diff --git a/README.md b/README.md index 13a91c1..4edd030 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,14 @@ # DeepPhe Stream Multi-Container Stack - release branch -This multi-container docker stack consists of the following 2 containers: +This multi-container docker stack consists of the following 2 contaienrs: -- 1: `dphe-stream-nginx` (reverse proxy and load balancer) -- 2: `dphe-stream` (document and patient summary REST API) +- 1 : `dphe-stream-nginx` (reverse proxy) +- 2 : `dphe-stream` (document and patient summary REST API) ## Changes needed to make a release -- 1: Place the source code zip file, for instance `v0.1.0-cr-release.zip`, to the directory `dphe-stream`. This zip file will be used to build the `dphe-stream` docker image. -- 2: Edit the `dphe-stream/Dockerfile` and specify to use the target release version, for instance `0.1.0`. +- 1: Place the source code zip file, for instance `v0.2.0-cr-release.zip`, to the directory `dphe-stream`. And this zip file will be used to build the `dphe-stream` docker image. +- 2: Edit the `dphe-stream/Dockerfile` and specify to use the target release version, for instance `0.2.0`. ## Overview of tools @@ -17,9 +17,9 @@ This multi-container docker stack consists of the following 2 containers: Note: Docker Compose requires Docker to be installed and running first. -## Docker post-installation configurations +### Docker post-installation configurations -The Docker daemon binds to a Unix socket instead of a TCP port. By default, that Unix socket is owned by the user root and other users can only access it using sudo. The Docker daemon always runs as the root user. +The Docker daemon binds to a Unix socket instead of a TCP port. By default that Unix socket is owned by the user root and other users can only access it using sudo. The Docker daemon always runs as the root user. If you're using Linux and you don't want to preface the docker command with sudo, you can add users to the `docker` group: @@ -31,51 +31,57 @@ The log out and log back in so that your group membership is re-evaluated. If te Note: the following instructions with docker commands are based on managing Docker as a non-root user. -## Docker build +## Build docker images -### Specify authentication token +### Specify auth token -Before starting building the child images, specify the auth token in `dphe-stream/deepphe.properties`. This auth token will be used later when interacting with the REST API calls via the standard HTTP request `Authorization` header with the Bearer scheme in the form of: +Before starting building the child images, specify the auth token in `dphe-stream/deepphe.properties`. This auth token will be used later when interacting with the REST API calls via the standard HTTP request `Authorization` header with the Bearer scheme: ```` Authorization: Bearer ```` -This auth layer as a gateway will apply to all the HTTP requests before they can reach to the actual API endpoints. +This auth layer applies to all the REST API requests before they can reach to the actual API endpoints. -A default token is provided in the `dphe-stream/deepphe.propertiers` file. For greater security, it is strongly advised that you change this token to a new value for any deployed instance. +A default token is provided in the `dphe-stream/deepphe.propertiers` file. For greater security, it is strongly advised that you change this token to a new value for deployment instance. -### Build docker images +### Build `dphe-stream-nginx` and `dphe-stream` images -Under the project root directory where we can find the `docker-compose.yml`: +Next go back to the project root directory where you can find the `docker-compose.yml`: ```` -docker-compose build +docker-compose build --no-cache ```` -#### Start up services +### Vulnerability scanning for local images + +Vulnerability scanning for Docker local images allows us to review the security state of the container images and take actions to fix issues identified during the scan, resulting in more secure deployments. The `scan` command is available by default in Docker version 20.10.x and newer. + +``` +docker scan --dependency-tree --file ./dphe-stream/Dockerfile dphe-stream:0.2.0-cr +docker scan --dependency-tree --file ./dphe-stream-nginx/Dockerfile dphe-stream-nginx:0.2.0-cr +``` + +## Start up services There are two configurable environment variables to keep in mind before starting up the containers: - `HOST_UID`: the user id on the host machine to be mapped to all the containers. Default to 1000 if not set or null. - `HOST_GID`: the user's group id on the host machine to be mapped to all the containers. Default to 1000 if not set or null. -We can set and verify the environment variable like below: +We can use the default values if the ouput of the below command is 1000 for both `uid` and `gid` of the current user who's going to spin up the containers. ```` -export HOST_UID=1000 -echo $HOST_UID -export HOST_GID=1000 -echo $HOST_GID +id ```` -In security practice, the processes within a running container should not run as root, or assume that they are root. The system user on the host machine should be in the docker group, and it should also be the user who builds the images and starts the containers. That's why we wanted to use this user's UID and GID within the containers to avoid security holes and file system permission issues as well. +In security practice, the processes within a running container should not run as root, or assume that they are root. The system user on the host machine should be in the docker group and it should also be the user who builds the images and starts the containers. That's why we wanted to use this user's UID and GID within the containers to avoid security holes and file system permission issues as well. ```` docker-compose up -d ```` -This command spins up all the services (in the background and leaves them running) defined in the `docker-compose.yml` and aggregates the output of each container. +This command spins up all the services (in the background as detached mode and leaves them running) defiened in the `docker-compose.yml` and aggregates the output of each container. Make sure the port `8080` and `8181` are not already allocated, otherwise the containers would fail to start. Note: the initialization of containers takes some time, you can use the following command in another terminal window to monitor the progress: @@ -83,12 +89,13 @@ Note: the initialization of containers takes some time, you can use the followin docker-compose logs -f --tail="all" ```` + +## Interact with the DeepPhe REST API + You will have the following API base URL for the REST API container: - `dphe-stream`: `http://localhost:8080/deepphe` -## Interact with the REST API - Please remember that you'll need to send over the auth token (specified prior the docker build) in the `Authorization` header for each HTTP request: ```` @@ -165,6 +172,8 @@ curl -i -X GET http://localhost:8080/deepphe/summarizePatient/patient/patientX \ -H "Authorization: Bearer AbCdEf123456" ```` +## Manage the contaners + ### Shell into the running container Sometimes you may want to shell into a running container to check more details, this can be done by: @@ -197,14 +206,47 @@ This command stops both containers of this project and removes them as well the Note: At this time DeepPhe Stream could be run with a single container. The multi-container stack exists to facilitate addition future workflows that may require additional containers. -## Run integration tests manually +## Integration tests -Once the containers are up running, we can run some integration tests written in Python within the `dphe-stream-nginx` container manually to verify the pipeline output by submitting some sample reports to the REST API. +Once the containers are up running, we can execute some integration tests written in Python to verify the pipeline output by submitting some sample reports to the REST API. The tests will be executed against the `dphe-stream-nginx` container, which proxies the requests to the backend REST API service. -The test cases and configuration are located at `dphe-stream-dock/dphe-stream-nginx/integration-test`. If a different auth token is specified during the image creation phase, that same auth token should be specified in the `test.cfg` as well. +The test cases and configuration are located at `dphe-stream-dock/dphe-stream-nginx/integration-test`. If a different auth token is specified during the image creation phase, that same auth token should be specified int he `test.cfg` as well. + +### Run the tests manually within the container ```` docker exec -it dphe-stream-nginx bash cd integration-test/ python3 test.py ```` + +### Add more tests and run against the container + +We can also add more test cases within the `dphe-stream-nginx/integration-test` directory to improve the coverage and run the tests against the running contianers. To do so, we can create a Python virtual environment and install the dependencies: + +``` +python3 -m venv venv +source venv/bin/activate +pip install -r requirements.txt +``` + +Once the test changes are made, we can run it: + +``` +python3 test.py +``` + +### Trigger the tests via docker healthcheck + +In the `docker-compose.yml` file, uncomment the healthcheck section with configuration changes if you prefer the tests to be triggered automatically against the running container on a periodic basis. + +``` +# Uncommnet the healthcheck section with desired configuration settings to determine if the state of the container is healthy +# This healthcheck triggers the python tests based on the options: interval, timeout and start_period +# healthcheck: +# test: ["CMD", "python3", "/usr/src/app/integration-test/test.py"] +# interval: 5m30s +# timeout: 30s +# retries: 3 +# start_period: 30s +``` \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 1f664a3..7cf2077 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -5,7 +5,7 @@ services: build: context: ./dphe-stream # Build the image with name and tag - image: dphe-stream:0.1.0-cr + image: dphe-stream:0.2.0-cr hostname: dphe-stream container_name: dphe-stream init: true @@ -19,14 +19,14 @@ services: - "8181:8080" volumes: # Make log accessible on host - - "./dphe-stream/logs:/usr/src/app/v0.1.0-cr-release/dphe-stream-rest/logs" + - "./dphe-stream/logs:/usr/src/app/v0.2.0-cr-release/dphe-stream-rest/logs" networks: - dphe-stream-network dphe-stream-nginx: build: ./dphe-stream-nginx # Build the image with name and tag - image: dphe-stream-nginx:0.1.0-cr + image: dphe-stream-nginx:0.2.0-cr hostname: dphe-stream-nginx container_name: dphe-stream-nginx init: true @@ -37,6 +37,14 @@ services: ports: # Map host machine port 8080 to container port 8080 (since nginx runs as non-root) - "8080:8080" + # Uncommnet the healthcheck section with desired configuration settings to determine if the state of the container is healthy + # This healthcheck triggers the python tests based on the options: interval, timeout and start_period + # healthcheck: + # test: ["CMD", "python3", "/usr/src/app/integration-test/test.py"] + # interval: 5m30s + # timeout: 30s + # retries: 3 + # start_period: 30s volumes: # Make log accessible on host - "./dphe-stream-nginx/logs:/usr/src/app/logs" diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc10_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc10_NOTE.txt new file mode 100644 index 0000000..99a7f47 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc10_NOTE.txt @@ -0,0 +1,21 @@ +=================================================================== +Report ID.....................10,doc10 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20110301 1015 +Record Type...................NOTE +Patient DOB...................04/01/1960 + + +CLINICAL HISTORY: The patient is a 51 year old woman with newly diagnosed invasive lobular carcinoma of the left breast. She is ER positive, PR positive and HER2/NEU negative. + +Briefly the patient was diagnosed in January of 2010 with metastatic breast cancer of the right breast. She was stage 2A (T1, N1, M0). She received chemotherapy with Adriamycin and Carboplatin followed by Abraxane. She underwent a right mastectomy with axillary lymph node dissection on 7/10/10. The surgical margins were negative and she received radiation therapy to the right breast and axilla area. She is being maintained on oral Tamoxifen. + +INTERIM HISTORY: She noticed a small nodule in her left breast. Mammography obtained on 1/31/10 revealed a firm mass in the lower outer left breast position that measures 1x2 cm. Ultrasound performed on 1/31/10 showed a 1.1x1.2x2.1 cm hypoechoic mass at the 4 o’clock region. The mass was highly suggestive of a malignancy. She underwent a left breast segmental mastectomy with left axillary lymph node biopsy on 2/1/11. Pathology came back as stage IA (pT1a, pN0) invasive lobular carcinoma with a focus of lobular carcinoma in situ of the left breast, lower outer quadrant, 4 o’clock position. + + +Physical Exam: The patient’s physical examination shows a well healed left surgical incision. The previous incision of the right breast is without masses. There are no signs of infection, swelling or erythema. She denies any pain, fever, nausea or vomiting. + +Impression: A 51 year old woman with stage 1A (pT1a, pN0) invasive lobular carcinoma and LCIS of the left breast S/P segmental mastectomy and left axillary lymph node biopsy. + +Recommendations: She will undergo radiation therapy to the left breast. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc1_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc1_RAD.txt new file mode 100644 index 0000000..bd11b61 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc1_RAD.txt @@ -0,0 +1,22 @@ +=================================================================== +Report ID.....................1,doc1 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20100123 1045 +Record Type...................RAD +Patient DOB...................04/01/1960 + +CLINICAL HISTORY: +This is a 50 year old peri-menopausal female who underwent mammogram on 1/28/09 for a palpable lump in the right breast. Ultrasonography revealed a 1.2x3.4x5.6 cm hypoechoic mass in the upper inner quadrant at the 1 0’clock position. Ultrasonography also revealed an abnormally thickened lymph node in the right axilla which had a thickened cortex of 7 mm. She now presents for U/S guided core biopsy of the mass and the abnormal lymph node. +PROCEDURE: +Ultrasound guided core biopsy of right breast 1 o’clock abnormality with clip placement +Ultrasound guided core biopsy of right axilla abnormal lymph node with clip placement + +FINDINGS: +The right breast and axilla were sterilely prepped and draped in the usual standard fashion. First the right 1 o’clock position 5 cm from the nipple was targeted. Local anesthesia was obtained with 2% xylocaine. A small skin incision was made. Under ultrasound guidance from a medial approach, 2 passes with a 14 gauge biopsy device were performed and sent to pathology. A clip was placed. +Then attention was turned to the right abnormal axillary lymph node. Local anesthesia was obtained with 2% xylocaine. A small skin incision was made. Under ultrasound guidance from an inferomedial approach, 2 passes with a 14 gauge biopsy device were performed and sent to pathology. A clip was placed at the site of the biopsy. +The wounds were cleaned and dressed. The patient tolerated the procedure well, and there were no complications. +Post procedure mammogram of the right breast demonstrated adequate clip placement. +IMPRESSION: +Uncomplicated ultrasound guided core biopsies of the right breast at the 1 o’clock position and abnormal right axillary lymph node. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc2_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc2_SP.txt new file mode 100644 index 0000000..f2c9033 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc2_SP.txt @@ -0,0 +1,38 @@ +=================================================================== +Report ID.....................2,doc2 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20100123 1315 +Record Type...................SP +Patient DOB...................04/01/1960 + + + +CLINICAL HISTORY: +This 50 year old peri-menopausal female is S/P ultrasound guided core biopsy of a suspicious lump in the right breast and an abnormal axillary lymph node. + + + + +FINAL DIAGNOSIS: +PART 1: RIGHT BREAST ULTRASOUND GUIDED CORE BIOPSY +A. INFILTRATING DUCTAL CARCINOMA, NUCLEAR GRADE 3 +B. FOCAL DUCTAL CARCINOMA IN SITU, NUCLEAR GRADE 2 + +PART 2: RIGHT AXILLARY LYMPH NODE ULTRASOUND GUIDED CORE BIOPSY +A. METASTATIC CARCINOMA INVLOVING LYMPH NODE CORES + + +IMMUNOHISTOCHEMISTRY: + +RESULT H-SCORE + +ESTROGEN RECEPTOR - NEGATIVE 0 + +PROGESTERONE RECEPTOR - NEGATIVE 0 + +HER2/NEU - NEGATIVE 0 + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc3_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc3_NOTE.txt new file mode 100644 index 0000000..79de7d8 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc3_NOTE.txt @@ -0,0 +1,24 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20100131 1015 +Record Type...................NOTE +Patient DOB...................04/01/1960 + +CLINICAL HISTORY: +This is a 50 year old peri-menopausal female with clinical stage 2A (T1,N2,M0) triple negative infiltrating ductal carcinoma and DCIS of the right breast. An enlarged right axillary lymph node was biopsied and found to be positive for metastatic disease. MRI revealed a tumor 1.9 cm in diameter. She presents now to discuss options for treatment. + +INTERIM HISTORY: +Patient seen post biopsy for evaluation and management of newly diagnosed infiltrating ductal carcinoma of the right breast with a focus of DCIS. She underwent a U/S core biopsy of the right breast and lymph node on 1/23/10 which revealed infiltrating ductal carcinoma. Breast MRI on 1/25/10 demonstrated a right breast malignancy at the 1 o’clock position measuring 1.2x3.4x5.6 cm. MRI also showed a left axillary lymphadenopathy. MRI of the left breast was without malignancy. PET/CT on 1/26/10 showed no evidence of distant metastases. +Physical Exam: Well appearing female in NAD +VS: BP 120/80, Pulse 71, Temp 97.0 +HEENT: NC/AT, PERRL, EOMI, sclera non-icteric +Neck: Supple, no masses, thyroid not enlarged +LUNGS: CTA, No wheezes, rales, rhonchi +COR: RRR, No murmurs, rubs or gallops +ABD: Soft, non-tender, non-distended, No HSM. +EXT: Good pulses, No clubbing, cyanosis or edema + +IMPRESSION: +On review of the patient’s screening and diagnostic imaging and biopsy results she has a stage IIA (T1,N2,M0) infiltrating ductal carcinoma of the right breast with metastatic lymph node in the right axilla. She will be treated with neoadjuvant chemotherapy consisting of Adriamycin and Carboplatin for 4 cycles followed by weekly Abraxane. We will obtain a mammography midway through therapy to assess tumor response. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc4_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc4_NOTE.txt new file mode 100644 index 0000000..6ef82a3 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc4_NOTE.txt @@ -0,0 +1,21 @@ +=================================================================== +Report ID.....................4,doc4 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20100531 1145 +Record Type...................NOTE +Patient DOB...................04/01/1960 + +DIAGNOSIS: Stage 2A (T1,N2,M0) infiltrating ductal carcinoma of the right breast triple negative. +INTERIM HISTORY: Patient returns for ongoing management of biopsy proven right breast cancer with axillary lymph node metastasis. Her initial visit was on 1/21/2010. Breast examination at that time was significant for a 2 cm palpable lump in the upper inner quadrant of the right breast at the 1 o’clock position. She also had multiple abnormally enlarged right axillary lymph nodes. She has completed 4 cycles of Adriamycin and Carboplatin. She is currently undergoing therapy with Abraxane and has completed 9 of 12 cycles. She has tolerated her chemotherapy well without nausea, vomiting or diarrhea. Breast MRI on 5/25/10 revealed the mass at the 1 o’clock position measuring 1.0x2.9x3.5 cm from previous 1.2x3.4x5.6 cm. The metastatic right axillary lymph node now measures 4.0 mm from previous 7.0 mm. PET/CT on 5/26/10 showed no evidence of distant metastases. +Physical Exam: Well appearing female in NAD +VS: BP 120/80, Pulse 72, Temp 97.2 +HEENT: NC/AT, PERRL, EOMI, sclera non-icteric +Neck: Supple, no masses, thyroid not enlarged +LUNGS: CTA, No wheezes, rales, rhonchi +COR: RRR, No murmurs, rubs or gallops +ABD: Soft, non-tender, non-distended, No HSM. +EXT: Good pulses, No clubbing, cyanosis or edema + +IMPRESSION: +Patient has had a partial response to neoadjuvant chemotherapy for triple negative infiltrating ductal carcinoma of the right breast. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc5_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc5_SP.txt new file mode 100644 index 0000000..1b943b4 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc5_SP.txt @@ -0,0 +1,41 @@ +=================================================================== +Report ID.....................5,doc5 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20100710 1015 +Record Type...................SP +Patient DOB...................04/01/1960 + +CLINICAL HISTORY: +This 51 year old peri-menopausal female is S/P neoadjuvant chemotherapy for infiltrating ductal carcinoma of the right breast with left axillary lymph node metastasis. Recent imaging showed significant tumor shrinkage. She was admitted for right breast mastectomy with axillary lymph node dissection. + +FINAL DIAGNOSIS: +PART 1: RIGHT BREAST MODIFIED RADICAL MASTECTOMY +A. INFILTRATING DUCTAL CARCINOMA IN THE UPPER INNER QUADRANT, 1.3 CM IN GREATEST DIMENSION ASSOCIATED WITH MICROCALCIFICATIONS, NUCLEAR GRADE 3 +B. FOCAL DUCTAL CARCINOMA IN SITU, 0.1 CM IN DIAMETER WITHOUT CALCIFICATIONS, NUCLEAR GRADE 2 +C. SURGICAL MARGINS ARE NEGATIVE + +PART 2: RIGHT AXILLARY LYMPH NODE DISSECTION +A. TWO OUT OF 10 AXILLARY LYMPH NODES POSITIVE FOR METASTATIC CARCINOMA (2/10) +B. LARGEST METASTATIC TUMOR MEASURES 2 MM +C. NO EXTRACAPSULAR EXTENSION IS IDENTIFIED + + +IMMUNOHISTOCHEMISTRY: + +RESULT H-SCORE + +ESTROGEN RECEPTOR - NEGATIVE 0 + +PROGESTERONE RECEPTOR - NEGATIVE 0 + +HER2/NEU - NEGATIVE 0 + + +T STAGE, PATHOLOGIC: pT1 +N STAGE, PATHOLOGIC: pN2 +M STAGE, PATHOLOGIC: pM0 + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc6_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc6_NOTE.txt new file mode 100644 index 0000000..2f37b01 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc6_NOTE.txt @@ -0,0 +1,14 @@ +=================================================================== +Report ID.....................6,doc6 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20100830 1115 +Record Type...................NOTE +Patient DOB...................04/01/1960 + + +CLINICAL HISTORY: This is a 51 year old peri-menopausal female with stage 2A (T1 N2 M0) infiltrating ductal carcinoma of the right breast with right axillary lymph node metastases. She is ER negative, PR negative and HER2 negative. She is status post 4 cycles of Adriamycin and Carboplatin followed 12 cycles of Abraxane. She underwent a right breast modified radical mastectomy and right axillary lymph node dissection on 7/10/10. She was started Tamoxifen on 7/30/2010. +INTERIM HISTORY: Her surgical incision is completely healed. She has no redness, erythema, irritation or signs of infection. She underwent a chest CT for radiation therapy planning which revealed no evidence of any lymphadenopathy in the visualized field. There were post-surgical changes in the right breast and right axilla. No evidence of metastatic disease. She received radiation to her right breast with additional treatment to the tumor bed. +On physical exam she looks and feels well. VSS. Cardiac exam reveals a normal S1 and S2 without murmurs, rubs or gallops. Lungs are clear to auscultation without wheezes, rales or rhonchi. Abdomen is soft, non-tender without hepatosplenomegaly. Extremities are without clubbing, cyanosis or edema. +IMPRESSION: +Patient is a pleasant 51 year old female with stage 2A (T1,N2,M0)infiltrating ductal carcinoma of the left breast with left axillary lymph node metastases S/P neoadjuvant chemotherapy and radiation therapy. She will continue on Tamoxifen. She has no evidence of disease and we will see her in 6 months. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc7_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc7_NOTE.txt new file mode 100644 index 0000000..b4c1609 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc7_NOTE.txt @@ -0,0 +1,22 @@ +=================================================================== +Report ID.....................7,doc7 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20110201 1015 +Record Type...................NOTE +Patient DOB...................04/01/1960 + + +CLINICAL HISTORY: The patient is a 51 year old woman who presents for 6 month follow up visit for history of stage IIA (T1, N2, M0) infiltrating ductal carcinoma of the right breast with metastatic left axillary lymph nodes. ER negative, PR negative and Her2 negative. + +Briefly the patient was diagnoses a year ago in January of 2010 with metastatic breast cancer of the left breast. She received chemotherapy with Adriamycin and Carboplatin followed by Abraxane. She underwent a right mastectomy with axillary lymph node dissection on 7/10/10. The surgical margins were negative and she received radiation therapy to the right breast and axilla area. She is being maintained on Tamoxifen and comes in for follow up. + + +INTERIM HISTORY: She has been noticing an increase in size of a small nodule in her left breast. Mammography obtained on 1/31/10 revealed a firm mass in the lower outer left breast position that measures 1x2 cm. Ultrasound performed on 1/31/10 showed a 1.1x1.2x2.1 cm hypoechoic mass at the 4 o’clock region. This mass is highly suggestive of a malignancy. + + +Physical Exam: The patient’s physical examination demonstrates a firm round mass in the lower outer quadrant of the left breast. The rest of her examination reveals a well healed surgical incision of the right breast. The axillary wound is well healed. No signs of bruising and no infection are noted. She denies any pain, fever, nausea or vomiting. + +Impression: A 51 year old woman with stage 2A infiltrating ductal carcinoma of the right breast S/P chemotherapy, mastectomy and radiation comes in with a new left breast nodule. She will undergo an ultrasound guided core biopsy of the mass. + +Recommendations: She will undergo an ultrasound guided core biopsy of the mass. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc8_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc8_SP.txt new file mode 100644 index 0000000..b644bcb --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc8_SP.txt @@ -0,0 +1,38 @@ +=================================================================== +Report ID.....................8,doc8 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20110203 1230 +Record Type...................SP +Patient DOB...................04/01/1960 + + + +CLINICAL HISTORY: +A 51 year old woman with A history of stage 2A infiltrating ductal carcinoma of the right breast S/P chemotherapy, mastectomy and radiation. She now has a suspicious lump in the right breast and an abnormal axillary lymph node. + + + + +FINAL DIAGNOSIS: +PART 1: LEFT BREAST ULTRASOUND GUIDED CORE BIOPSY +A. INVASIVE LOBULAR CARCINOMA, NUCLEAR GRADE 1 +B. LOBULAR CARCINOMA IN SITU, NUCLEAR GRADE 1 + +PART 2: LEFT AXILLARY LYMPH NODE ULTRASOUND GUIDED CORE BIOPSY +A. ONE LYMPH NODE NEGATIVE FOR METASTATIC CARCINOMA + + +IMMUNOHISTOCHEMISTRY: + +RESULT H-SCORE + +ESTROGEN RECEPTOR - POSITIVE 140 + +PROGESTERONE RECEPTOR - POSITIVE 100 + +HER2/NEU - NEGATIVE 0 + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc9_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc9_SP.txt new file mode 100644 index 0000000..edc3638 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient1/fake_patient1_doc9_SP.txt @@ -0,0 +1,44 @@ +=================================================================== +Report ID.....................9,doc9 +Patient ID....................pt123123123 +Patient Name..................Fake Patient1 +Principal Date................20110215 1230 +Record Type...................SP +Patient DOB...................04/01/1960 + +CLINICAL HISTORY: +A 51 year old woman with biopsy proven invasive lobular carcinoma of the left breast status post left segmental mastectomy. She has a history of stage 2A infiltrating ductal carcinoma of the right breast S/P chemotherapy, mastectomy and radiation. + +FINAL DIAGNOSIS: +PART 1: LEFT BREAST SEGMENTAL MASTECTOMY +A. INVASIVE LOBULAR CARCINOMA, 0.3 CM IN GREATEST DIMENSION NUCLEAR GRADE 1 +B. FOCAL LOBULAR CARCINOMA IN SITU, NUCLEAR GRADE 2 +C. FOCAL DUCTAL CARCINOMA IN SITU, NUCLEAR GRADE 2 +D. SURGICAL MARGINS ARE NEGATIVE +E. CHANGES CONSISTENT WITH PREVIOUS CORE BIOPSY + +PART 2: LEFT AXILLARY LYMPH NODE #1, BIOPSY +A. ONE LYMPH NODE NEGATIVE FOR TUMOR (0/1) + +PART 3: LEFT AXILLARY LYMPH NODE #2, BIOPSY +A. TWO LYMPH NODES NEGATIVE FOR TUMOR (0/2) + + +IMMUNOHISTOCHEMISTRY: + +RESULT H-SCORE + +ESTROGEN RECEPTOR - POSITIVE 140 + +PROGESTERONE RECEPTOR - POSITIVE 100 + +HER2/NEU - NEGATIVE 0 +HER2/NEU (FISH) – NOT AMPLIFIED + +T STAGE PATHOLOGIC: pT1a +N STAGE PATHOLOGIC: pN0 +M STAGE PATHOLOGIC: N/A Not applicable + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc1_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc1_NOTE.txt new file mode 100644 index 0000000..171024d --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc1_NOTE.txt @@ -0,0 +1,25 @@ +=================================================================== +Report ID.....................1,doc1 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20091103 1045 +Record Type...................NOTE +Patient DOB...................06/21/1958 + +Chief complaint: Patient with a new hard palpable lump in the left breast. +History of Present Illness: Patient is a 51 year old peri-menopausal female who has no previous complaints or symptoms, presents with a new hard palpable lump in the left breast. On self-examination she noticed a lump in her left breast in October of 2009. +Overall, she is feeling well. She has good energy level and her ECOG performance status is 0. She denies fever, chills, sweats, nausea, vomiting, diarrhea or constipation. There is no change in bowel or bladder habits. +I had a long discussion with the patient and her husband. She will get a Mammogram and return for results. +Allergies: No known drug allergies. +Physical Examination: +GENERAL: The patient is a middle aged female who is alert and in no distress. +HEENT: NC/AT PERRLA, sclera are clear, no lesions. +NECK: Supple without lymphadenopathy. +HEART: RRR without murmurs. +BREASTS: Left breast with palpable lump near 2 o’clock position. Right breast is without mass or abnormalities. +ABDOMEN: Soft, non-tender, non-distended, no masses. +BACK: No CVAT +EXTREMITIES: No clubbing, cyanosis or edema. +Assessment: Patient with a palpable lump in the left breast, scheduled for Mammogram. + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc2_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc2_RAD.txt new file mode 100644 index 0000000..a783b37 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc2_RAD.txt @@ -0,0 +1,25 @@ +=================================================================== +Report ID.....................2,doc2 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20091130 1135 +Record Type...................RAD +Patient DOB...................06/21/1958 +CLINICAL HISTORY: +51 year old peri-menopausal female who presents with a new hard palpable lump in the left breast. +TECHNIQUE: +Full field digital mammography with CAD was performed including routine views of both breasts, spot magnification views on the right with a full 90 degree lateral and spot compression views on the left. +Left breast and axillary ultrasound was performed. +FINDINGS: +Heterogeneously dense fibro glandular tissue is present throughout both breasts limiting the sensitivity of the mammogram. There is no evidence of mass or calcifications in the right breast. +A large firm mass is seen in the upper outer left breast at the 2 o’clock region. The mass measures 1x2 cm on the CC view. Calcifications are seen adjacent to the mass. +Ultrasound evaluation was performed on the area and a 1.3x3.2x5.1 cm hypoechoic mass is seen in the left breast at the 2 o’clock region. +Ultrasound of the left axillary lymph nodes was performed revealing multiple abnormally thickened lymph nodes. The largest lymph node has a thickened cortex of at least 6 mm. +IMPRESSION: +A large hypoechoic mass at the 2 o’clock location of the left breast is highly suggestive of a malignancy. The mass measures 1.3x3.2x5.1 cm. Ultrasound core biopsy is recommended. +Abnormal left axillary lymph nodes are highly suspicious of metastatic disease. +MR evaluation of extent of disease is recommended. +ASSESSMENT AND RECOMMENDATIONS: +ACR BI-RADS Category: 5 (Breast Imaging Left) Highly suggestive for malignancy. +RECOMMENDATION: Ultrasound guided core biopsy +OVERALL ASSESSMENT: 5 (Highly suggestive for malignancy. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc3_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc3_RAD.txt new file mode 100644 index 0000000..a33c1b4 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc3_RAD.txt @@ -0,0 +1,25 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20091130 1345 +Record Type...................RAD +Patient DOB...................06/21/1958 + +CLINICAL HISTORY: +51 year old peri-menopausal female who presents with a new hard palpable lump in the left breast. Patient is here for ultrasound guided core biopsy. +PROCEDURE TITLE: +Targeted ultrasound left breast. +Ultrasound guided core biopsy of left 2 o’clock abnormality. +Clip placement. +Ultrasound guided core biopsy of left axillary abnormal lymph node. +Clip placement. +Post procedure left breast mammogram. +PROCEDURE AND FINDINGS: +The left breast and axilla were sterilely prepped and draped in the usual standard fashion. First the left 2 o’clock position 5 cm from the nipple was targeted. Local anesthesia was obtained with 2% xylocaine. A small skin incision was made. Under ultrasound guidance from a medial approach, 2 passes with a 14 gauge biopsy device were performed and sent to pathology. A wing clip was placed at the 2 o’clock position 5 cm from the nipple under ultrasound guidance. +Then attention was turned to the left abnormal axillary lymph node. Local anesthesia was obtained with 2% xylocaine. A small skin incision was made. Under ultrasound guidance from an inferomedial approach, 2 passes with a 14 gauge biopsy device were performed and sent to pathology. A coil clip was placed at the site of the biopsy. +The wounds were cleaned and dressed. The patient tolerated the procedure well, and there were no complications. +Post procedure mammogram of the left breast demonstrated adequate clip placement. +IMPRESSION: +Uncomplicated ultrasound guided core biopsies of the left breast at the 2 o’clock position and abnormal left axillary lymph node. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc4_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc4_SP.txt new file mode 100644 index 0000000..cc00c4a --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc4_SP.txt @@ -0,0 +1,32 @@ +=================================================================== +Report ID.....................4,doc4 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20091130 1530 +Record Type...................SP +Patient DOB...................06/21/1958 + + +FINAL DIAGNOSIS: +PART 1: BREAST, LEFT, 2 O' CLOCK, ULTRASOUND GUIDED CORE BIOPSY +A. INVASIVE DUCTAL CARCINOMA, NUCLEAR GRADE 3. +B. FOCAL DUCTAL CARCINOMA IN SITU, NUCLEAR GRADE 2-3. +PART 2: LYMPH NODE, LEFT AXILLA, ULTRASOUND GUIDED CORE BIOPSY + METASTATIC CARCINOMA INVOLVING LYMPH NODE CORES. +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: positive, H-score: 90 +Progesterone Receptor: positive, H-score: 60 +Her2/NEU: negative, 0 +Her2/NEU (FISH): Not applicable +GROSS DESCRIPTION: +The specimen is received in formalin in two properly labeled containers. +Part 1 is labeled with the patient's name, and "left breast at 2 +o'clock". It consists of 2 cylindrical portions of white-yellow focally hemorrhagic fibrous cores. +Formalin exposure time: 50 hours and 25 minutes +Part 2 is labeled with the patient's name, and "left axilla lymph +node". It consists of two cylindrical portions of white-yellow focally hemorrhagic fibrous cores. +Formalin exposure time: 52 hours and 25 minutes. + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc5_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc5_RAD.txt new file mode 100644 index 0000000..f746654 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc5_RAD.txt @@ -0,0 +1,22 @@ +=================================================================== +Report ID.....................5,doc5 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20091206 1445 +Record Type...................RAD +Patient DOB...................06/21/1958 + +51 year old peri-menopausal female with newly diagnosed with left breast Invasive ductal carcinoma and DCIS on biopsy presents for MRI for evaluation of extent of disease. +TECHNIQUE: +Bilateral breast MRI with and without IV contrast. +FINDINGS: +There are post biopsy changes seen in the retro areolar region aspect of the left breast at the post biopsy site. +There is abnormal enhancement seen in this location compatible with patient’s history of malignancy. +There is increased enhancement seen in the inferior aspect of the left breast at the 2 o’clock position measuring 1.2 cm. +There are other multiple benign appearing enhancing masses seen in both the right and left breasts. +None of the remaining masses appear worrisome for malignancy based upon MRI criteria. +IMPRESSION: +BIRADS CATEGORY: 5 +There is a malignant appearing area of enhancement in the left breast which does correspond to the patient’s history of recent diagnosis of malignancy. +She has been scheduled to see a Medical Oncologist, as well as a Surgeon. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc6_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc6_NOTE.txt new file mode 100644 index 0000000..5dd53fc --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc6_NOTE.txt @@ -0,0 +1,30 @@ +=================================================================== +Report ID.....................6,doc6 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20100130 1525 +Record Type...................NOTE +Patient DOB...................06/21/1958 + +DIAGNOSIS: Stage IIIA (T3 N2 M0) invasive ductal carcinoma of the left breast, ER positive, PR positive and HER2 negative. + +Therapy: Completed 8 cycles of Taxotere. + +REASON FOR VISIT: Assess response to neoadjuvant chemotherapy. + +Patient returns to the office today for ongoing management of biopsy-proven left breast cancer with axillary lymph node metastasis. +Her initial office visit was on November 3, 2009. +Her clinical breast examination at that time was significant for a 2 cm palpable mass in the upper outer aspect of the left breast at the 2 o’clock position. +She also had multiple abnormally enlarged left axillary lymph nodes. + +She had core biopsies of the left breast mass and the left axillary lymph node. Pathology confirmed the diagnosis of invasive ductal carcinoma of the left breast with metastases to the left axillary lymph node. + +She completed 4 cycles of chemotherapy with Adriamycin and Cytoxan. +She has now completed 8 of a planned 12 cycles of Taxotere. She has tolerated her chemotherapy without significant sequela. + +She denies any hospitalizations. + +Her past medical history, surgical history, medications, and allergies were reviewed as noted in the electronic medical record. + +IMPRESSION: Patient has had a partial response to neoadjuvant chemotherapy for a locally advanced, ER positive, PR positive and HER2 negative, left breast cancer. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc7_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc7_SP.txt new file mode 100644 index 0000000..bcc198b --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc7_SP.txt @@ -0,0 +1,30 @@ +=================================================================== +Report ID.....................7,doc7 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20100220 1645 +Record Type...................SP +Patient DOB...................06/21/1958 + +PATIENT HISTORY: 51 year-old female with triple negative invasive ductal carcinoma of the left breast with multiple positive axillary lymph nodes. Status post neoadjuvant chemotherapy. + + +FINAL DIAGNOSIS: +LEFT BREAST, MODIFIED RADICAL MASTECTOMY +A. INVASIVE DUCTAL CARCINOMA, MAIN TUMOR MASS IN THE 2 O’CLOCK REGION IN THE UPPER OUTER QUADRANT +B. SURGICAL MARGINS ARE NEGATIVE. +C. CHANGES CONSISTENT WITH PREVIOUS CORE BIOPSY +D. TUMOR IS ESTROGEN RECEPTOR NEGATIVE, PROGESTERONE RECEPTOR NEGATIVE, HER-2/NEU NEGATIVE +E. CHANGES CONSISTENT WITH STATUS POST CHEMOTHERAPY. +F. TWO OUT OF EIGHT AXILLARY LYMPH NODES POSITIVE FOR METASTATIC CARCINOMA (2/8). + +HORMONE RECEPTOR IMMUNOHISTOCHEMISTRY +RESULT +ESTROGEN Positive 90 +PROGESTERONE Positive 60 +HER-2/NEU Negative 0 + +T STAGE PATHOLOGIC: pT3 +N STAGE PATHOLOGIC: pN2 +M STAGE PATHOLOGIC: pM0 + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc8_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc8_NOTE.txt new file mode 100644 index 0000000..72c8c25 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc8_NOTE.txt @@ -0,0 +1,23 @@ +=================================================================== +Report ID.....................8,doc8 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20100301 1015 +Record Type...................NOTE +Patient DOB...................06/21/1958 + + +Reason For Visit: Post op breast surgery + +Diagnosis: IIIA (T3, N2, M0) Left breast cancer: ER positive, PR positive, and Her2 negative. + +Procedure: Left modified radical mastectomy and axillary lymph node dissection on January 30, 2010. + +Interim History: The patient is a 51 year old woman who presents for her postoperative visit. The operation was performed without complication and her recovery has been uneventful. + +Physical Exam: The patient’s physical examination demonstrates a well healed surgical incision of the left breast. The axillary wound is well healed. +No signs of bruising and no infection are noted. The breasts appear symmetric. The overall cosmetic outcome is good + +Impression: A 51 year old woman with stage 3A invasive ductal carcinoma of the left breast, treated with modified radical mastectomy and axillary lymph node dissection. + +Recommendations: The patient’s surgical management is now complete. She has a Medical Oncology consult 3/10/10, to discuss systemic therapies as indicated. Radiation Oncology consult on 3/29/10 to discuss required adjuvant breast irradiation. She will return to office in 6 months for a follow-up visit. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc9_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc9_NOTE.txt new file mode 100644 index 0000000..c7356f8 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient2/fake_patient2_doc9_NOTE.txt @@ -0,0 +1,21 @@ +=================================================================== +Report ID.....................9,doc9 +Patient ID....................pt246246246 +Patient Name..................Fake Patient2 +Principal Date................20100819 1130 +Record Type...................NOTE +Patient DOB...................06/21/1958 +Reason for Visit: Back Pain. + +History of Present Illness: +52 year old female admitted with severe back pain. She rates the pain as 10/10 and located in the thoracic spine. The pain has been ongoing for this patient since July of this year. She has been followed in the pain service and has been receiving injections. Spinal injections with the pain service have not helped with the pain. The pain is also associated with worsening fatigue and shortness of breath. Patient reports increase weakness. MRI was recommended but patient declined. Instead she underwent a CT scan. +CT spine appears to have extensive metastatic disease of the vertebral column as well as pulmonary nodules that have not been seen well previously. Based on these new findings she will need a CT of the chest/abdomen and pelvis to evaluate for any further lesions. +Past Medical History: +Patient with known history of left breast cancer stage IIIA status post left modified radical mastectomy with metastatic disease to the left axillary lymph node. She is status post chemotherapy with Adriamycin, Cytoxan and Taxotere. She also received Radiation Therapy as an outpatient. +As per last visit with oncology in May of this year, it appeared the patient was in remission. +Since then patient has had worsening back pain and did not have MRI because of claustrophobia. + +IMPRESSION: +52 year old female admitted with severe back pain found to have pulmonary lesions and compression fracture of Thoracic spine concerning for underlying metastatic disease. +CT scan revealed small pleural effusions right greater than left with atelectasis. New 6 mm pulmonary nodule is seen in the right lower lobe. New 4 mm nodule is seen in the right upper lobe. Additional 2 mm nodules are seen in the left middle lobe. There are bony metastasis seen in the vertebral column at T9 and T10. Additionally there are metastatic deposits in the left sixth rib and right fifth rib. +Patient has metastatic disease from her previously treated stage 3A invasive ductal carcinoma of the left breast, ER, PR positive and HER2 negative. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc1_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc1_NOTE.txt new file mode 100644 index 0000000..6081333 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc1_NOTE.txt @@ -0,0 +1,25 @@ +=================================================================== +Report ID.....................1,doc1 +Patient ID....................pt135135135 +Patient Name..................Fake Patient3 +Principal Date................20100116 1045 +Record Type...................NOTE +Patient DOB...................11/12/1966 + +Chief complaint: Patient with newly diagnosed right breast cancer. +History of Present Illness: Patient is a 44 year old-female seen for management of recently diagnosed right breast cancer. She was asymptomatic at the time of her yearly mammogram in December of 2009. Mammogram showed architectural distortion associated with calcifications in the upper outer quadrant of the right breast. Ultrasound showed an irregular hypoechoic mass at the 10 o’clock position measuring approximately 1.5x1.9x1.0 cm. Core needle biopsy on 1/3/2010 showed an invasive ductal carcinoma, ER positive, PR positive, HER2/NEU negative by FISH. +Her past medical history is significant for diagnosis of breast cancer in 2001 when she found a lump in her left breast during self-exam. At that time she had a biopsy done and had stage 2B adenocarcinoma. She underwent adjuvant chemotherapy and then had a left mastectomy followed by XRT. +Overall, she is feeling well. She has good energy level and her ECOG performance status is 0. She denies fever, chills, sweats, nausea, vomiting, diarrhea or constipation. There is no change in bowel or bladder habits. +Physical Examination: +GENERAL: The patient alert and in no distress. +HEENT: NC/AT PERRLA, sclera are clear, no lesions. +NECK: Supple without lymphadenopathy. +HEART: RRR without murmurs. +BREASTS: Right breast with healing incision at previous biopsy site. Left breast has previous mastectomy scar. +ABDOMEN: Soft, non-tender, non-distended, no masses. +BACK: No CVAT +EXTREMITIES: No clubbing, cyanosis or edema. + +Assessment: Patient is a 44 year-old female with clinical stage II (T2 N0 M0) invasive ductal carcinoma of the right breast associated with DCIS. She will proceed with a right breast segmental mastectomy and sentinel lymph node biopsy. + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc2_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc2_SP.txt new file mode 100644 index 0000000..f391d98 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc2_SP.txt @@ -0,0 +1,34 @@ +=================================================================== +Report ID.....................2,doc2 +Patient ID....................pt135135135 +Patient Name..................Fake Patient3 +Principal Date................20100201 1545 +Record Type...................SP +Patient DOB...................11/12/1966 + +PATIENT HISTORY: 44 year-old female with biopsy proven invasive ductal carcinoma of the right breast with history of stage 2B left breast adenocarcinoma status post neoadjuvant chemotherapy, right mastectomy and radiation therapy. + + +FINAL DIAGNOSIS: +RIGHT BREAST, SEGMENTAL MASTECTOMY +PART 1: +A. 2 FOCI OF INVASIVE DUCTAL CARCINOMA, 2.1 AND 1.1 CM IN THE 10 O’CLOCK REGION IN THE UPPER OUTER QUADRANT +B. DCIS, SOLID TYPE, REPRESENTING 4% OF THE TUMOR VOLUME. +C. MARGINS FREE OF TUMOR. +D. MICROCALCIFICATIONS ASSOCIATED WITH TUMOR. +PART 2: +E. RIGHT AXILLA, SENTINEL LYMPH NODE EXCISION, ONE LYMPH NODE POSITIVE FOR METASTATIC CARCINOMA. + +HORMONE RECEPTOR IMMUNOHISTOCHEMISTRY +RESULT +ESTROGEN POSITIVE 150 +PROGESTERONE POSITIVE 160 +HER-2/NEU NEGATIVE 0 +HER-2/NEU (FISH) NOT AMPLIFIED + +T STAGE: PT2 +N STAGE: PN1 +M STAGE: NOT APPLICABLE + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc3_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc3_NOTE.txt new file mode 100644 index 0000000..6114f58 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc3_NOTE.txt @@ -0,0 +1,23 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt135135135 +Patient Name..................Fake Patient3 +Principal Date................20100210 1015 +Record Type...................NOTE +Patient DOB...................11/12/1966 + + + +Reason For Visit: Post op breast surgery + +Diagnosis: Stage II (T2, N1, M0) invasive ductal carcinoma of the right breast: ER positive, PR positive, and Her2 negative by FISH. + +Procedure: Right segmental mastectomy and right axilla, sentinel lymph node excision on February 1, 2010. + +Interim History: The patient is a 44 year old woman who presents for her postoperative visit. The operation was performed without complication and her recovery has been uneventful. + +Physical Exam: The patient’s physical examination demonstrates a well healed surgical incision of the right breast. The axillary wound is well healed. No signs of bruising and no infection are noted. She denies any pain, fever, nausea or vomiting. + +Impression: A 44 year old woman with stage 2 invasive ductal carcinoma of the right breast, treated with segmental mastectomy and axillary, sentinel lymph node excision. + +Recommendations: The patient is to have a right axillary lymph node dissection due to multifocal carcinoma and micro-metastases in the sentinel lymph node. Further treatment plan to be discussed after this procedure. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc4_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc4_SP.txt new file mode 100644 index 0000000..4592c25 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc4_SP.txt @@ -0,0 +1,30 @@ +=================================================================== +Report ID.....................4,doc4 +Patient ID....................pt135135135 +Patient Name..................Fake Patient3 +Principal Date................20100301 1530 +Record Type...................SP +Patient DOB...................11/12/1966 + + +FINAL DIAGNOSIS: +PART 1: LYMPH NODES, RIGHT AXILLA, DISSECTION +A. 12 OF 19 LYMPH NODES POSITIVE FOR METASTATIC BREAST CARCINOMA. +B. LARGEST METASTATESES MEASURE UP TO 1.9 CM + + +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: POSITIVE +Progesterone Receptor: POSITIVE +Her2/NEU: NEGATIVE +Her2/NEU (FISH): Not applicable + +GROSS DESCRIPTION: +The specimen is received in formalin in two properly labeled containers. +Part 1 is labeled with the patient's name, and "RIGHT axilla lymph +node". It consists of two cylindrical portions of white-yellow focally hemorrhagic fibrous cores. +Formalin exposure time: 52 hours and 25 minutes. + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc5_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc5_NOTE.txt new file mode 100644 index 0000000..c7ca211 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc5_NOTE.txt @@ -0,0 +1,24 @@ +=================================================================== +Report ID.....................5,doc5 +Patient ID....................pt135135135 +Patient Name..................Fake Patient3 +Principal Date................20100311 1525 +Record Type...................NOTE +Patient DOB...................11/12/1966 + +Reason for Visit: Post op right axillary lymph node dissection. + +Diagnosis: Stage II (T2, N1, M0) right invasive ductal breast carcinoma with metastatic disease to the right axillary lymph nodes: ER positive, PR positive, and Her2 negative. + +Procedure: Right axillary lymph node dissection on March 1, 2010. + +Interim History: The patient is a 44 year old female who presents for her postoperative visit following axillary lymph node dissection for metastatic breast cancer. The procedure was performed without complication and her recovery has been uneventful. + +PMH: Her past medical history is significant for diagnosis of breast cancer in 2001 when she found a lump in her left breast during self-exam. At that time she had a biopsy done and had stage 2B adenocarcinoma. She underwent adjuvant chemotherapy and then had a left mastectomy followed by XRT. + +Physical Exam: The patient’s physical examination demonstrates a healing axillary wound. There is no erythema, swelling, redness or edema. No signs of bruising and no infection are noted. She denies any fever or pain. + +Impression: A 44 year old female with stage 2 invasive ductal carcinoma of the right breast, treated with a right segmental mastectomy and right axillary lymph node dissection. + +Recommendations: The patient’s surgical management is now complete. She has a Medical Oncology consult 3/25/10, to discuss systemic therapies as indicated. Radiation Oncology consult to follow, to discuss required adjuvant breast irradiation. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc6_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc6_NOTE.txt new file mode 100644 index 0000000..aa03e20 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc6_NOTE.txt @@ -0,0 +1,23 @@ +=================================================================== +Report ID.....................6,doc6 +Patient ID....................pt135135135 +Patient Name..................Fake Patient3 +Principal Date................20100325 1125 +Record Type...................NOTE +Patient DOB...................11/12/1966 + +DIAGNOSIS: Stage II (T2 N1 M0) invasive ductal carcinoma of the right breast, metastatic to right axillary lymph nodes. ER positive, PR positive, Her2 negative. + +REASON FOR VISIT: Discuss chemotherapy. + +Patient returns to the office today for management of invasive ductal carcinoma of the right breast with axillary lymph node metastasis. +Her initial office visit was on January 16, 2010. + +I discussed treatment options with her and her husband. I recommended chemotherapy with Doxorubicin and Paclitaxel. She will come in next week to start this regimen. + +PMH: Her past medical history is significant for diagnosis of breast cancer in 2001 when she found a lump in her left breast during self-exam. At that time she had a biopsy done and had stage 2B adenocarcinoma. She underwent adjuvant chemotherapy and then had a left mastectomy followed by XRT. + +Physical Exam: The patient’s physical examination demonstrates a healing axillary wound. There is no erythema, swelling, redness or edema. No signs of bruising and no infection are noted. She denies any fever or pain. + +IMPRESSION: Patient is a 44 year-old female with stage 2, invasive ductal carcinoma of the right breast s/p right segmental mastectomy followed by right axillary lymph node dissection for metastatic disease. She will receive 4 cycles of Doxorubicin and Paclitaxel. We will monitor her for any side effects and will re-assess her response after the 4th cycle. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc7_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc7_NOTE.txt new file mode 100644 index 0000000..4fd4844 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc7_NOTE.txt @@ -0,0 +1,31 @@ +=================================================================== +Report ID.....................7,doc7 +Patient ID....................pt135135135 +Patient Name..................Fake Patient3 +Principal Date................20100508 1045 +Record Type...................NOTE +Patient DOB...................11/12/1966 + +DIAGNOSIS: Stage II (T2 N1 M0) invasive ductal carcinoma of the right breast, metastatic to right axillary lymph nodes. ER positive, PR positive, Her2 negative. + +REASON FOR VISIT: 3rd cycle of Doxorubicin and Paclitaxel. + +Patient returns to the office today for management of invasive ductal carcinoma of the right breast with axillary lymph node metastasis. +Her initial office visit was on January 16, 2010. + +She has received two cycles of chemotherapy with Doxorubicin and Paclitaxel. She has tolerated chemotherapy well with minimal nausea and vomiting. Her blood counts have remained stable with WBC 10.01, HGB 17, HCT 50.6, PLT 290. BUN and CR have been within normal limits. + +PMH: Her past medical history is significant for diagnosis of breast cancer in 2001 when she found a lump in her left breast during self-exam. At that time she had a biopsy done and had stage 2B adenocarcinoma. She underwent adjuvant chemotherapy and then had a left mastectomy followed by XRT. + +Physical Exam: Blood pressure 114/80, temperature 97.6, pulse 72 +GEN: She is nontoxic, non-cachectic appearing. +HEAD: NC/AT with Alopecia +EYES: Anicteric +ENT: No oral lesions. +HEART: RRR, no murmurs, rubs or gallops. +LUNGS: Clear to auscultation bilaterally. +ADB: Non-tender. Non-distended. No HSM. +EXT: No clubbing, cyanosis or edema. + +IMPRESSION: Patient is a 44 year-old female with stage 2, invasive ductal carcinoma of the right breast s/p right segmental mastectomy followed by right axillary lymph node dissection for metastatic disease. She has received 2 cycles of Doxorubicin and Paclitaxel. She is admitted for her third cycle. She has tolerated chemotherapy reasonably well with minimal side-effects. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc8_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc8_NOTE.txt new file mode 100644 index 0000000..7146e63 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient3/fake_patient3_doc8_NOTE.txt @@ -0,0 +1,21 @@ +=================================================================== +Report ID.....................8,doc8 +Patient ID....................pt135135135 +Patient Name..................Fake Patient3 +Principal Date................20100624 1230 +Record Type...................NOTE +Patient DOB...................11/12/1966 + +Reason for Visit: Back Pain. + +History of Present Illness: +44 year old female admitted with severe back pain. She rates the pain as 10/10 and located in the lower back. The pain has been ongoing for this patient since the beginning of June. She did not complete her 4th cycle of chemotherapy due to the severe back pain. She will get a CT scan. + +CT spine appears to show extensive metastatic disease of the lumbar vertebra as well as pulmonary nodules that were not seen previously. Based on these new findings she will need a CT of the chest/abdomen and pelvis to evaluate for any further lesions. +Past Medical History: +Patient with history of right breast cancer stage II status post right segmental mastectomy followed by right axillary lymph node dissection for metastatic disease to the right axillary lymph node. She had received 3 cycles of chemotherapy with Doxorubicin and Paclitaxel with minimal side-effects. She had complained of back pain shortly after receiving her 4th cycle. She underwent a CT of the spine which revealed metastatic disease in the lumbar vertebra. + +IMPRESSION: +44 year old female admitted with severe back pain found to have pulmonary lesions and compression fracture of Lumbar spine concerning for metastatic disease. +CT scan revealed a 6 mm pulmonary nodule in the right lower lobe and a 4 mm nodule is seen in the right upper lobe. Additional 2 mm nodules are seen in the left middle lobe. There are bony metastases seen in the lumbar vertebra. Addition metastatic deposits are seen in the left sixth rib and right fifth rib. +She is scheduled to be seen by radiation therapy for treatment recommendations. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc1_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc1_NOTE.txt new file mode 100644 index 0000000..cce1c5e --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc1_NOTE.txt @@ -0,0 +1,26 @@ +=================================================================== +Report ID.....................1,doc1 +Patient ID....................pt567567567 +Patient Name..................Fake Patient4 +Principal Date................20110310 1025 +Record Type...................NOTE +Patient DOB...................01/15/1949 + +Reason for Visit: Patient is a 62 year old post-menopausal female with a long history of lumpy breasts. She felt a mass on her right breast on self-examination that she hadn’t noticed before. She also felt another lump in her left breast which she described as hard and painful. + +Interim History: The patient is a 62 year old female who presents for evaluation of the masses. The patient’s recent mammography on March 1, 2011 revealed a lobulated mass in the upper inner quadrant of the right breast at 2 o’clock position that measured 1.2x3.0 cm. Mammography also revealed a nodular mass in the upper inner quadrant of the left breast at 11 o’clock position that measured 2 cm in diameter. +Ultrasound evaluation was performed on the area of the right breast and a 1.1x2.2x3.3 cm hypoechoic mass is seen in the 2 o’clock region. Ultrasound of the left breast at 11 o’clock revealed a 1.1x1.2x1.2 cm mass. Ultrasound of the right axillary lymph nodes was performed showing multiple thickened lymph nodes. Ultrasound of the left axilla revealed normal appearing lymph nodes. + +Past History: She has a history of left ovarian carcinoma, treated with total abdominal hysterectomy, bilateral salpingo-oophorectomy in July 2002. She received neoadjuvant chemotherapy with Taxol and Carboplatin. + +Physical Exam: Health appearing female in NAD. +HEENT: NC/AT, PERRL, EOMI, Sclera non icteric +NECK: Supple, no masses +LUNGS: CTA, no wheezes, rales, rhonchi +CARDIAC: RRR. No murmurs, rubs or gallops +ADB: Soft, NT, ND, No HSM +EXT: No clubbing, cyanosis or edema + + +Impression: A 62 year old female with bilateral breast masses seen on mammography and ultrasound scheduled for core biopsy of the right breast mass as well as the left breast nodule. She will return to discuss further treatment options once pathology is finalized. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc2_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc2_RAD.txt new file mode 100644 index 0000000..a5b42c0 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc2_RAD.txt @@ -0,0 +1,22 @@ +=================================================================== +Report ID.....................2,doc2 +Patient ID....................pt567567567 +Patient Name..................Fake Patient4 +Principal Date................20110312 1045 +Record Type...................RAD +Patient DOB...................01/15/1949 +CLINICAL HISTORY: +62 year old post-menopausal female with a new hard palpable lump in the left breast and a new mass in the right breast for ultrasound guided core biopsy. +PROCEDURE TITLE: +Targeted ultrasound right breast +Ultrasound core biopsy of right 2 o’clock mass +Targeted ultrasound of left breast +Ultrasound core biopsy of left 11 o’clock mass +Ultrasound guided core biopsy of right axillary abnormal lymph node + +PROCEDURE AND FINDINGS: +The right breast and axilla were sterilely prepped and draped in the usual standard fashion. First the right 2 o’clock position 5 cm from the nipple was targeted. Local anesthesia was obtained with 2% xylocaine. A small skin incision was made. Under ultrasound guidance from a medial approach, 2 passes with a 14 gauge biopsy device were performed and sent to pathology. A wing clip was placed at the 2 o’clock position 5 cm from the nipple under ultrasound guidance. +Then attention was turned to the right abnormal axillary lymph node. Local anesthesia was obtained with 2% xylocaine. A small skin incision was made. Under ultrasound guidance from an inferomedial approach, 2 passes with a 14 gauge biopsy device were performed and sent to pathology. A coil clip was placed at the site of the biopsy. +The left breast was sterilely prepped and draped in the usual standard fashion. The left 11 o’clock position 3 cm from the nipple was targeted. Local anesthesia was obtained with 2% xylocaine. A small skin incision was made. Under ultrasound guidance from a medial approach, 2 passes with a 14 gauge biopsy device were performed and sent to pathology. A wing clip was placed at the 11 o’clock position 3 cm from the nipple under ultrasound guidance. +IMPRESSION: +Uncomplicated ultrasound guided core biopsies of the right breast at the 2 o’clock position, the left breast at the 11 o’clock position and the abnormal right axillary lymph node. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc3_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc3_SP.txt new file mode 100644 index 0000000..4e01b21 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc3_SP.txt @@ -0,0 +1,36 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt567567567 +Patient Name..................Fake Patient4 +Principal Date................20110312 1530 +Record Type...................SP +Patient DOB...................01/15/1949 + + +CLINICAL HISTORY: +62 year old female with a new hard palpable lump in the left breast and a new mass in the right breast for ultrasound guided core biopsy. + + +FINAL DIAGNOSIS: +PART 1: BREAST, RIGHT, 2 O' CLOCK, ULTRASOUND GUIDED CORE BIOPSY +A. INVASIVE DUCTAL CARCINOMA, NUCLEAR GRADE 2. +B. INVASIVE CARCINOMA 2.0 CM +C. MICROCALCIFICATIONS ASSOCIATED WITH MALIGNANT TUMOR +PART 2: RIGHT, AXILLARY LYMPH NODE, ULTRASOUND GUIDED CORE BIOPSY +A: METASTATIC BREAST CARCINOMA +PART 3: BREAST, LEFT, 11 O’CLOCK, ULTRASOUND GUIDED CORE BIOPSY +A: INVASIVE LOBULAR CARCINOMA, NUCLEAR GRADE 2. +B: CARCINOMA MEASURES 1.6 CM +C: ATYPICAL LOBULAR HYPERPLASIA + + +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: positive, H-score: 250 +Progesterone Receptor: positive, H-score: 100 +Her2/NEU: positive, 3+ + + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc4_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc4_NOTE.txt new file mode 100644 index 0000000..d398e2e --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc4_NOTE.txt @@ -0,0 +1,33 @@ +=================================================================== +Report ID.....................4,doc4 +Patient ID....................pt567567567 +Patient Name..................Fake Patient4 +Principal Date................20110404 1025 +Record Type...................NOTE +Patient DOB...................01/15/1949 + + +DIAGNOSIS: Stage IIIB (T3 N2 M0) invasive ductal carcinoma of the right breast, and invasive lobular carcinoma of the left breast. ER positive, PR positive, HER2 positive. + +Therapy: 7 of planned 12 cycles of Taxotere. + +REASON FOR VISIT: Assess response to neoadjuvant chemotherapy. + +Patient returns to the office today for ongoing management of biopsy-proven bilateral breast cancer with right axillary lymph node metastases. Her initial visit was on March 10, 2011 at which time her clinical breast examination revealed a new mass in the right breast biopsy revealing invasive ductal carcinoma and a lump in the left breast biopsy revealing invasive lobular carcinoma. She also had multiple abnormally enlarged right axillary lymph nodes. + +She completed 4 cycles of chemotherapy with Adriamycin and Cytoxan. +She is now admitted for cycle 7 of 12 planned cycles of Taxotere. She has tolerated her chemotherapy without significant sequela. + +Past History: She has a history of left ovarian carcinoma, treated with total abdominal hysterectomy, bilateral salpingo-oophorectomy in July 2002. She received neoadjuvant chemotherapy with Taxol and Carboplatin. + +Physical Exam: Health appearing female in NAD. +HEENT: NC/AT, PERRL, EOMI, Sclera non icteric +NECK: Supple, no masses +LUNGS: CTA, no wheezes, rales, rhonchi +CARDIAC: RRR. No murmurs, rubs or gallops +ADB: Soft, NT, ND, No HSM +EXT: No clubbing, cyanosis or edema + + +IMPRESSION: Patient is a 62 year old post-menopausal female who has had a partial response to neoadjuvant chemotherapy for her bilateral breast carcinoma. We will re-assess patient’s disease after the 12th cycle of Taxotere. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc5_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc5_NOTE.txt new file mode 100644 index 0000000..a98bf93 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc5_NOTE.txt @@ -0,0 +1,31 @@ +=================================================================== +Report ID.....................5,doc5 +Patient ID....................pt567567567 +Patient Name..................Fake Patient4 +Principal Date................20110625 1115 +Record Type...................NOTE +Patient DOB...................01/15/1949 + + +DIAGNOSIS: Stage IIIB (T3 N2 M0) invasive ductal carcinoma of the right breast, and invasive lobular carcinoma of the left breast. ER positive, PR positive, HER2 positive. + +Therapy: Completed 4 cycles of Adriamycin and Cytoxan and 12 cycles of Taxotere. + +REASON FOR VISIT: Assess response to neoadjuvant chemotherapy. + +Patient returns to the office today for ongoing management of biopsy-proven bilateral breast cancer with right axillary lymph node metastases. Her initial visit was on March 10, 2011 at which time her clinical breast examination revealed a new mass in the right breast biopsy revealing invasive ductal carcinoma and a lump in the left breast biopsy revealing invasive lobular carcinoma. She also had multiple abnormally enlarged right axillary lymph nodes. + +She is being seen to assess her response to chemotherapy. Breast MRI on 6/21/11 showed tumor responded to chemotherapy. Right breast mass now measures 1.0x1.9x2.0 cm from previous 1.1x2.2x3.3 cm. Left breast mass now measures 1.0x1.0x1.0 cm from previous 1.1x1.2x1.2 cm. Right axillary lymph node metastasis now measures 2.0x1.9 cm form previous 3.2x2.5 cm. + +Past History: She has a history of left ovarian carcinoma, treated with total abdominal hysterectomy, bilateral salpingo-oophorectomy in July 2002. She received neoadjuvant chemotherapy with Taxol and Carboplatin. + +Physical Exam: Health appearing female in NAD. +HEENT: NC/AT, PERRL, EOMI, Sclera non icteric +NECK: Supple, no masses +LUNGS: CTA, no wheezes, rales, rhonchi +CARDIAC: RRR. No murmurs, rubs or gallops +ADB: Soft, NT, ND, No HSM +EXT: No clubbing, cyanosis or edema + +IMPRESSION: Patient has had a good response to neoadjuvant chemotherapy for her bilateral breast carcinoma. She will now proceed with bilateral mastectomies and right axillary dissection. + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc6_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc6_SP.txt new file mode 100644 index 0000000..54dce0c --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc6_SP.txt @@ -0,0 +1,40 @@ +=================================================================== +Report ID.....................6,doc6 +Patient ID....................pt567567567 +Patient Name..................Fake Patient4 +Principal Date................20110712 1030 +Record Type...................SP +Patient DOB...................01/15/1949 + + +CLINICAL HISTORY: +This is a 62 year old female with stage IIIB (T3 N2 M0) invasive ductal carcinoma of the right breast and invasive lobular carcinoma of the right breast. ER positive, PR positive, HER2 positive. She is S/P 4 cycles of Adriamycin and Cytoxan and 12 cycles of Taxotere. + + + + +FINAL DIAGNOSIS: +PART 1: BREAST, RIGHT, 2 O' CLOCK, TOTAL MASTECTOMY +A. INVASIVE DUCTAL CARCINOMA, NUCLEAR GRADE 2. +B. INVASIVE CARCINOMA 1.5 CM +C. MICROCALCIFICATIONS ASSOCIATED WITH MALIGNANT TUMOR +PART 2: RIGHT, AXILLARY LYMPH NODE, DISSECTION +A: TEN LYMPH NODES, NEGATIVE FOR NEOPLASM (0/10) +PART 3: BREAST, LEFT, 11 O’CLOCK, TOTAL MASTECTOMY +A: INVASIVE LOBULAR CARCINOMA, NUCLEAR GRADE 2. +B: CARCINOMA MEASURES 1.0 CM +C: ATYPICAL LOBULAR HYPERPLASIA + +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: positive, H-score: 250 +Progesterone Receptor: positive, H-score: 100 +Her2/NEU: positive, 3+ + +T STAGE: PT3 +N STAGE: PN2 +M STAGE: PM0 + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc7_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc7_NOTE.txt new file mode 100644 index 0000000..8a5ae1c --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient4/fake_patient4_doc7_NOTE.txt @@ -0,0 +1,26 @@ +=================================================================== +Report ID.....................7,doc7 +Patient ID....................pt567567567 +Patient Name..................Fake Patient4 +Principal Date................20110727 1115 +Record Type...................NOTE +Patient DOB...................01/15/1949 + + + +Reason For Visit: Post op breast surgery + +Diagnosis: IIIB (T3, N2, M0) invasive ductal carcinoma of the right breast and invasive lobular carcinoma of the left breast. ER positive, PR positive, and Her2 positive. + +Procedure: On 7/12/11 the patient underwent bilateral total mastectomy with right breast specimen revealing invasive ductal carcinoma and right axillary lymph node dissection. Lymph nodes were negative for malignancy. Left breast specimen revealed invasive lobular carcinoma. + +Interim History: The patient is a 62 year old woman who presents for her postoperative visit. The operation was performed without complication and her recovery has been uneventful. + +Past Medical History: She has a history of left ovarian carcinoma, treated with total abdominal hysterectomy, bilateral salpingo-oophorectomy in July 2002. She received neoadjuvant chemotherapy with Taxol and Carboplatin. + + +Physical Exam: The patient’s physical examination demonstrates a well healed surgical incision of the right breast. The axillary wound is well healed. No signs of bruising and no infection are noted. She denies any pain, fever, nausea or vomiting. + +Impression: A 62 year old woman with stage 3B invasive ductal carcinoma of the right breast, and invasive lobular carcinoma of the left breast, treated with bilateral total mastectomy and left axillary lymph node excision. + +Recommendations: She will be seen by Radiation Oncology to begin treatment to the breast. Patient was started on Tamoxifen. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc10_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc10_NOTE.txt new file mode 100644 index 0000000..b5abb5e --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc10_NOTE.txt @@ -0,0 +1,14 @@ +=================================================================== +Report ID.....................10,doc10 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20100215 1300 +Record Type...................NOTE +Patient DOB...................08/01/1972 + +CHIEF COMPLAINT: Patient with invasive ductal carcinoma of the left breast now seen for newly diagnosed metastatic disease to the lung confirmed on biopsy. +CLINICAL HISTORY: She presented to the EW with SOB, CP and abdominal pain on 2/5/10. She underwent a CT of the chest and abdomen the next day. CT showed multiple pulmonary nodules in both lungs and a metastatic nodule in the left lobe of the liver. She had a biopsy of the left lower lobe lung mass that confirmed metastatic disease consistent with her known breast primary. She was diagnosed with invasive ductal carcinoma of the left breast with left axillary lymph nodes metastases. She received 4 cycles of Adriamycin and Cytoxan followed by 12 cycles of Taxotere. She underwent a total mastectomy of the left breast with left axillary lymph node dissection on 9/2/09. At the time of surgery she was a stage 3A (T3, N2, M0) ER positive, PR positive and HER2/NEU negative. Her surgery was performed without complication and her recovery has been uneventful. She has been on Tamoxifen since October 2009. She has tolerated this well without any significant side effects. +Past Medical History: She has a history of a right ovarian cyst and endometriosis. +Physical Exam: Reveals an ill-appearing female in moderate distress. Cardiac exam showed normal S1 and S2 with no murmurs. Extremities were without edema. Lung exam with coarse breath sounds in both lungs. Exam of the abdomen reveal tenderness in the lower abdomen. +IMPRESSION: +Patient with stage 3A (T3, N2, M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases diagnosed on 5/5/09. She now has metastatic disease the lungs and liver. She will receive Docetaxel and Bevacizumab. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc1_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc1_RAD.txt new file mode 100644 index 0000000..7de6192 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc1_RAD.txt @@ -0,0 +1,22 @@ +=================================================================== +Report ID.....................1,doc1 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20090505 1015 +Record Type...................RAD +Patient DOB...................08/01/1972 +CLINICAL HISTORY: +37 year old female presents with a new hard palpable lump in the left breast. Mammography in April 2009 revealed a suspicious mass in the left breast with an enlarged left axillary lymph node. She now comes in for ultrasound and diagnostic mammography of the left breast lumps. +Procedure performed: +Ultrasound core biopsy of left 1 o’clock and 2 o’clock masses +Ultrasound guided core biopsy of left axillary abnormal lymph node + + +PROCEDURE AND FINDINGS: +Digital diagnostic mammography of the left breast with CAD was performed. Full medial lateral and magnification views confirm the presence of a 1.0 cm ill-defined mass at the 1 o’clock position and a 1.1 cm mass at the 2 o’clock position of the left breast. A left axillary view shows 2 abnormal dense round lymph nodes measuring 2.4 cm and 2.0 cm. +Sonography of the left breast confirms a 1.0x1.0x0.8 cm hypoechoic mass at the 1 o’clock position and a 1.1x1.0x1.0 cm hypoechoic mass at the 2 o’clock position. +Sonography of the left axilla demonstrates 2 abnormal lymph nodes, both with cortical thickening. This is worrisome for metastatic disease. +IMPRESSION: +Ill-defined masses located in the left breast at 1 o’clock and 2 o’clock positions are highly suspicious for malignancy. Ultrasound guided core biopsies of the 2 masses was performed. Ultrasound guided core biopsy of the abnormal left axillary lymph node was also performed. +ACR BI-RADS category (left breast): 4 – Suspicious for malignancy. +Abnormal left axillary lymph node highly suspicious for metastatic disease. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc2_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc2_SP.txt new file mode 100644 index 0000000..760da8e --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc2_SP.txt @@ -0,0 +1,35 @@ +=================================================================== +Report ID.....................2,doc2 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20090505 1530 +Record Type...................SP +Patient DOB...................08/01/1972 + + +CLINICAL HISTORY: +37 year old female with a new hard palpable lump in the left breast and an abnormal left axillary lymph node status post ultrasound guided core biopsy. + + +FINAL DIAGNOSIS: +PART 1: BREAST, LEFT, 1 O' CLOCK, ULTRASOUND GUIDED CORE BIOPSY +A. INVASIVE DUCTAL CARCINOMA, NUCLEAR GRADE 2. +B. DUCTAL CARCINOMA IN SITU, NUCLEAR GRADE 2 +C. MICROCALCIFICATIONS ASSOCIATED WITH MALIGNANT TUMOR +PART 2: LEFT, AXILLARY LYMPH NODE, ULTRASOUND GUIDED CORE BIOPSY +A: METASTATIC DISEASE CONSISTANT WITH BREAST PRIMARY IN TWO OF TWO LYMPH NODES (2/2) +PART 3: BREAST, LEFT, 2 O’CLOCK, ULTRASOUND GUIDED CORE BIOPSY +A: INVASIVE DUCTAL CARCINOMA, NUCLEAR GRADE 2. +B: DUCTAL CARCINOMA IN SITU, NUCLEAR GRADE 2 +C: ATYPICAL LOBULAR HYPERPLASIA + +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: positive, H-score: 100 +Progesterone Receptor: positive, H-score: 45 +Her2/NEU: negative, 1+ + + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc3_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc3_NOTE.txt new file mode 100644 index 0000000..cb0abce --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc3_NOTE.txt @@ -0,0 +1,20 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20090510 1015 +Record Type...................NOTE +Patient DOB...................08/01/1972 + +CLINICAL HISTORY: This is a 37 year old pre-menopausal female with a newly diagnosed left breast cancer. She felt a lump in the upper outer quadrant of the left breast. Breast imaging on 5/5/09 revealed multiple areas of concern. She went to have 2 biopsies at the 1 o’clock and 2 o’clock positions that showed invasive ductal carcinoma. These were ER positive, PR positive and HER2/NEU negative. She presents now to discuss options for treatment. +Past Medical History: She has a history of a right ovarian cyst and endometriosis. +Physical Exam: Health appearing young female in NAD +VS: BP 120/80, Pulse 71, Temp 97.0 +HEENT: NC/AT, PERRL, EOMI, sclera non-icteric +Neck: Supple, no masses, thyroid not enlarged +LUNGS: CTA, No wheezes, rales, rhonchi +COR: RRR, No murmurs, rubs or gallops +ABD: Soft, non-tender, non-distended +EXT: Good pulses, No clubbing, cyanosis or edema +IMPRESSION: +Patient with newly diagnoses clinical stage 3A (T3,N2,M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases. Recommendation was made for her to start chemotherapy with Adriamycin and Cytoxan for 4 cycles, followed by 12 cycles of Taxotere. We will assess tumor response midway through therapy. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc4_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc4_NOTE.txt new file mode 100644 index 0000000..f248b45 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc4_NOTE.txt @@ -0,0 +1,16 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20090630 1015 +Record Type...................NOTE +Patient DOB...................08/01/1972 + +DIAGNOSIS: 37 year old female with clinical stage 3A (T3, N2, M0) invasive ductal carcinoma of the left breast +THERAPY: Completed 6 cycles of Taxotere. +CLINICAL HISTORY: This is a 37 year old pre-menopausal female with a newly diagnosed invasive ductal carcinoma of the left breast. She returns for ongoing management. Her clinical breast exam that time was significant for a 1.0 cm palpable mass at the 1 o’clock position of the left breast and a 2.0 cm palpable mass at the 2 o’clock position of the left breast both in the upper outer quadrant. Imaging also revealed enlarged left axillary lymph nodes. She went to have 2 biopsies at the 1 o’clock and 2 o’clock positions that showed invasive ductal carcinoma. These were ER positive, PR positive and HER2/NEU negative. She presents for assessment of tumor response to neoadjuvant chemotherapy. She completed 4 cycles of Adriamycin and Cytoxan. She also has completed 6 of 12 planned cycles of Taxotere. +Past Medical History: She has a history of a right ovarian cyst and endometriosis. +Physical Exam: Health appearing young female in NAD. She has tolerated chemotherapy with minimal side-effects. She has had no fever, nausea, vomiting, chest pain or diarrhea. Cardiac exam showed normal S1 and S2 with no murmurs. Extremities were without edema. + +IMPRESSION: +Patient has had a partial response to chemotherapy. Recent imaging showed decrease in size of the invasive tumor at 1 o’clock measuring 0.8 cm from 1.0 cm and the invasive tumor at 2 o’clock now measuring 1.0 cm from 2.0 cm. Metastatic left axillary lymph nodes now measure 0.9 and 1.5 cm from previous 2.4 and 2.0 cm respectfully. Patient with clinical stage 3A (T3, N2, M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases showing tumor response to chemotherapy. Final recommendation will be made following the completion of Taxotere. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc5_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc5_SP.txt new file mode 100644 index 0000000..3c4e67c --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc5_SP.txt @@ -0,0 +1,39 @@ +=================================================================== +Report ID.....................5,doc5 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20090902 1420 +Record Type...................SP +Patient DOB...................08/01/1972 + +CLINICAL HISTORY: +This is a 38 year old pre-menopausal female with invasive ductal carcinoma of the left breast, metastatic to the left axillary lymph nodes. Clinical stage 3A, S/P neoadjuvant chemotherapy, left mastectomy and axillary lymph node dissection. + +FINAL DIAGNOSIS: +PART 1: LEFT BREAST, MODIFIED RADICAL MASTECTOMY + • INVASIVE DUCTAL CARCINOMA, NUCLEAR GRADE 2, TUMOR MASS IN THE 1 O’CLOCK REGION IN THE UPPER OUTER QUADRANT + • INVASIVE DUCTAL CARINOMA, NUCLEAR GRADE 2, TUMOR MASS IN THE 2 O’CLOCK REGION IN THE UPPER OUTER QUADRANT + • DUCTAL CARCINOMA IN SITU, NUCLEAR GRADE 2 + • SURGICAL MARGINS ARE NEGATIVE + • CHANGES CONSISTANT WITH PREVIOUS CORE BIOPSY + • CHANGES CONSISTANT WITH S/P CHEMOTHERAPY + • MICROCALCIFICATIONS ASSOCIATED WITH MALIGNANT +PART 2: LEFT AXILLARY LYMPH NODE DISSECTION +A: 2 OUT OF 6 AXILLARY LYMPH NODES POSITIVE FOR METASTATIC CARCINOMA (2/6) + +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: positive, H-score: 100 +Progesterone Receptor: positive, H-score: 45 +Her2/NEU: negative, 1+ +Her2/NEU (FISH): Not Amplified + +Pathologic Stage +T Stage: PT3 +N Stage: PN2 +M Stage: PM0 + + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc6_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc6_NOTE.txt new file mode 100644 index 0000000..49d327e --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc6_NOTE.txt @@ -0,0 +1,15 @@ +=================================================================== +Report ID.....................6,doc6 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20091001 1300 +Record Type...................NOTE +Patient DOB...................08/01/1972 + +DIAGNOSIS: 38 year old female with clinical stage 3A (T3, N2, M0) invasive ductal carcinoma of the left breast +INTERIM HISTORY: This is a 38 year old pre-menopausal female with invasive ductal carcinoma of the left breast. She IS S/P left breast mastectomy with left axillary lymph node dissection on 9/2/09. The operation was performed without complication and her recovery has been uneventful. Her clinical breast exam in early May of 2009 was significant for a 1.0 cm palpable mass at the 1 o’clock position of the left breast and a 2.0 cm palpable mass at the 2 o’clock position of the left breast both in the upper outer quadrant. Imaging also revealed enlarged left axillary lymph nodes. She went to have 2 biopsies at the 1 o’clock and 2 o’clock positions that showed invasive ductal carcinoma. These were ER positive, PR positive and HER2/NEU negative. She completed 4 cycles of Adriamycin and Cytoxan and 12 cycles of Taxotere prior to her surgery. +Past Medical History: She has a history of a right ovarian cyst and endometriosis. +Physical Exam: Health appearing young female in NAD. There is a well-healed surgical scar of the left breast. There are no signs of bruising, erythema or infection. She has had no fever, nausea, vomiting, chest pain or diarrhea. Cardiac exam showed normal S1 and S2 with no murmurs. Extremities were without edema. + +IMPRESSION: +Patient with stage 3A (T3, N2, M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases. She returns for discussion of maintenance therapy. Recommendation is made to start Tamoxifen. She will follow up with me in 6 months. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc7_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc7_NOTE.txt new file mode 100644 index 0000000..cde043f --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc7_NOTE.txt @@ -0,0 +1,15 @@ +=================================================================== +Report ID.....................7,doc7 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20100205 0300 +Record Type...................NOTE +Patient DOB...................08/01/1972 + +CHIEF COMPLAINT: Patient admitted with shortness of breath, chest pain and abdominal pain. +CLINICAL HISTORY: This is a 38 year old presenting to the EW with SOB, CP and abdominal pain. She was diagnosed with invasive ductal carcinoma of the left breast with left axillary lymph nodes metastases. She received 4 cycles of Adriamycin and Cytoxan followed by 12 cycles of Taxotere. She underwent a total mastectomy of the left breast with left axillary lymph node dissection on 9/2/09. At the time of surgery she was a stage 3A (T3, N2, M0) ER positive, PR positive and HER2/NEU negative. Her surgery was performed without complication and her recovery has been uneventful. She has been on Tamoxifen since October 2009. She has tolerated this well without any significant side effects. +Past Medical History: She has a history of a right ovarian cyst and endometriosis. +Physical Exam: Reveals an ill-appearing female in moderate distress. Cardiac exam showed normal S1 and S2 with no murmurs. Extremities were without edema. Lung exam with coarse breath sounds in both lungs. Exam of the abdomen reveal tenderness in the lower abdomen. + +IMPRESSION: +Patient presented with chest and abdominal pain and shortness of breath. She was diagnosed with stage 3A (T3, N2 ,M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases on 5/5/09. She was started on maintenance therapy with Tamoxifen in October 2009. We will obtain a CT scan of the chest to rule out pneumonia or metastatic disease. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc8_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc8_RAD.txt new file mode 100644 index 0000000..292dd0f --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc8_RAD.txt @@ -0,0 +1,19 @@ +=================================================================== +Report ID.....................8,doc8 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20100206 1015 +Record Type...................RAD +Patient DOB...................08/01/1972 + +CLINICAL HISTORY: +38 year old female with a history of left breast invasive ductal carcinoma metastatic to axillary lymph nodes on Tamoxifen presents with chest pain and shortness of breath. She is here for CT of the chest and abdomen. +Technique: Serial helical images were obtained at 2.0 mm increments from the lung apices to the abdomen. + +FINDINGS: +Lungs: +There are small pleural effusions on the left associated with atelectasis. There are larger pleural effusions on the right. A 3 mm nodule is seen in the right middle lobe of the lung. A 4 mm nodule is seen in the left lower lung. Additional 2 mm pulmonary nodules in the right lower lobe are noted. +Abdomen: +Abdominal CT showed new 2 mm nodules in the left lobe of the liver. +IMPRESSION: +New pulmonary nodules in both lungs and a new nodule in the left lobe of the liver are concerning for malignancy. Biopsy of the lung nodules was recommended. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc9_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc9_SP.txt new file mode 100644 index 0000000..b42b849 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient5/fake_patient5_doc9_SP.txt @@ -0,0 +1,32 @@ +=================================================================== +Report ID.....................9,doc9 +Patient ID....................pt101102103 +Patient Name..................Fake Patient5 +Principal Date................20100207 1230 +Record Type...................SP +Patient DOB...................08/01/1972 + + + +CLINICAL HISTORY: +The patient is a 38-year-old female with a history of metastatic breast carcinoma. + +PRE-OP DIAGNOSIS: Lung mass +POST-OP DIAGNOSIS: Lung mass +PROCEDURE: Bronchoscopy, EBUS + + + +FINAL DIAGNOSIS: + +LUNG, LEFT LOWER LOBE, BRONCHOSCOPIC BIOPSY + +METASTATIC POORLY DIFFERENTIATED CARCINOMA CONSISTENT WITH BREAST PRIMARY. + +IMMUNOHISTOCHEMISTRY +HER2/NEU: NEGATIVE (NOT AMPLIFIED) + + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/#fake_patient6_doc4_NOTE.txt# b/dphe-stream-nginx/integration-test/reports/fake_patient6/#fake_patient6_doc4_NOTE.txt# new file mode 100644 index 0000000..9057116 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/#fake_patient6_doc4_NOTE.txt# @@ -0,0 +1,36 @@ +=================================================================== +Report ID.....................4,doc4 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20100830 1415 +Record Type...................NOTE +Patient DOB...................05/01/1941 +CLINICAL HISTORY: This is a 69 year old post-menopausal female with a +newly diagnosed invasive ductal carcinoma of the left breast. She is +ER positive, PR negative and HER2 positive. She presents now to +discuss options for treatment. +INTERIM HISTORY: She underwent a U/S core biopsy of the left breast +and lymph node on 8/18/10 which revealed invasive ductal +carcinoma. Breast MRI on 8/20/10 demonstrated a left breast malignancy +at the 4 o’clock position measuring 1.2x1.3x1.1 cm. MRI also showed a +left axillary lymphadenopathy. MRI of the right breast showed +post-surgical changes consistent previous lumpectomy and changes +consistent with radiation therapy. PET/CT on 8/24/10 showed no +evidence of distant metastases. +PMH: She has a history DCIS of the right breast ER and PR positive +diagnosed in January of 1999. She was stage 0 (pTis, pNx).She +underwent a right segmental mastectomy on 2/1/99 followed by +re-excision for positive margins. She started Tamoxifen in March of +2009 followed by radiation therapy from April to May 1999. +Physical Exam: Well appearing female in NAD +VS: BP 120/80, Pulse 71, Temp 97.0 +HEENT: NC/AT, PERRL, EOMI, sclera non-icteric +Neck: Supple, no masses, thyroid not enlarged +LUNGS: CTA, No wheezes, rales, rhonchi +COR: RRR, No murmurs, rubs or gallops +ABD: Soft, non-tender, non-distended, No HSM. +EXT: Good pulses, No clubbing, cyanosis or edema +IMPRESSION: +Patient with 2A (T1,N1,M0) invasive ductal carcinoma of the left +breast with left axillary lymph node metastases. She will start +chemotherapy with Taxotere and Carboplatin. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc1_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc1_RAD.txt new file mode 100644 index 0000000..32c59e2 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc1_RAD.txt @@ -0,0 +1,18 @@ +=================================================================== +Report ID.....................1,doc1 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20100816 1045 +Record Type...................RAD +Patient DOB...................05/01/1941 +CLINICAL HISTORY: +Patient is a 69 year old post-menopausal female presenting for evaluation of a left breast lump and enlarged left axillary lymph node identified on routine screening mammography performed on 8/8/10. + +MAMMOGRAPHY: +Digital diagnostic mammography of the left breast was performed. Full lateral inferior and magnification views confirm the presence of a 1.0 cm ill-defined mass at the 4 o’clock position of the left breast. A left axillary view shows 2 abnormal dense round lymph nodes measuring 3.0 cm and 2.1 cm. +Sonography of the left breast confirms a 1.0x0.8x0.7 cm hypoechoic mass at the 4 o’clock central position. This mass has an irregular shape and no other masses are seen. +Sonography of the left axilla demonstrates 2 abnormal lymph nodes, both with cortical thickening. This is worrisome for extra-nodal extension and favors a diagnosis of metastatic disease. +IMPRESSION: +There is a suspicious 1.0 cm solid mass located in the left breast at 4 o’clock. There are 2 palpable enlarged left axillary lymph nodes. Ultrasound guided core biopsy the left breast mass is recommended. Ultrasound guided core biopsy of the abnormal left axillary lymph node was recommended. +ACR BI-RADS category (left breast): 5 – Highly suggestive of malignancy. +Abnormal left axillary lymph node highly suspicious for metastatic disease. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc2_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc2_RAD.txt new file mode 100644 index 0000000..e9bfaf7 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc2_RAD.txt @@ -0,0 +1,17 @@ +=================================================================== +Report ID.....................2,doc2 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20100818 1245 +Record Type...................RAD +Patient DOB...................05/01/1941 + +CLINICAL HISTORY: +Patient is a 69 year old female who returns for ultrasound guided core biopsy of the 1.0 cm solid mass at the 4 o’clock position of the left breast and the 3.0 cm palpable left axillary lymph node. + +TECHNIQUE: +The left breast was prepped in the usual sterile fashion. Under ultrasound guidance 2cc of 1% lidocaine was injected. A small incision in the skin was made. Core biopsy was performed using a 14 gauge needle. Two passes were made directly through the lesion. A clip was placed at the biopsy site. +The left axilla was prepped in the usual sterile fashion. Under ultrasound guidance 2cc of 1% lidocaine was injected. A small incision in the skin was made. Core biopsy was performed using a 14 gauge needle. Two passes were made directly through the lesion. A clip was placed at the biopsy site. +Post procedure digital mammography was obtained and shows the clips at the sites of the lesions. +IMPRESSION: +Successful core biopsy of a 1.0 cm left breast mass and a 3.0 cm left axillary lymph node has been performed under ultrasound guidance. The specimens were sent to pathology. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc3_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc3_SP.txt new file mode 100644 index 0000000..161f743 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc3_SP.txt @@ -0,0 +1,34 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20100818 1130 +Record Type...................SP +Patient DOB...................05/01/1941 + + + +CLINICAL HISTORY: +69 year old female with a mass in the left breast and a palpable left axillary lymph node status post ultrasound guided core biopsy. She had a history of DCIS of the right breast diagnosed in 1999. + + +FINAL DIAGNOSIS: +PART 1: BREAST, LEFT, 4 O' CLOCK, ULTRASOUND GUIDED CORE BIOPSY +A. INVASIVE DUCTAL CARCINOMA, NUCLEAR GRADE 2. +B. DUCTAL CARCINOMA IN SITU, NUCLEAR GRADE 2 + +PART 2: LEFT, AXILLARY LYMPH NODE, ULTRASOUND GUIDED CORE BIOPSY +A: INVASIVE DUCTAL CARCINOMA, NUCLEAR GRADE 2 + + + +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: positive, H-score: 60 +Progesterone Receptor: NEGATIVE, H-score: 0 +Her2/NEU: POSITIVE, 3+ + + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc4_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc4_NOTE.txt new file mode 100644 index 0000000..ad045ae --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc4_NOTE.txt @@ -0,0 +1,20 @@ +=================================================================== +Report ID.....................4,doc4 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20100830 1415 +Record Type...................NOTE +Patient DOB...................05/01/1941 +CLINICAL HISTORY: This is a 69 year old post-menopausal female with a newly diagnosed invasive ductal carcinoma of the left breast. She is ER positive, PR negative and HER2 positive. She presents now to discuss options for treatment. +INTERIM HISTORY: She underwent a U/S core biopsy of the left breast and lymph node on 8/18/10 which revealed invasive ductal carcinoma. Breast MRI on 8/20/10 demonstrated a left breast malignancy at the 4 o’clock position measuring 1.2x1.3x1.1 cm. MRI also showed a left axillary lymphadenopathy. MRI of the right breast showed post-surgical changes consistent previous lumpectomy and changes consistent with radiation therapy. PET/CT on 8/24/10 showed no evidence of distant metastases. +PMH: She has a history DCIS of the right breast ER and PR positive diagnosed in January of 1999. She was stage 0 (pTis, pNx).She underwent a right segmental mastectomy on 2/1/99 followed by re-excision for positive margins. She started Tamoxifen in March of 2009 followed by radiation therapy from April to May 1999. +Physical Exam: Well appearing female in NAD +VS: BP 120/80, Pulse 71, Temp 97.0 +HEENT: NC/AT, PERRL, EOMI, sclera non-icteric +Neck: Supple, no masses, thyroid not enlarged +LUNGS: CTA, No wheezes, rales, rhonchi +COR: RRR, No murmurs, rubs or gallops +ABD: Soft, non-tender, non-distended, No HSM. +EXT: Good pulses, No clubbing, cyanosis or edema +IMPRESSION: +Patient with 2A (T1,N1,M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases. She will start chemotherapy with Taxotere and Carboplatin. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc5_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc5_NOTE.txt new file mode 100644 index 0000000..83936cb --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc5_NOTE.txt @@ -0,0 +1,14 @@ +=================================================================== +Report ID.....................5,doc5 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20101115 1045 +Record Type...................NOTE +Patient DOB...................05/01/1941 + +CLINICAL HISTORY: This is a 69 year old post-menopausal female with metastatic invasive ductal carcinoma of the left breast. She is ER positive, PR negative and HER2 positive. She has completed 3 cycles of Taxotere and Carboplatin. She comes in to assess response to therapy. +INTERIM HISTORY: She has experienced some nausea and vomiting treated with anti-emetics and diarrhea treated with Lomotil. Briefly she was diagnosed with invasive ductal carcinoma of the left breast on biopsy dated 8/18/10. She was found to have metastatic disease to the left axillary lymph node. Decision was made to start her on Taxotere and Carboplatin and re-assess tumor response to chemotherapy. +On physical exam she looks and feels well. VSS. MRI of the left breast reveals decrease in tumor size which now measures 0.9x1.0x0.8 cm from previous 1.2x1.3x1.1 cm. The left axillary lymph node now measures 2.0x1.9 cm from previous 3.0x2.0 cm. +PMH: She has a history DCIS of the right breast ER and PR positive diagnosed in January of 1999. She was stage 0 (pTis, pNx). She underwent a right segmental mastectomy on 2/1/99 followed by re-excision for positive margins. She started Tamoxifen in March of 2009 followed by radiation therapy from April to May 1999. +IMPRESSION: +Patient with clinical stage 2A (T1,N1,M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases with tumor regression S/P 3 cycles of Taxotere and Carboplatin. She will return after her 6th cycle to discuss surgery. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc6_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc6_NOTE.txt new file mode 100644 index 0000000..6036419 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc6_NOTE.txt @@ -0,0 +1,14 @@ +=================================================================== +Report ID.....................6,doc6 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20110217 1445 +Record Type...................NOTE +Patient DOB...................05/01/1941 + +CLINICAL HISTORY: This is a 69 year old post-menopausal female who at initial presentation showed invasive ductal carcinoma of the left breast with left axillary lymph node metastases. She is ER positive, PR negative and HER2 positive. She has completed 6 cycles of Taxotere and Carboplatin. She comes in to discuss further therapy. +INTERIM HISTORY: She has tolerated chemotherapy with some nausea and vomiting treated with anti-emetics and diarrhea treated with Lomotil. She stated that she notices decrease in tumor in the left breast. Breast MRI from 2/1/11 confirms this with the left breast cancer now measuring 0.5x0.6x0.1 cm from 1.2x1.3x1.1 cm on original MRI dated 8/20/10. The metastatic left axillary lymph node now measures 1.9 cm from previous 3.0 cm. Mammography confirmed the findings. +PMH: She has a history DCIS of the right breast ER and PR positive diagnosed in January of 1999. She was stage 0 (pTis, pNx). She underwent a right segmental mastectomy on 2/1/99 followed by re-excision for positive margins. She started Tamoxifen in March of 2009 followed by radiation therapy from April to May 1999. +On physical exam she looks and feels well. VSS. Cardiac exam reveals normal S1 and S2 without murmurs, rubs or gallops. Lungs are clear to auscultation without wheezes, rales or rhonchi. Abdomen is soft, non-tender without hepatosplenomegaly. Extremities are without clubbing, cyanosis or edema. +IMPRESSION: +Patient is a pleasant 69 year old female with clinical stage 2A (T1,N1,M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases with tumor regression S/P 6 cycles of Taxotere and Carboplatin. She is scheduled to have a left breast mastectomy and left axillary lymph node dissection. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc7_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc7_SP.txt new file mode 100644 index 0000000..80b6b8e --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc7_SP.txt @@ -0,0 +1,37 @@ +=================================================================== +Report ID.....................7,doc7 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20110301 1115 +Record Type...................SP +Patient DOB...................05/01/1941 + +CLINICAL HISTORY: +69 year old female with invasive ductal carcinoma of the left breast and axillary lymph nodes status post neoadjuvant chemotherapy. She had a history of DCIS of the right breast diagnosed in 1999. + + +FINAL DIAGNOSIS: +PART 1: BREAST, LEFT, SEGMENTAL MASTECTOMY +A. S/P NEOADJUVANT CHEMOTHERAPY FOR INVASIVE DUCTAL CARCINOMA, +NUCLEAR GRADE 2 WITH METASTASES TO THE LEFT AXILLARY LYMPH NODES +B. MARGINS ARE CLEAR +C. NO RESIDUAL CARCINOMA IDENTIFIED + +PART 2: LEFT, AXILLARY LYMPH NODES +A: 24 AXILLARY LYMPH NODES, FREE OF TUMOR (0/24) + + + +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: positive, H-score: 60 +Progesterone Receptor: NEGATIVE, H-score: 0 +Her2/NEU: POSITIVE, 3+ + +PATHOLOGIC STAGE +T STAGE: T1 +N STAGE: N1 +M STAGE: MO + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc8_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc8_NOTE.txt new file mode 100644 index 0000000..9635116 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient6/fake_patient6_doc8_NOTE.txt @@ -0,0 +1,14 @@ +=================================================================== +Report ID.....................8,doc8 +Patient ID....................pt789789789 +Patient Name..................Fake Patient6 +Principal Date................20110415 1115 +Record Type...................NOTE +Patient DOB...................05/01/1941 + +CLINICAL HISTORY: This is a 69 year old post-menopausal female with clinical stage 2A (T1 N1 M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases. She is ER positive, PR negative and HER2 positive. She is status post 6 cycles of Taxotere and Carboplatin followed by left breast segmental mastectomy and left axillary lymph node dissection performed on 3/1/11. +INTERIM HISTORY: Her surgical incision is completely healed. She has no redness, erythema, irritation or signs of infection. She has limited range of motion from her axillary surgery and has been encouraged to perform exercises for mobility. She presents for Radiation Therapy consultation. The patient started on single agent Herceptin on 4/1/11. +PMH: She has a history DCIS of the right breast ER and PR positive diagnosed in January of 1999. She was stage 0 (pTis, pNx). She underwent a right segmental mastectomy on 2/1/99 followed by re-excision for positive margins. She started Tamoxifen in March of 2009 followed by radiation therapy from April to May 1999. +On physical exam she looks and feels well. VSS. Cardiac exam reveals normal S1 and S2 without murmurs, rubs or gallops. Lungs are clear to auscultation without wheezes, rales or rhonchi. Abdomen is soft, non-tender without hepatosplenomegaly. Extremities are without clubbing, cyanosis or edema. +IMPRESSION: +Patient is a pleasant 69 year old female with clinical stage 2A (T1,N1,M0) invasive ductal carcinoma of the left breast with left axillary lymph node metastases S/P neoadjuvant chemotherapy with pathologic complete response (T0 N0) to receive radiation therapy to he left breast and tumor bed. She will continue on Herceptin. We will plan to see her after completion of radiation therapy. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc1_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc1_RAD.txt new file mode 100644 index 0000000..7ae2e9a --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc1_RAD.txt @@ -0,0 +1,23 @@ +=================================================================== +Report ID.....................1,doc1 +Patient ID....................pt357357357 +Patient Name..................Fake Patient7 +Principal Date................20100510 1045 +Record Type...................RAD +Patient DOB...................03/01/1938 + +CLINICAL HISTORY: +This is a 72 year old post-menopausal female who on recent screening mammogram on 5/4/10 revealed a suspicious lump of the left breast. + +TECHNIQUE: +Spot compression views of the left breast were obtained with ultrasound of the left breast and left axilla. +FINDINGS: +There are calcifications in the left breast at 10 o’clock position. Findings are suspicious for carcinoma. The mass measures greater than 8 cm. +Left breast ultrasound revealed a lobulated mass in the superior region measuring 1.7X1.6X1.5 CM. An additional 9x12 mm irregular shaped mass located at the 11 o’clock position measuring 2.9 cm. +Ultrasound of the left axilla showed a 17 mm lymph node with focal thickening of the cortex. +IMPRESSION: +Findings are consistent with multifocal carcinoma of the left breast. A thickened left axillary lymph node is noted and suspicious for metastatic disease. +ACR BI-RADS category (left breast): 5 – Highly suspicious for malignancy. +Abnormal left axillary lymph node highly suspicious for metastatic disease. +RECOMMENDATION: +The patient is scheduled for U/S guided biopsy of the left breast mass and abnormal left axillary lymph node. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc2_RAD.txt b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc2_RAD.txt new file mode 100644 index 0000000..85bb0eb --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc2_RAD.txt @@ -0,0 +1,21 @@ +=================================================================== +Report ID.....................2,doc2 +Patient ID....................pt357357357 +Patient Name..................Fake Patient7 +Principal Date................20100516 1045 +Record Type...................RAD +Patient DOB...................03/01/1938 + +CLINICAL HISTORY: +Patient is a 72 year old female who returns for ultrasound guided core biopsy of the left breast mass and the abnormal left axillary lymph node found on mammogram. +PROCEDURE: +U/S guided core biopsy of mass in 10 o’clock position of left breast with clip placement +U/S guided core biopsy of mass in 11 o’clock position of left breast with clip placement +U/S guided core biopsy of abnormal left axillary lymph node with clip placement + +TECHNIQUE: +Sonography of the left breast mass at 10 o’clock was performed. The left breast was prepped in the usual sterile fashion. Under ultrasound guidance 2cc of 1% lidocaine was injected. A small skin incision was made. Under ultrasound guidance 2 passes were made with a 14 gauge needle. Clip was placed. Under ultrasound guidance 2 passes were made with a 14 gauge needle of the left breast mass at the 11 o’clock position. Clip was placed. +Sonography of the left axilla revealed 2 abnormal lymph nodes. One lymph node located in the superior axilla measuring 4 mm and another inferior axilla measuring 5 mm. A small incision in the skin was made. Core biopsy was performed using a 14 gauge needle. Two passes were made directly through the lesion. A clip was placed at the biopsy site. +Post procedure digital mammography was obtained and shows the clips at the sites of the lesions. +IMPRESSION: +Successful core biopsies of the suspicious masses at 10 o’clock and 11 o’clock position of the left breast. Successful core biopsy of suspicious left axillary lymph node. The specimens were sent to pathology. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc3_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc3_SP.txt new file mode 100644 index 0000000..ddad4e9 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc3_SP.txt @@ -0,0 +1,38 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt357357357 +Patient Name..................Fake Patient7 +Principal Date................20100516 1130 +Record Type...................SP +Patient DOB...................03/01/1938 + + + +CLINICAL HISTORY: +72 year old female with a mass in the left breast and a palpable left axillary lymph node status post ultrasound guided core biopsy. + + + +FINAL DIAGNOSIS: +PART 1: BREAST, LEFT, 10 O' CLOCK, ULTRASOUND GUIDED CORE BIOPSY +A. INFILTRATING DUCTAL CARCINOMA, NUCLEAR GRADE 2. +B. MICROCALCIFICATIONS IN BIOPSY SPECIMEN + +PART 2: BREAST, LEFT, 11 O’CLOCK, ULTRASOUND GUIDED CORE BIOPSY + • DUCTAL CARCINOMA IN SITU, NUCLEAR GRADE 2 + +PART 2: LEFT, AXILLARY LYMPH NODE, ULTRASOUND GUIDED CORE BIOPSY +A: BENIGN LYMPH NODE + + + +COMMENT: +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: POSITIVE, H-score: 190 +Progesterone Receptor: POSITIVE, H-score: 180 +Her2/NEU: NEGATIVE, 1+ + + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc4_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc4_NOTE.txt new file mode 100644 index 0000000..1805ca5 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc4_NOTE.txt @@ -0,0 +1,21 @@ +=================================================================== +Report ID.....................4,doc4 +Patient ID....................pt357357357 +Patient Name..................Fake Patient7 +Principal Date................20100525 1415 +Record Type...................NOTE +Patient DOB...................03/01/1938 +CLINICAL HISTORY: This is a 72 year old post-menopausal female who felt a lump in her left breast which on biopsy revealed infiltrating ductal carcinoma and DCIS of the left breast. An enlarged left axillary lymph node was biopsied and found to be benign. She is ER positive, PR positive and HER2 negative. MRI revealed a tumor 6.0 cm in diameter. She presents now to discuss options for treatment. +INTERIM HISTORY: Patient seen post biopsy for evaluation and management of newly diagnosed infiltrating ductal carcinoma of the left breast with associated DCIS. She underwent a U/S core biopsy of the left breast and lymph node on 5/16/10 which revealed infiltrating ductal carcinoma. Breast MRI on 5/20/10 demonstrated a left breast malignancy at the 10 o’clock position measuring 1.2x1.3x1.1 cm. MRI also showed a left axillary lymphadenopathy. MRI of the right breast was without malignancy. PET/CT on 5/22/10 showed no evidence of distant metastases. +PMH: She has Chronic Lymphocytic Leukemia diagnosed in May of 2002 receiving immunosuppressive therapy with Alemtuzumab. WBC has been normal and recent bone marrow biopsy showed stable disease. +Physical Exam: Well appearing female in NAD +VS: BP 120/80, Pulse 71, Temp 97.0 +HEENT: NC/AT, PERRL, EOMI, sclera non-icteric +Neck: Supple, no masses, thyroid not enlarged +LUNGS: CTA, No wheezes, rales, rhonchi +COR: RRR, No murmurs, rubs or gallops +ABD: Soft, non-tender, non-distended, No HSM. +EXT: Good pulses, No clubbing, cyanosis or edema + +IMPRESSION: +On review of the patient’s screening and diagnostic imaging there is an abnormality noted with significant calcifications extending posteriorly in the left breast. She is scheduled to undergo a left breast mastectomy with axillary lymph node dissection. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc5_SP.txt b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc5_SP.txt new file mode 100644 index 0000000..22f48d0 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc5_SP.txt @@ -0,0 +1,43 @@ +=================================================================== +Report ID.....................5,doc5 +Patient ID....................pt357357357 +Patient Name..................Fake Patient7 +Principal Date................20100621 1330 +Record Type...................SP +Patient DOB...................03/01/1938 +CLINICAL HISTORY: +72 year old female with infiltrating ductal carcinoma of the left breast status post left breast total mastectomy and axillary lymph node dissection. + +FINAL DIAGNOSIS: +PART 1: LEFT BREAST, TOTAL MASTECTOMY +A. INFILTRATING DUCTAL CARCINOMA +B. 2 FOCI OF INVASIVE CARCINOMA, NUCLEAR GRADE 3 +C. LARGER FOCUS 1.8 CM AT 10 O’CLOCK +D. SMALLER FOCUS 1.1 CM AT 11 O’CLOCK +E. DUCTAL CARCINOMA IN SITE WITH CALCIFICATIONS,NUCLEAR GRADE 2 +F. SURGICAL MARGINS ARE NEGATIVE + +PART 2: LEFT AXILLARY SENTINEL LYMPH NODE #1 BIOPSY +A. ONE LYMPH NODE WITH METASTATIC CARCINOMA (1/1) + +PART 3: LEFT AXILLARY SENTINEL LYMPH NODE #2 BIOPSY +A. ONE LYMPH NODE NEGATIVE FOR MALIGNANCY (0/1) + +PART 2: LEFT AXILLARY LYMPH NODE DISSECTION +A: TWELVE LYMPH NODES NEGATIVE FOR MALIGNANCY (0/12) + +COMMENT: + +HORMONE IMMUNOHISTOCHEMISTRY: +Estrogen Receptor: POSITIVE, H-score: 190 +Progesterone Receptor: POSITIVE, H-score: 180 +Her2/NEU: NEGATIVE, 1+ + +PATHOLOGIC STAGE +PT1 +PN1mi +PMX + + + + diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc6_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc6_NOTE.txt new file mode 100644 index 0000000..015f225 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc6_NOTE.txt @@ -0,0 +1,22 @@ +=================================================================== +Report ID.....................6,doc6 +Patient ID....................pt357357357 +Patient Name..................Fake Patient7 +Principal Date................20100712 1415 +Record Type...................NOTE +Patient DOB...................03/01/1938 + +CLINICAL HISTORY: This is a 72 year old post-menopausal female with Stage 1B (T1, N1mi, M0) infiltrating ductal carcinoma and DCIS of the left breast. She is ER positive, PR positive and HER2 negative. +INTERIM HISTORY: Patient underwent a left modified radical mastectomy with left axillary sentinel lymph node biopsy and left axillary lymph node dissection on 6/21/10. Pathology revealed infiltrating ductal carcinoma of the left breast, 1.8 cm, nuclear grade 3. Lympho-vascular invasion was present. Surgical margins were negative. Fourteen (14) lymph nodes were removed with one positive for metastatic carcinoma. She has a well healed left mastectomy incision without signs of infection, erythema or swelling. +PMH: She has Chronic Lymphocytic Leukemia diagnosed in May of 2002 receiving immunosuppressive therapy with Alemtuzumab. WBC has been normal and recent bone marrow biopsy showed stable disease. +Physical Exam: Well appearing female in NAD +VS: BP 120/80, Pulse 71, Temp 97.0 +HEENT: NC/AT, PERRL, EOMI, sclera non-icteric +Neck: Supple, no masses, thyroid not enlarged +LUNGS: CTA, No wheezes, rales, rhonchi +COR: RRR, No murmurs, rubs or gallops +ABD: Soft, non-tender, non-distended, No HSM. +EXT: Good pulses, No clubbing, cyanosis or edema + +IMPRESSION: +Patient’s surgical management is now complete. She is to be seen by Medical Oncology to discuss systemic therapy. She also has an appointment to see Radiation Oncology for post-surgical radiation to the breast. diff --git a/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc7_NOTE.txt b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc7_NOTE.txt new file mode 100644 index 0000000..5d30fb9 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/fake_patient7/fake_patient7_doc7_NOTE.txt @@ -0,0 +1,23 @@ +=================================================================== +Report ID.....................7,doc7 +Patient ID....................pt357357357 +Patient Name..................Fake Patient7 +Principal Date................20101026 1015 +Record Type...................NOTE +Patient DOB...................03/01/1938 +CLINICAL HISTORY: This is a 72 year old post-menopausal female with Stage 1B (T1, N1mi, M0) infiltrating ductal carcinoma and DCIS of the left breast. She is ER positive, PR positive and HER2 negative. +INTERIM HISTORY: She returns having been on Anastrozole for 3 months. She has tolerated therapy well without significant side effects. She completed radiation therapy to the left breast with additional treatment to the tumor bed in August 2010. +Briefly she was diagnosed with left breast infiltrating ductal carcinoma by biopsy on 5/16/10. She underwent a left modified radical mastectomy with left axillary sentinel lymph node biopsy and left axillary lymph node dissection on 6/21/10. Pathology revealed infiltrating ductal carcinoma of the left breast, 1.8 cm, nuclear grade 3. Lympho-vascular invasion was present. Surgical margins were negative. Fourteen (14) lymph nodes were removed with one positive for metastatic carcinoma. She has a well healed left mastectomy incision without signs of infection, erythema or swelling. +PMH: She has Chronic Lymphocytic Leukemia diagnosed in May of 2002 receiving immunosuppressive therapy with Alemtuzumab. WBC has been normal and recent bone marrow biopsy showed stable disease. +Physical Exam: Well appearing female in NAD +VS: BP 120/80, Pulse 71, Temp 97.0 +HEENT: NC/AT, PERRL, EOMI, sclera non-icteric +NECK: Supple, no masses, thyroid not enlarged +LUNGS: CTA, No wheezes, rales, rhonchi +BREAST: left breast with well healed surgical scar without skin breakdown or burns. +COR: RRR, No murmurs, rubs or gallops +ABD: Soft, non-tender, non-distended, No HSM. +EXT: Good pulses, No clubbing, cyanosis or edema + +IMPRESSION: +She has tolerated her therapy with Anastrozole reasonably well. We will continue to see her every 6 months. diff --git a/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc1_RAD.txt b/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc1_RAD.txt new file mode 100644 index 0000000..7cbead0 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc1_RAD.txt @@ -0,0 +1,54 @@ +=================================================================== +Report ID.....................1,doc1 +Patient ID....................pt123456789 +Patient Name..................PatientX +Principal Date................20100121 1345 +Record Type...................RAD +=================================================================== +[Report de-identified (Limited dataset compliant) by De-ID v.6.24.5.1] + +CLINICAL HISTORY: +50 year old peri-menopausal female who presents with new hard palpable lump +in the left breast. + +TECHNIQUE: +Full field digital mammography with CAD was performed including +routine views of both breasts, spot magnification views on the right +with a full 90 degree lateral and spot compression views on the left. + +Left breast and axillary ultrasound evaluation was performed. + +COMPARISON: +This study is compared to previous examinations dating back to 2004. + +FINDINGS: +Heterogeneously dense fibroglandular tissue is present throughout +both breasts limiting the sensitivity of the mammogram. There is no evidence +of mass or calcifications in the right breast. + +A large firm mass is seen in the upper outer left breast at the 12:30 +o'clock region. The mass measures 1x2 cm on the CC view. Calcifications are +seen adjacent to the mass. + +Ultrasound evaluation was performed on the area and a 1.2x3.4x5.6 cm hypoechoic +mass is seen in the left breast at the 12:30 o'clock region. + +Ultrasound of the left axillary lymph nodes were performed revealing multiple +abnormally thickened lymph nodes. The largest lymph node has a thickened cortex +of at least 7 mm. + +IMPRESSION: +A large hypoechoic mass at the 10:30 location of the left breast is highly +suggestive of a malignancy. The mass measures 1.2x3.4x5.6 cm. Ultrasound guided +core biopsy is recommended. + +Abnormal left axillary lymph nodes are highly suspicious of metastatic disease. + +MR evaluation of extent of disease is recommended. + +ASSESSMENT AND RECOMMENDATIONS: +ACR BI-RADS Category: +5: (Breast Imaging Left) Highly suggestive for malignancy +RECOMMENDATION:Ultrasound guided core biopsy +OVERALL ASSESSMENT: +5 - Highly suggestive for malignancy \ No newline at end of file diff --git a/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc2_SP.txt b/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc2_SP.txt new file mode 100644 index 0000000..eafd6f3 --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc2_SP.txt @@ -0,0 +1,89 @@ +=================================================================== +Report ID.....................2,doc2 +Patient ID....................pt123456789 +Patient Name..................PatientX +Principal Date................20100130 1215 +Record Type...................SP +=================================================================== +[Report de-identified (Limited dataset compliant) by De-ID v.6.24.5.1] + + +FINAL DIAGNOSIS: +PART 1: BREAST, LEFT, MODIFIED RADICAL MASTECTOMY +A. INVASIVE DUCTAL CARCINOMA IN UPPER OUTER QUADRANT, 1.3 CM IN +GREATEST DIMENSION ASSOCIATED WITH MICROCALCIFICATIONS. +B. NOTTINGHAM SCORE 8/9 (TUBULES 2, NUCLEAR GRADE 3, MITOTIC RATE 3) +NOTTINGHAM GRADE 3. +C. NO DEFINITE LYMPHOVASCULAR INVASION IDENTIFIED. +D. SURGICAL MARGINS ARE NEGATIVE. +E. TUMOR IS ESTROGEN RECEPTOR NEGATIVE, PROGESTERONE RECEPTOR NEGATIVE, +HER-2/NEU NEGATIVE WITH A KI-67 INDEX OF 45%. +F. NO EVIDENCE OF IN-SITU COMPONENT SEEN. +PART 2: AXILLARY LYMPH NODES, LEFT, BIOPSY +A. TWO OUT OF TEN AXILLARY LYMPH NODES POSITIVE FOR METASTATIC +CARCINOMA (2/10). +B. LARGEST METASTATIC TUMOR MEASURES 2.5 CM IN GREATEST DIMENSION. +C. NO EXTRACAPSULAR EXTENSION IS IDENTIFIED. + +COMMENT: +Immunostaining for AE1/AE3 supports the status of the axillary lymph node. + +Pathologist: Person9, M.D. +** Report Electronically Signed Out ** +By Pathologist: Person9, M.D. +1/30/2010 15:21 +My signature is attestation that I have personally reviewed the submitted +material(s) and the final diagnosis reflects that evaluation. + +GROSS DESCRIPTION: +The specimen is received fixed, labeled with the patient's name, initials, +medical record number and "left radical modified breast mastectomy". + +CASE SYNOPSIS: +SYNOPTIC - PRIMARY INVASIVE CARCINOMA OF BREAST +LATERALITY: Left +PROCEDURE: Modified radical mastectomy +LOCATION: Upper outer quadrant +Clock position: 12:30 +SIZE OF TUMOR: Maximum dimension invasive component: 13 mm +MULTICENTRICITY/MULTIFOCALITY OF INVASIVE FOCI: +No +TUMOR AGGREGATE SIZE: Sum of the sizes of multiple invasive tumors: +TUMOR TYPE (invasive component): Ductal adenocarcinoma +NOTTINGHAM SCORE: 8 Nuclear grade: 3 +Tubule formation: 2 +Mitotic activity score: 3 +Nottingham grade (1, 2, 3): 3 +ANGIOLYMPHATIC INVASION: No +DERMAL LYMPHATIC INVASION: No +CALCIFICATION: Yes +TUMOR TYPE, IN SITU: Not present +Percent of tumor occupied by in situ component: 0 % +SURGICAL MARGINS INVOLVED BY INVASIVE COMPONENT: +No +Distance of invasive tumor to closest margin: 10 mm +SURG MARGINS INVOLVED BY IN SITU COMPONENT: +No +Distance of in situ disease to closest margin: +PAGET's DISEASE OF NIPPLE: No +LYMPH NODES POSITIVE: 2 +LYMPH NODES EXAMINED: 10 +METHOD(S) OF LYMPH NODE EXAMINATION: +H/E stain +ONLY KERATIN POSITIVE CELLS ARE PRESENT: +No +SIZE OF NODAL METASTASES: Diameter of largest lymph node metastasis: 15 mm +LYMPH NODE METASTASIS(-ES) WITH EXTRACAPSULAR EXTENSION: +No +METASTASES TO IPSILATERAL INTERNAL MAMMARY LYMPH NODE (IF APPLICABLE): +No +SKIN INVOLVED (ULCERATION): No +NON-NEOPLASTIC BREAST TISSUE: ADH, FCD +T STAGE, PATHOLOGIC: pT1c +N STAGE, PATHOLOGIC: pN1a +M STAGE: Not applicable +ESTROGEN RECEPTORS: negative, H-score: 0 +PROGESTERONE RECEPTORS: negative, H-score: 0 +HER2/NEU: negative, 0 +HER2/NEU (FISH): Not applicable +-------------------------------------------------------- diff --git a/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc3_NOTE.txt b/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc3_NOTE.txt new file mode 100644 index 0000000..37d4d8b --- /dev/null +++ b/dphe-stream-nginx/integration-test/reports/patientX/patientX_doc3_NOTE.txt @@ -0,0 +1,29 @@ +=================================================================== +Report ID.....................3,doc3 +Patient ID....................pt123456789 +Patient Name..................PatientX +Principal Date................20101202 +Record Type...................NOTE +=================================================================== +[Report de-identified (Limited dataset compliant) by De-ID v.6.24.5.1] + + +DIAGNOSIS: Stage IIA (T1 N1 M0) infiltrating ductal carcinoma, left breast, +triple negative. + +Therapy completed 9 cycles of weekly Abraxane. + +REASON FOR VISIT: Assess response to neoadjuvant chemotherapy. + +Patient92 returns to the office today for ongoing management of biopsy-proven left breast cancer with axillary lymph node metastasis. +Her initial office visit was on September 30, 2010. +Her clinical breast examination at that time was significant for a 2 cm palpable mass in the upper outer aspect of the left breast extending from 12:30 o'clock. +She also had multiple abnormally enlarged left axillary lymph nodes. + +She has now completed 9 of a planned 12 cycles of weekly Abraxane. +She has tolerated her chemotherapy overall without significant sequela. +She denies any hospitalizations. + +Her past medical history, surgical history, medications, and allergies were reviewed as noted in the electronic medical record. + +IMPRESSION: Partial response to neoadjuvant chemotherapy for a locally advanced, triple negative, left breast cancer. \ No newline at end of file diff --git a/dphe-stream-nginx/integration-test/test.cfg b/dphe-stream-nginx/integration-test/test.cfg index e62757b..c365172 100644 --- a/dphe-stream-nginx/integration-test/test.cfg +++ b/dphe-stream-nginx/integration-test/test.cfg @@ -1,4 +1,14 @@ [TEST] AUTH_TOKEN = AbCdEf123456 -BASE_URL = http://localhost:8080/deepphe/ -REPORT = patientX/patientX_doc1_RAD.txt \ No newline at end of file +REST_API_BASE_URL = http://localhost:8080/deepphe/ + +[REPORTS] +PATIENT_X_REPORT = reports/patientX/patientX_doc1_RAD.txt +FAKE_PATIENT_1_REPORT = reports/fake_patient1/fake_patient1_doc1_RAD.txt +FAKE_PATIENT_2_REPORT = reports/fake_patient2/fake_patient2_doc1_NOTE.txt +FAKE_PATIENT_3_REPORT = reports/fake_patient3/fake_patient3_doc1_NOTE.txt +FAKE_PATIENT_4_REPORT = reports/fake_patient4/fake_patient4_doc2_RAD.txt +FAKE_PATIENT_5_REPORT = reports/fake_patient5/fake_patient5_doc1_RAD.txt +FAKE_PATIENT_6_REPORT = reports/fake_patient6/fake_patient6_doc1_RAD.txt +FAKE_PATIENT_7_REPORT = reports/fake_patient7/fake_patient7_doc1_RAD.txt + diff --git a/dphe-stream-nginx/integration-test/test.py b/dphe-stream-nginx/integration-test/test.py index 6477aaa..bc1c586 100644 --- a/dphe-stream-nginx/integration-test/test.py +++ b/dphe-stream-nginx/integration-test/test.py @@ -16,9 +16,26 @@ config.read(Path(__file__).absolute().parent / 'test.cfg') user_token = config['TEST']['AUTH_TOKEN'] + # Remove trailing slash / from URL base to avoid "//" caused by config with trailing slash -base_url = config['TEST']['BASE_URL'].strip('/') -report = config['TEST']['REPORT'] +base_url = config['TEST']['REST_API_BASE_URL'].strip('/') + +report_tuples = config.items('REPORTS') + +logger.debug(config.items('REPORTS')) + + +#################################################################################################### +## Non-test Functions +#################################################################################################### + +def parse_patient_and_report(report_rel_path): + val_list = report_rel_path.split("/") + patient_name = val_list[1] + report_name = val_list[2] + + return patient_name, report_name + """ Create a dict of HTTP Authorization header with Bearer token @@ -44,102 +61,128 @@ def create_request_headers(user_token): return headers_dict +#################################################################################################### +## Test Cases +#################################################################################################### + class TestRestApi(unittest.TestCase): def test_summarize_doc(self): with self.assertRaises(Exception) as context: broken_function() - target_url = f'{base_url}/summarizeDoc/doc/doc1' - request_headers = create_request_headers(user_token) - # Add content-type header - request_headers['content-type'] = 'text/plain' + for (key, report_rel_path) in report_tuples: + patient_name, report_name = parse_patient_and_report(report_rel_path) - report_text = (Path(__file__).absolute().parent / report).read_text() + target_url = f'{base_url}/summarizeDoc/doc/{report_name}' + request_headers = create_request_headers(user_token) + # Add content-type header + request_headers['content-type'] = 'text/plain' - logger.debug(report_text) + report_text = (Path(__file__).absolute().parent / report_rel_path).read_text() - # HTTP GET - response = requests.get(url = target_url, headers = request_headers, data = report_text) + #logger.debug(report_text) - result_dict = response.json() - - logger.debug(result_dict) + # HTTP GET + # The requests package attempts to auto-encode the data for transfer and fallback is latin-1 + # Specify to encode with utf-8 to avoid encoding error + response = requests.get(url = target_url, headers = request_headers, data = report_text.encode('utf-8')) - expr = ('id' in result_dict) and (result_dict['id'] == 'doc1') + result_dict = response.json() + + #logger.debug(result_dict) - self.assertTrue(expr, "doc1 summarized") + expr = ('id' in result_dict) and (result_dict['id'] == report_name) + + self.assertTrue(expr, f"Message: {report_name} summarized") def test_summarize_patient_doc(self): with self.assertRaises(Exception) as context: broken_function() - target_url = f'{base_url}/summarizePatientDoc/patient/patientX/doc/doc1' - request_headers = create_request_headers(user_token) - # Add content-type header - request_headers['content-type'] = 'text/plain' + for (key, report_rel_path) in report_tuples: + patient_name, report_name = parse_patient_and_report(report_rel_path) + + target_url = f'{base_url}/summarizePatientDoc/patient/{patient_name}/doc/{report_name}' + request_headers = create_request_headers(user_token) + # Add content-type header + request_headers['content-type'] = 'text/plain' - report_text = (Path(__file__).absolute().parent / report).read_text() + report_text = (Path(__file__).absolute().parent / report_rel_path).read_text() - logger.debug(report_text) + #logger.debug(report_text) - # HTTP PUT - response = requests.put(url = target_url, headers = request_headers, data = report_text) + # HTTP PUT + # The requests package attempts to auto-encode the data for transfer and fallback is latin-1 + # Specify to encode with utf-8 to avoid encoding error + response = requests.put(url = target_url, headers = request_headers, data = report_text.encode('utf-8')) - result_dict = response.json() - - logger.debug(result_dict) + result_dict = response.json() + + #logger.debug(result_dict) - expr = ('id' in result_dict) and (result_dict['id'] == 'patientX') + expr = ('id' in result_dict) and (result_dict['id'] == patient_name) - self.assertTrue(expr, "patientX doc1 summarized") + self.assertTrue(expr, "Message: {patient_name} {report_name} summarized") def test_queue_patient_doc(self): with self.assertRaises(Exception) as context: broken_function() - target_url = f'{base_url}/queuePatientDoc/patient/patientX/doc/doc1' - request_headers = create_request_headers(user_token) - # Add content-type header - request_headers['content-type'] = 'text/plain' + for (key, report_rel_path) in report_tuples: + patient_name, report_name = parse_patient_and_report(report_rel_path) - report_text = (Path(__file__).absolute().parent / report).read_text() + target_url = f'{base_url}/queuePatientDoc/patient/{patient_name}/doc/{report_name}' + request_headers = create_request_headers(user_token) + # Add content-type header + request_headers['content-type'] = 'text/plain' - logger.debug(report_text) + report_text = (Path(__file__).absolute().parent / report_rel_path).read_text() - # HTTP PUT - response = requests.put(url = target_url, headers = request_headers, data = report_text) + #logger.debug(report_text) - result_dict = response.json() - - logger.debug(result_dict) + # HTTP PUT + # The requests package attempts to auto-encode the data for transfer and fallback is latin-1 + # Specify to encode with utf-8 to avoid encoding error + response = requests.put(url = target_url, headers = request_headers, data = report_text.encode('utf-8')) - # {'name': 'Document Queued', 'value': 'Added patinetX doc1 to the Text Processing Queue.'} - expr = ('name' in result_dict) and (result_dict['name'] == 'Document Queued') + result_dict = response.json() + + #logger.debug(result_dict) - self.assertTrue(expr, "patientX doc1 queued up") + # {'name': 'Document Queued', 'value': 'Added patientX patientX_doc1_RAD.txt to the Text Processing Queue.'} + expr = ('name' in result_dict) and (result_dict['value'] == f'Added {patient_name} {report_name} to the Text Processing Queue.') + + self.assertTrue(expr, "Message: {patient_name} {report_name} queued up") def test_summarize_patient(self): with self.assertRaises(Exception) as context: broken_function() - target_url = f'{base_url}/summarizePatient/patient/patientX' - request_headers = create_request_headers(user_token) + for (key, report_rel_path) in report_tuples: + patient_name, report_name = parse_patient_and_report(report_rel_path) + + target_url = f'{base_url}/summarizePatient/patient/{patient_name}' + request_headers = create_request_headers(user_token) + + # HTTP GET + response = requests.get(url = target_url, headers = request_headers) - # HTTP GET - response = requests.get(url = target_url, headers = request_headers) + result_dict = response.json() + + #logger.debug(result_dict) - result_dict = response.json() - - logger.debug(result_dict) + expr = ('id' in result_dict) and (result_dict['id'] == patient_name) - expr = ('id' in result_dict) and (result_dict['id'] == 'patientX') + self.assertTrue(expr, "Message: {patient_name} summarized") - self.assertTrue(expr, "patientX summarized") +#################################################################################################### +## Run test.py as script +#################################################################################################### if __name__ == '__main__': unittest.main() \ No newline at end of file diff --git a/dphe-stream/Dockerfile b/dphe-stream/Dockerfile index f69b9f6..88bfa1d 100644 --- a/dphe-stream/Dockerfile +++ b/dphe-stream/Dockerfile @@ -20,7 +20,7 @@ RUN yum update -y && \ curl -fsSL https://archive.apache.org/dist/maven/maven-3/$MAVEN_VERSION/binaries/apache-maven-$MAVEN_VERSION-bin.tar.gz | tar xzf - -C /usr/share && \ mv /usr/share/apache-maven-$MAVEN_VERSION /usr/share/maven && \ ln -s /usr/share/maven/bin/mvn /usr/bin/mvn && \ - unzip v0.1.0-cr-release.zip && \ + unzip v0.2.0-cr-release.zip && \ yum clean all # Set environment variables for Java and Maven @@ -31,13 +31,13 @@ ENV M2 $M2_HOME/bin ENV PATH $M2:$PATH # Install local dependencies -RUN mvn -f /usr/src/app/v0.1.0-cr-release/dphe-onto-db/pom.xml clean install -DskipTests && \ - mvn -f /usr/src/app/v0.1.0-cr-release/dphe-neo4j/pom.xml clean install -DskipTests && \ - mvn -f /usr/src/app/v0.1.0-cr-release/dphe-core/pom.xml clean install -DskipTests && \ - mvn -f /usr/src/app/v0.1.0-cr-release/dphe-stream/pom.xml clean install -DskipTests +RUN mvn -f /usr/src/app/v0.2.0-cr-release/dphe-onto-db/pom.xml clean install -DskipTests && \ + mvn -f /usr/src/app/v0.2.0-cr-release/dphe-neo4j/pom.xml clean install -DskipTests && \ + mvn -f /usr/src/app/v0.2.0-cr-release/dphe-core/pom.xml clean install -DskipTests && \ + mvn -f /usr/src/app/v0.2.0-cr-release/dphe-stream/pom.xml clean install -DskipTests # Change directory to build the REST API application jar -WORKDIR /usr/src/app/v0.1.0-cr-release/dphe-stream-rest +WORKDIR /usr/src/app/v0.2.0-cr-release/dphe-stream-rest # Remove the default application.properties # Remove the default deepphe.properties @@ -67,6 +67,6 @@ ENTRYPOINT ["/usr/local/bin/entrypoint.sh"] EXPOSE 8080 # Start the rest api server on port 8080 running as non-root -# Note: since the current work dir is /usr/src/app/v0.1.0-cr-release/dphe-stream-rest, the logs will be generated here too -# Thus we use /usr/src/app/v0.1.0-cr-release/dphe-stream-rest/logs for the volume mount in docker-compose.yml -CMD ["java", "-jar","-Xmx6G","/usr/src/app/v0.1.0-cr-release/dphe-stream-rest/target/deepphe-stream-rest-0.1.0-cr.jar"] +# Note: since the current work dir is /usr/src/app/v0.2.0-cr-release/dphe-stream-rest, the logs will be generated here too +# Thus we use /usr/src/app/v0.2.0-cr-release/dphe-stream-rest/logs for the volume mount in docker-compose.yml +CMD ["java", "-jar","-Xmx6G","/usr/src/app/v0.2.0-cr-release/dphe-stream-rest/target/deepphe-stream-rest-0.2.0-cr.jar"]