end-of-file-fixer

.github/workflows/main.yml

@@ -32,4 +32,4 @@ jobs:
           . venv/bin/activate
           pushd src/lib
           python -m pip install -r requirements.txt -r requirements-dev.txt
-          python -m pytest SmiServices/*.py
+          python -m pytest SmiServices/*.py

doc/annotation_service_docker.md

@@ -89,4 +89,3 @@ docker exec -it $(docker ps|grep annotation_server|awk '{print$1}') /bin/bash
 docker login
 docker push howff/annotation_server
 ```
-

doc/cui_sop.txt

@@ -280,4 +280,3 @@ sort -u <(jq -r < *lts/doc0001.json '.annotations[]|.cui') <(jq -r < *lts/doc011
   sed -e "s/^/'/" -e "s/$/'/" | paste -s -d ','
 
 explain analyze select semehr_results from semehr_results where sopinstanceuid = any (array(select SOPInstanceUID from cui_sop where cui IN ('C0000726','C0001511','C0003611', ..., 'C4553491')));
-

src/data/mtsamples_ihi_docs/doc0005.txt

@@ -19,5 +19,3 @@
 10.  There is a color Doppler suggestive of a patent foramen ovale with lipomatous hypertrophy of the interatrial septum.
 
 11.  The study was somewhat technically limited and hence subtle abnormalities could be missed from the study.
-
-

src/data/mtsamples_ihi_docs/doc0010.txt

@@ -25,5 +25,3 @@ IMPRESSION:
 1.  Normal LV systolic function.
 
 2.  Ejection fraction estimated around 60%.
-
-

src/data/mtsamples_ihi_docs/doc0016.txt

@@ -7,5 +7,3 @@ IMPRESSION/PLAN:
  We are going to put her on two weeks of Optifast at around 900 calories.  I have also explained the risks and potential complications of laparoscopic cholecystectomy to her in detail including bleeding, infection, deep venous thrombosis, pulmonary embolism, injury to the small intestine, stomach, liver, leak from the cystic duct, common bile duct, and possible need for ERCP and further surgery.  This surgery is going to be planned for October 6.  This is for cholelithiasis prior to her Lap-Banding procedure.
 
 I have also reviewed with her the risks and potential complications of laparoscopic gastric banding including bleeding, infection, deep venous thrombosis, pulmonary embolism, slippage of the band, erosion of the band, injury to the esophagus, stomach, small intestine, large intestine, spleen, liver, injury to the band, port, or tubing necessitating replacement of the band, port, or tubing among other potential complications and she understands.  We are going to proceed for laparoscopic gastric banding.  I have reviewed her entire chart in detail.  I have also gone over with her the Fairfield County Bariatrics consent form for banding and all the risks.  She has also signed the St. Vincent's Hospital consent form for Lap-Banding.  She has taken the preoperative quiz for banding.  She has signed the preop and postop instructions, and understands them and we reviewed them.  She has taken the quiz and done fairly well.  We have reviewed with her any potential other issues and I have answered her questions.  She is planned for surgical intervention.
-
-

src/data/mtsamples_ihi_docs/doc0018.txt

@@ -17,5 +17,3 @@ I was able to access her port.  She does have an AP standard low profile.  I asp
 ASSESSMENT:
 
   The patient is status post lap band adjustments, doing well, has a total of 7 mL within her band, tolerated water postprocedure.  She will come back in two weeks for another adjustment as needed.
-
-

src/data/mtsamples_ihi_docs/doc0021.txt

@@ -17,5 +17,3 @@ CONCLUSION:
 1.  Focus of abnormal increased tracer activity overlying the right parietal region of the skull.  CT scanning of magnetic resonance imaging of the skull and brain could be done for further assessment if it is clinically indicated.
 
 2.  There is probably some degree of urinary retention.
-
-

src/data/mtsamples_ihi_docs/doc0025.txt

@@ -1,3 +1 @@
 CHIEF COMPLAINT:
-
-

src/data/mtsamples_ihi_docs/doc0062.txt

@@ -51,5 +51,3 @@ Non-emergency department courses.  It is thought that this patient should procee
 ASSESSMENT AND PLAN: 
 
  Penile mass.  The patient does have a large pedunculated penile mass.  He will be referred to the urologist who is on-call today.  The patient will need this mass excised and biopsied.  The patient verbalized understanding the plan of followup and is discharged in satisfactory condition from the ER.
-
-

src/data/mtsamples_ihi_docs/doc0108.txt

@@ -25,5 +25,3 @@ The patient had a very thin patent processus vaginalis leading to a rather sizea
 DESCRIPTION OF OPERATION: 
 
  The patient came to the operating room and had an uneventful induction of inhalation anesthetic.  A peripheral IV was placed, and we conducted a surgical time-out to reiterate all of The patient's important identifying information and to confirm that we were indeed going to perform a left inguinal hernia and hydrocele repair.  After preparation and draping was done with chlorhexidine based prep solution, a local infiltration block as well as an ilioinguinal and iliohypogastric nerve block was performed with 0.25% Marcaine with dilute epinephrine.  A curvilinear incision was made low in the left inguinal area along one of prominent skin folds.  Soft tissue dissection was carried down through Scarpa's layer to the external oblique fascia, which was then opened to expose the underlying spermatic cord structures.  The processus vaginalis was dissected free from the spermatic cord structures, and the distal hydrocele sac was widely opened and drained of its fluid contents.  The processus vaginalis was cleared back to peritoneal reflection at the deep inguinal ring and a high ligation was performed there using both the transfixing and a mass ligature of 3-0 Vicryl.  After the excess hydrocele and processus vaginalis tissue was excised, the spermatic cord structures were replaced and the external oblique and Scarpa's layers were closed with interrupted 3-0 Vicryl sutures.  Subcuticular 5-0 Monocryl and Steri-Strips were used for the final skin closure.  The patient tolerated the operation well.  He was awakened and taken to the recovery room in good condition.  Blood loss was minimal.  No specimen was submitted.
-
-

src/data/mtsamples_ihi_docs/doc0123.txt

@@ -63,5 +63,3 @@ PLAN:
 3.  Prescriptions same as #2.  Also referred her for a barium swallow series to rule out a stricture.
 
 4.  Ortho Tri-Cyclen Lo.
-
-

src/data/mtsamples_ihi_docs/doc0128.txt

@@ -3,5 +3,3 @@ There is normal and symmetrical filling of the caliceal system.  Subsequent film
 IMPRESSION:
 
   Negative intravenous urogram.
-
-

src/data/mtsamples_ihi_docs/doc0133.txt

@@ -73,5 +73,3 @@ HOSPITAL COURSE:
  The patient was admitted to the hospital after inability to place a ureteral stent via ureteroscopy and cystoscopy.  He was made NPO.  He had a fever at first time with elevated creatinine.  He was also evaluated and treated by Dr. X, for fluid management, hypertensive management, and gave him some hydralazine and Lasix to improve his urine output, in addition to manage his blood pressure.  Once the percutaneous tube was placed, we found that his urine culture grew Pseudomonas, so he was kept on Fortaz, and was switched over to ciprofloxacin without difficulty.  He, otherwise, did well with continuing decrease his creatinine at the time of discharge to home.
 
 The patient was discharged home in stable condition with ciprofloxacin, enalapril, and recommendation for followup in Urology in 1 to 2 weeks for the surgical correction in 2 to 3 weeks of repeat pyeloplasty or possible ureterocalicostomy.  The patient had draining nephrostomy tube without difficulty.
-
-

src/data/mtsamples_ihi_docs/doc0143.txt

@@ -5,5 +5,3 @@ PREOPERATIVE DIAGNOSES:
 2.  History of bladder carcinoma.
 
 POSTOPERATIVE DIAGNOSIS:
-
-

src/data/mtsamples_ihi_docs/doc0157.txt

@@ -17,5 +17,3 @@ IMPRESSION:
 PLAN:  
 
 The patient came in followup for his routine care with Dr. X, but should not need any further routine surgical followup unless he develops any type of difficulty with this surgical wound.  If that does occur, we will be happy to see him back at any time.
-
-

src/data/mtsamples_ihi_docs/doc0211.txt

@@ -19,5 +19,3 @@ RESULTS
 IMPRESSION: 
 
  Normal coronary angiogram.
-
-

src/data/mtsamples_ihi_docs/doc0234.txt

@@ -15,5 +15,3 @@ ANESTHESIA:
   Monitored anesthesia care with regional anesthesia applied by surgeon with local.
 
 COMPLICATIONS:
-
-

src/data/mtsamples_ihi_docs/doc0240.txt

@@ -19,5 +19,3 @@ PROCEDURE #2:
 DESCRIPTION OF PROCEDURE #2:
 
   Both groins were prepped and draped.  The patient was placed at 10 degrees head-up position.  A Cook 4-French double-lumen 8-cm catheter kit was opened.  Using the 21-gauge needle that comes with the kit, several attempts were made to insert central venous and then an arterial line in the left groin.  There were several successful punctures of these vessels, but I was unable to advance Seldinger wire.  After removal of the needles, the area was compressed digitally for approximately 5 minutes.  There was a small hematoma that was not growing.  Initially, the left leg was mildly mottled with prolonged capillary refill of approximately 3 seconds.  Using 1% lidocaine, I infiltrated the vessels of the groin both medial and lateral to the vascular sheath.  Further observation, the capillary refill and circulation of the left leg became more than adequate.  The O2 saturation monitor that was on the left toe functioned well throughout the procedures, from the beginning to the end.  At the end of the procedure, the circulation of the leg was intact.
-
-

src/data/mtsamples_ihi_docs/doc0291.txt

@@ -17,5 +17,3 @@ DESCRIPTION OF PROCEDURE:
 The patient tolerated the procedure fairly well, but almost at the end of it she said that she was feeling like fainting and therefore we carefully withdrew the needle.  At that time, it was getting difficult to withdraw fluid anyway and we allowed her to lie down and after a few minutes the patient was feeling fine.  At any rate, we gave her bolus of 250 mL of normal saline and the patient returned to her room for additional hours of observation.  We then thought that if she was doing fine, then we will send her home.
 
 A chest x-ray was performed after the procedure which showed a dramatic reduction of the amount of pleural fluid and then there was no pneumothorax or no other obvious complications of her procedure.
-
-

src/data/mtsamples_ihi_docs/doc0322.txt

@@ -45,5 +45,3 @@ PROCEDURE IN DETAIL:
 PLAN:  
 
 Our plan will be to pull the drains in 48 hours.  We will then continue to watch the patient's fever curve and follow her white count to see how she is responding to the operative and medical therapies.
-
-

src/data/mtsamples_ihi_docs/doc0354.txt

@@ -1,5 +1,3 @@
 PROCEDURE IN DETAIL:
 
   After appropriate operative consent was obtained, the patient was brought supine to the operating room and placed on the operating room table.  After intravenous sedation was administered a retrobulbar block consisting of 2% Xylocaine with 0.75% Marcaine and Wydase was administered to the right eye without difficulty.  The patient's right eye was prepped and draped in a sterile ophthalmic fashion and the procedure begun.  A wire lid speculum was inserted into the right eye and a 360-degree conjunctival peritomy was performed at the limbus.  The 4 rectus muscles were looped and isolated using 2-0 silk suture.  The retinal periphery was then inspected via indirect ophthalmoscopy.
-
-

src/data/mtsamples_ihi_docs/doc0398.txt

@@ -17,5 +17,3 @@ Lesion was removed.  Attention was turned toward the area.  Pressure was held an
 The skin and the area were closed with 5-0 nylon suture.  All counts were correct.  The procedure was closed.  A sterile dressing was applied.  There were no complications.  The patient had no neurovascular deficits, etc.
 
  after this minor punch biopsy procedure.
-
-

src/data/mtsamples_ihi_docs/doc0402.txt

@@ -17,5 +17,3 @@ COMPLICATIONS:
 PROCEDURE:
 
   The area around the lesion was anesthetized after she gave consent for her procedure.  Punch biopsy including some portion of lesion and normal tissue was performed.  Hemostasis was completed with pressure holding.  The biopsy site was approximated with non-dissolvable suture.  The area was hemostatic.  All counts were correct and there were no complications.  The patient tolerated the procedure well.  She will see us back in approximately five days.
-
-

src/data/mtsamples_ihi_docs/doc0426.txt

@@ -9,5 +9,3 @@ O -
 A -
 
  1.  Plantar fasciitis.
-
-

src/data/mtsamples_ihi_docs/doc0436.txt

@@ -5,5 +5,3 @@ PROCEDURE PERFORMED:
 DESCRIPTION OF PROCEDURE:
 
   The patient was identified by myself on presentation to the angiography suite.  His right arm was prepped and draped in sterile fashion from the antecubital fossa up.  Under ultrasound guidance, a #21-gauge needle was placed into his right cephalic vein.  A guidewire was then threaded through the vein and advanced without difficulty.  An introducer was then placed over the guidewire.  We attempted to manipulate the guidewire to the superior vena cava; however, we could not pass the point of the subclavian vein and we tried several maneuvers and then opted to do a venogram.  What we did was we injected approximately 4 mL of Visipaque 320 contrast material through the introducer and did a mapping venogram and it turned out that the cephalic vein was joining into the subclavian vein.  It was very tortuous area.  We made several more attempts using the mapping system to pass the glide over that area, but we were unable to do that.  Decision was made at that point then to just do a midline catheter.  The catheter was cut to 20 cm, then we inserted back to the introducer.  The introducer was removed.  The catheter was secured by two #3-0 silk sutures.  Appropriate imaging was then taken.  Sterile dressing was applied.  The patient tolerated the procedure nicely and was discharged from Angiography in satisfactory condition back to the general floor.  We may make another attempt in the near future using a different approach.
-
-

src/data/mtsamples_ihi_docs/doc0467.txt

@@ -35,5 +35,3 @@ Coil embolization of patent ductus arteriosus.
 MANAGEMENT:  
 
 The case to be discussed at Combined Cardiology/Cardiothoracic Surgery case conference.  The patient will require a cardiologic followup in 6 months and 1 year's time including clinical evaluation and echocardiogram.  Further patient care be directed by Dr. X.
-
-

src/data/mtsamples_ihi_docs/doc0562.txt

@@ -25,5 +25,3 @@ DESCRIPTION OF PROCEDURE:
  The patient was brought to the operating room and placed in a supine position.  The right foot was prepared and draped in usual sterile manner.  Anesthesia was achieved utilizing a 50:50 mixture of 2% lidocaine plain with 0.5 Marcaine plain infiltrated just proximal to the first metatarsocuneiform joint.  Hemostasis was achieved utilizing a pneumatic ankle Tourniquet placed above the right ankle and inflated to a pressure of 225 mmHg.  At this time, attention was directed to the dorsal aspect of the right first metatarsophalangeal joint where dorsal linear incision approximately 3 cm in length was made.  The incision was deepened within the same plain taking care of the Bovie and retracted all superficial nerves and vessels as necessary.  The incision was then carried down to the underlying capsular structure once again taking care of the Bovie and retracted all superficial nerves and vessels as necessary.  The capsular incision following the same outline as the skin incision was made and carried down to the underlying bony structure.  The capsule was then freed from the underling bony structure utilizing sharp and blunt dissection.  Using a microsagittal saw, the medial and dorsal very prominent bony eminence were removed and the area was inspected for any remaining bony prominences following resection of bone and those noted were removed using a hand rasp.  At this time, attention was directed to the first inner space using sharp and blunt dissection.  Dissection was carried down to the underling level of the adductor hallucis tendon, which was isolated and freed from its phalangeal, sesamoidal, and metatarsal attachments.  The tendon was noted to lap the length and integrity for transfer and at this time was tenotomized taking out resection of approximately 0.5 cm to help prevent any re-fibrous attachment.  At this time, the lateral release was stressed and was found to be complete.  The extensor hallucis brevis tendon was then isolated using blunt dissection and was tenotomized as well taking out approximately 0.5-cm resection.  The entire area was copiously flushed 3 times using a sterile saline solution and was inspected for any bony prominences remaining and it was noted that the base of the proximal phalanx on the medial side due to the removal of the extensive buildup of the metatarsal head was going to be very prominent in nature and at this time was removed using a microsagittal saw.  The area was again copiously flushed and inspected for any abnormalities and/or prominences and none were noted.  At this time, attention was directed to the base of the first metatarsal where a second incision was made approximately 4 cm in length.  The incision was deepened within the same plain taking care of Bovie and retracted all superficial nerves and vessels as necessary.  The incision was then carried down to the level of the metatarsal and using sharp and blunt dissection periosteal capsule structures were freed from the base of the metatarsal and taking care to retract the long extensive tendon and any neurovascular structures to avoid any disruption.  At this time, there was a measurement made of 1 cm just distal to the metatarsocuneiform joint on the medial side and 2 cm distal to the metatarsocuneiform joint from the lateral aspect of the joint.  At this time, 0.5 cm was measured distal to that lateral measurement and using microsagittal saw, a wedge osteotomy was taken from the base with the apex of the osteotomy being medial, taking care to keep the medial cortex intact as a hinge.  The osteotomy site was feathered down until the osteotomy site could be closed with little tension on it and at this time using an OrthoPro screw 3.0 x 22 mm.  The screw was placed following proper technique.  The osteotomy site was found to be fixated with absolutely no movement and good stability upon manual testing.  A very tiny gap on the lateral aspect of the osteotomy site was found and this was filled in packing it with the cancellous bone that was left over from the wedge osteotomy.  The packing of the cancellous bone was held in place with bone wax.  The entire area was copiously flushed 3 times using a sterile saline solution and was inspected and tested again for any movement of the osteotomy site or any gapping and then removed.  At this time, a deep closure was achieved utilizing #2-0 Vicryl suture, subcuticular closure was achieved using #4-0 Vicryl suture, and skin repair was achieved at both surgical sites with #5-0 nylon suture in a running interlocking fashion.  The hallux was found to have excellent movement upon completion of the osteotomy and the second procedure of the McBride bunionectomy and the metatarsal was found to stay in excellent alignment with good stability at the proximal osteotomy site.  At this time, the surgical site was postoperatively injected with 0.5 Marcaine plain as well as dexamethasone 4 mg primarily.  The surgical sites were then dressed with sterile Xeroform, sterile 4x4s, cascading, and Kling with a final protective layer of fiberglass in a nonweightbearing cast fashion.  The tourniquet was dropped and color and temperature of all digits returned to normal.  The patient tolerated the anesthesia and the procedure well and left the operating room in stable condition.
 
 The patient has been given written and verbal postoperative instructions and has been instructed to call if she has any questions, problems, or concerns at any time with the numbers provided.  The patient has also been warned a number of times the importance of elevation and no weightbearing on the surgical foot.
-
-

src/data/mtsamples_ihi_docs/doc0597.txt

@@ -33,5 +33,3 @@ The cast was then reinforced with fiberglass.  The patient was awakened from ane
 PLAN:  
 
 The patient will be discharged home.  She will return in 3 weeks for cast removal and clinical examination.  She would likely be placed into a wrist-guard at that time.  She has a prescription for Tylenol with codeine elixir.
-
-