index called patient (used to show demographic charts). This copying will normally occur on a scheduled basis by EMERSE itself but to force the copying immediately (so that the changes can be seen immediately), follow the directions regarding Rebuilding Patient Indexes. For the standard setup on the virtual machine, use the following credentials to login:

username: emerse
password: demouser

You can check to see if the index has been updated by looking at the Solr admin page, by looking at the Last Modified time under Statistics. It won’t say 'complete', but it should report a very recent time frame, such as within the last few minutes. If not, wait until it is complete. Refresh the page from time to time to see if the Last Modified status has changed. Note, however, that erasing the prior data before loading the new data (which occurs when running the reload.sh script) will also result in a recent time frame for the Last Modified time. Therefore, also check that the Num Docs for the patient index matches the total number of patients added to the system.

Once this is complete, it is time to stop and then start Tomcat and Solr (password demouser will be required for each command) from the Terminal:

It may be necessary to wait a few minutes minutes until everything fully starts up again before trying EMERSE.

The Synchronize function should also have updated the patient counts as shown in the EMERSE UI. However, if for some reason it does not show up you may have to wait about 30 minutes for the Spring Scheduler within the app itself to auto-update these stats periodically. This also may require logging out of and then logging back into EMERSE for the change to be displayed in the application.

The virtual machine currently has the date range for the documents “hard-coded”, meaning that they will not change even if the actual imported documents have a different date range. This is a configuration option and can be changed. This won’t matter unless a search was done for a specific date range, otherwise EMERSE will always search across all documents regardless of dates. Nevertheless, it is possible to change this so that the system will dynamically change the date range to accurately reflect the dates of the documents. The following directions detail how this can be done:

The code that reads this properties file and updates the dates is embedded in the Java Virtual Machine (JVM) so it can’t be run automatically. However, it should update on its own about every 30-60 minutes once the properties file has been edited and saved, and Tomcat has been restarted.

New data (patients and documents) can be added after an initial loading of data. To do this, clear out the prior two spreadsheets (documentMetadata.xlsx and patientMetadata.xlsx) that were used to load the previous data. Also clear out the documents folder that contained the previous documents that needed to be loaded. Then add in just the new data to be loaded (new patients, new documents, and new document metadata) into the two spreadsheets, and add the documents to the documents folder. Then, simply go back to the directions in the section: “Using the scripts to load data into EMERSE” but run just these two scripts:

And finally, stop and start the servers:

For demonstration purposes it may be useful to include documents that are in PDF format since clinical documents are sometimes stored in that format. The directions below do not cover all aspects of handling PDFs, since it can be a complex task, but some basic instructions are provided. Also note that, as described elsewhere in this manual, this VM is provided primarily for demonstration purposes so if you plan to include any documents that contain real protected health information it is best to check with your local compliance and IT groups for guidance.

The following figure provides a high-level overview of the process for incorporating PDFs into the EMERSE VM, with more details described below.

Note that the location of the PDF directory in the example diagram above is not necessarily where that directory must be located. This is just for demonstration purposes. EMERSE has no built-in expectation of where PDFs should be located, but including them within the Tomcat webapps directory is a simple way to make them accessible to the web application.

The first step for incorporating a PDF into EMERSE is to determine if the PDF contains actual ‘text or just an image (a scan/photograph) of text. PDFs created from software such as Microsoft Word should already have the text incorporated inside the PDF, but if a document was scanned then it will likely contain only an image of the text. One way to tell the difference is to try to select, highlight, and copy the text inside the PDF and paste it into a word processor. If you can select, copy and paste it, then the text is already incorporated. If the text can’t be selected, copied, and pasted, then it is likely only an image. If the text is an image then you may need to use optical character recognition (OCR) software to turn the pictures of the text into actual computer text that can be copied or, in the case of EMERSE, extracted and indexed. There are various options for OCR, including one built into Adobe Acrobat, and there is also the open source Tesseract software that was developed by Google. OCR is not built into EMERSE.

If the text is already incorporated into the PDF then the next step is to extract the text and convert it to a document that Solr can handle natively, which would be either HTML or TXT. Details for how this can be done on a Mac are described in the section “Preparing documents for import: File Conversion.” One possible approach is to convert PDF to RTF and then RTF to HTML (to preserve any formatting), or to even simply convert PDF to TXT and just use the plain text file for importing into Solr. Note that Apache also provides a tool for extracting text from PDF (called “Tika”) that can work with Solr, but it is not an automated process—​in other words, you can’t just push a PDF document to Solr like you could a plain text or HTML document.

For the following example of how these PDFs can be incorporated into EMERSE, assume that the PDF text has been extracted and converted to a similarly named HTML document. Each PDF document should ideally have a name with no spaces (so it can easily be displayed within a web browser).

Store all of the PDF documents in a directory called PDFs (it can be any name, but for this example that is the name used). Then, in the corresponding HTML document with the extracted text, add a link to the original PDF from the HTML document. For example ssume that the original PDF is called document_12345.pdf and the corresponding HTML document with the extracted PDF text is called document_12345.html. The PDF document will be stored in a directory called PDFs (location of the directory is defined below), and the corresponding HTML document will be in the documents directory, which is the one used for importing the documents into Solr.

Inside the HTML document, within the body of the text, add a link to the PDF, for example:

Note that adding this link/URL could be done automatically with some simple coding such as identifying the <body> tag and appending the URL immediately after that.

At this point, the documents and metadata can be loaded into EMERSE using the directions provided elsewhere in this manual. The only other thing that needs to be done is to move the directory of PDFs (called PDFs) over the to virtual machine. That directory should be copied to:

/app/software/emerse/apache-tomcat-x.x.xx/webapps/emerse/

Currently, EMERSE can highlight the extracted text in the HTML document that EMERSE indexed, but EMERSE cannot highlight the corresponding text within the PDF itself. However, linking to the original PDF file containing the text should still be useful for users, and a user could still use the “Find” command (control-F on Windows, command-F on Mac) within the web browser or the PDF viewer to look for the text within the PDF. This can still be a timesaver.